ADAM

 

A computer program to simulate selective

breeding schemes for animals

 

 

 

 

 

 

 

 

 

 

Developed by:

 

Anders Christian Sørensen

Mark Henryon

Louise Dybdahl Pedersen

Saeid Ansari-Mahyari

Peer Berg

 

Department of Genetics and Biotechnology

Faculty of Agricultural Sciences

University of Aarhus

Blichers Allé 20, P.O. Box 50

DK-8830 Tjele

Denmark

 

Contact information

 

Anders Christian Sørensen                         Louise Dybdahl Pedersen

Phone: +45 8999 1321                            Phone: +45 8999 1660

Email: AndersC.Sorensen@agrsci.dk          Email: Louise.DybdahlPedersen@agrsci.dk

 

Updated

 

17/04/2009 (Version 167)


 

Index

Program description 5

Required files 5

Input.prm 5

Description of individual namelists: 7

&DESTINR 7

&RANDOM_NUMBER_SEED 7

&POPPRM 7

&CONTROLPARAMETERS 8

&BASEPOPULATION 13

&POPVARIABLES 17

&SELECTIONPARAMETERS 17

&SELECTION 18

&RULES

&EVA

&MATINGDESIGN 40

&MATINGHERDS 40

&GENERATIONSBACK 42

&OBSERVATIONS

&MATRICES 45

&DESIGN_MATRICES 46

&CONTROL_GENOME 47

&MARKER_NUMBERS 48

&MARKER_PARAMETERS 49

&MARKER_ALLELE_FREQUENCIES 50

&SAMPLE_MARKER_PARAMETERS 51

&QTL_PARAMETERS 52

&QTL_EFFECTS_FREQUENCIES 53

&SAMPLE_QTL_PARAMETERS 54

&SAMPLE_QTL_NUMBERS 55

&LD 56

&IBD 57

&IBD_PARAMETERS 59

&SELECTIVE_GENOTYPING 60

&GAS_PARAMETERS 60

&TEMPLATE_PARAMETERS 61

&FOUNDER_PARAMETERS 62

Examples: 63

Example 1 63

Example 2 65

Output files: 69

Description of individual output files: 69

accuracy.res 69

age_distribution_individual_selected.res 69

age_distribution_sires_selected.res 70

animal#.res 70

founder_representation#.res 70

marker#.res 70

mean_animal#.dat 70

mean_animal.dat 70

mean_obs#.res 70

mean_QTL#.res 70

mean_template#.res 70

mean_obs#.res 70

mean_QTL#.res 71

mean_template#.res 71

mean_timesteps.res 71

mean_timesteps_replicate.res 71

Mendelian_selection_differential.res 71

number_genotyped.res 71

obs#.res 71

qtl#.res 71

selection_differential.res 71

sire_contribution.res 72

template#.res 72

template_info#.res 72


 

1.              Program description

 

Program that simulates selective breeding schemes for animals. The program is

written in FORTRAN.

 

2.              Required files

 

Input file

input.prm, provides input parameters. File is located in the working directory.

Further details are provided below.

 

Script file

adam.script, job file that submits program to interactive system. File is

located in the working directory.

 

DMU files

The following files are required if DMU is called:

dmu4.adam.joba or dmu5.adam.joba, job files that submits DMU program to

interactive system

adam.dmu.dir, provides input parameters for DMU

adam.dmu.parm, provides variance components for DMU

 

The following files are also required if DMU is called for MABLUP:

dmu.mas.joba, script file that submits DMU program to interactive system

dmu_mas.dir, provides input parameters for DMU

mas.dmu.parm, provides variance components for DMU

ibd.joba, script file that submits IBD program to interactive system

 

Files are located in DESTINR (directory provided in input.prm)

 

EVA file(s)

The following file(s) is required if DMU is called:

EVA parameter file, provides input parameters for EVA. The name of the file(s) can be any text string. The file associated with each stage of EVA selection is specified in each EVA-selection stage of namelist &EVA.

 

EVA parameter file(s) is located in DESTINR (directory provided in input.prm)

 

3.              Input.prm

Complete list of input parameters (namelists).

&DESTINR 7

&RANDOM_NUMBER_SEED 7

&POPPRM 7

&CONTROLPARAMETERS 8

&BASEPOPULATION 13

&POPVARIABLES 17

&SELECTIONPARAMETERS 17

&SELECTION 18

&RULES 42

&EVA

&MATINGDESIGN 40

&MATINGHERDS 40

&GENERATIONSBACK 42

&OBSERVATIONS

&MATRICES 45

&DESIGN_MATRICES 46

&CONTROL_GENOME 47

&MARKER_NUMBERS 48

&MARKER_PARAMETERS 49

&MARKER_ALLELE_FREQUENCIES 50

&SAMPLE_MARKER_PARAMETERS 51

&QTL_PARAMETERS 52

&QTL_EFFECTS_FREQUENCIES 53

&SAMPLE_QTL_PARAMETERS 54

&SAMPLE_QTL_NUMBERS 55

&LD 56

&IBD 57

&IBD_PARAMETERS 59

&SELECTIVE_GENOTYPING 60

&GAS_PARAMETERS 60

&TEMPLATE_PARAMETERS 61

&FOUNDER_PARAMETERS 62

 

4.              Description of individual namelists:

 

&DESTINR

  reportR=destination     /

 

  **Task**

  Destination for report files.

 

  **Properties of name**

  destination           Definition: Destination for report files

                        Type: Character

                        Options: Any existing and accessible directory

                        Default: An existing and accessible directory must be

                                 provided

 

&RANDOM_NUMBER_SEED

  ran_seed=random_seed

  seed1=seed1

  seed2=seed2     /

 

  **Task**

  Input seed for random number generators in Randlib.

 

  **Properties of names**

  random_seed             Definition: Method used to generate the seed.

                          Type: Integer

                          Options:

                             0 Use specified seeds (seed1 and seed2).

                             1 Use /dev/urandom to generate two integer seeds.

                          Default: 0

 

  seed1, seed2            Definition: Integer seeds for initialising RANDLIB;

                                      used when random_seed=0.

                          Type: Integer*4

                          Options: -huge(1)≤seed1 and seed2≤huge(1)

                          Default: 12345678 and 98765432

 

  **Additional information**

  Seed1 and seed2 are only read when random_seed=0. When random_seed=0, seed1

  and seed2 should be specified.

 

&POPPRM

  npop=npop

  gestation_length=gestation_length

  nchrom=nchrom

  genotyped_at_birth=genotyped_at_birth

  OldAgeMales=OldAgeMales

  OldAgeFemales=OldAgeFemales     /

 

  **Task**

  Basic input for the populations.

 

  **Properties of names**

  npop                  Definition: Number of populations.

                        Type: Integer

                        Options: 1

                        Default: 1

 

  gestation_length      Definition: Gestation length

                        Type: Integer

                        Options: ³0

                        Default: 0

 

  nchrom                Definition: Number of chromosomes in the genome. A

                                    chromosome is defined as a single segment of

                                    DNA, whose inheritance is completely

                                    independent of any other chromosomes.

                        Type: Integer

                        Options: ³0

                        Default: 0

 

  genotyped_at_birth    Definition: Animals genotyped at birth

                        Type: character

                        Options:

                           yes Animals are genotyped at birth

                            no Animals are not genotyped at birth

                        Default: no

 

  OldAgeMales           Definition: Age at which males are culled for old age

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  OldAgeFemales         Definition: Age at which females are culled for old age

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  **Relation to other namelists**

  The following namelists are only read if nchrom>0: &CONTROL_GENOME, &LD, &IBD,

  &SELECTIVE_GENOTYPING, &MARKER_NUMBERS, &MARKER_PARAMETERS,

  &MARKER_ALLELE_FREQUENCIES, &SAMPLE_MARKER_PARAMETERS, &QTL_PARAMETERS,

  &QTL_EFFECTS_FREQUENCIES, &SAMPLE_QTL_PARAMETERS, &SAMPLE_QTL_NUMBERS,

  &IBD_PARAMETERS, &TEMPLATE_PARAMETERS, and &GAS_PARAMETERS.

 

  &SELECTION

  OldAgeMales and OldAgeFemales must be greater than the maximum reproduction

  ages of living males and females. The maximum reproduction ages are specified

  in namelist SELECTION, variable selection_scheme, via sex_code, age(2), and

  destiny_sel.

 

  **Additional information**

  No QTL or markers are simulated when nchrom=0

 

  When gestation_length 0, offspring are born in the same time step as parents

  are mated.

 

&CONTROLPARAMETERS

  ntime=ntime

  nrep=nrep

  cull_males=cull_males

  start_rep=start_rep

  print_replicate=print_replicate

  print_age_distribution_individual_selected=

                                   print_age_distribution_individual_selected

  print_age_distribution_sires_selected=print_age_distribution_sires_selected

  print_selection_differential=print_selection_differential

  print_accuracy=print_accuracy

  print_number_genotyped=print_number_genotyped

  print_sire_contribution=print_sire_contribution

  print_Mendelian_selection_differential=print_Mendelian_selection_differential

  time_steps_season=time_steps_season

  time_steps_year=time_steps_year

  data_time_steps=data_time_steps

  data_time_steps_mas=data_time_steps_mas

  constant_mendelian_variance=constant_mendelian_variance

  nRandomCullingGroups=nRandomCullingGroups

  RandomCullingGroups=sex  FirstAge  LastAge  proportion     /

 

NB! Number of lines provided for RandomCullingGroups must equal

    nRandomCullingGroups

 

  **Task**

  Input that controls the physical aspects of the simulation.

 

  **Properties of names**

  ntime                 Definition: Number of time steps

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  nrep                  Definition: Number of replicates simulated

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  cull_males            Definition: Defines whether surplus males are stored in

                                    memory

                        Type: Integer

                        Options:

                           0 Sampled males are stored in memory

                           1 Sampled males are only stored if the dam was

                             selected as a bull dam.

                        Default: 0

 

  start_rep             Definition: Starting replicate number

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  print_replicate       Definition: Controls whether information on each

                                    individual is outputted in files

                        Type: Integer

                        Options:

                           0 Simulated datasets are not stored.

                           1 Simulated datasets are stored in several files.

                        Default: 0

 

  print_age_distribution_individual_selected

                        Definition: Controls whether information on the age

                                    distribution of selected animals is

                                    outputted in the file

                                    ‘age_distribution_individual_selected.dat’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

                               distribution of selected animals for each

                               replicate, timestep, and stage of selection.

                        Default: no

 

  print_age_distribution_sires_selected

Definition: Controls whether information on the age

                                    distribution of sires of selected animals is

                                    outputted in the file

                                    ‘age_distribution_sires_selected.res’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

                               distribution of age of sires, at the time of

                               birth of their selected offspring for each

                               replicate, timestep, and stage of selection.

                        Default: no

 

  print_selection_differential

Definition: Controls whether information on the means of

                                    candidates and selected animals is outputted

                                    in the file ‘selection_differential.res’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

means of selected animals for each replicate,

timestep, and stage of selection.

                        Default: no

 

  print_accuracy        Definition: Controls whether information on the

                                    accuracies of candidates for selection is

                                    outputted in the file ‘accuracy.res’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

                               accuracy of candidates for each replicate,

                               timestep, and stage of selection.

                        Default: no

 

  print_number_genotyped

                        Definition: Controls whether information on the number

                                    of animals genotyped per timestep is

                                    outputted in the file number_genotyped.res’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

                               number of genotyped animals for each replicate

                               and timestep.

                        Default: no

 

  print_sire_contribution

Definition: Controls whether information on the number

                                    of sires of selected progeny and the

                                    variance of number of selected progeny per

                                    sire is outputted in the file

                                    ‘sire_contribution.res’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

                               number of sires and variance of progeny group

                               sizes for each replicate, timestep, and stage of

                               selection.

                        Default: no

 

  print_Mendelian_selection_differential

Definition: Controls whether information on the mean

                                    Mendelian sampling term of QTL for

                                    candidates and selected individuals is

                                    outputted in the file

                                    ‘Mendelian_selection_differential.res’.

                        Type: Character

                        Options:

                           no  No file produced.

                           yes File is generated holding information on the

                               mean Mendelian sampling term of QTL for

                               candidates and selected individuals for each

                               replicate, timestep, and stage of selection.

                        Default: no

 

  time_steps_season     Definition: Number of time steps per season; used to

                                    simulate HYS effects.

                        Type: Real

                        Options: ³0.0

                        Default: 1.0

 

  time_steps_year       Definition: Number of time steps per each year; needed

                                    to create report output files.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  data_time_steps       Definition: Number of previous time steps used in

                                    genetic evaluations.

                        Type: Integer

                        Options: ³1

                        Default: HUGE(1), largest possible integer

 

  data_time_steps_mas   Definition: Number of previous time steps used in

                                    genetic evaluation for MABLUP.

                        Type: Integer

                        Options: ³1

                        Default: HUGE(1), largest possible integer

 

  constant_mendelian_variance

                        Definition: Determines whether inbreeding of parents

                                    affects the variance of the Mendelian

                                    sampling term of the offspring

                        Type: Character

                        Options:

                             no  Uses inbreeding of parents to determine the

                                 variance of the Mendelian sampling term of the

                                 offspring

                            yes  Uses 0.5 for variance of the Mendelian sampling

                                 term of the offspring independent of the

                                 inbreeding of the parents

                        Default: no

 

  nRandomCullingGroups

                        Definition: Number of random-culling groups; number of

                                    lines specified in RandomCullingGroups

                        Type: Integer

                        Options: nRandomCullingGroups³0

                        Default: 0

 

  RandomCullingGroups=

  sex

                        Definition: Sex of animals to be randomly

                                    (involuntarily) culled

                        Type: Integer

                        Options:

                           1 Males

                           2 Females

                        Default: sex must be provided

 

  FirstAge

                        Definition: Youngest age of animals to be randomly

                                    culled

                        Type: Integer

                        Options:

                           FirstAge³-gestation_length

                        Default: FirstAge must be provided

 

  LastAge

                        Definition: Oldest age of animals to be randomly culled

                        Type: Integer

                        Options:

                           FirstAgeLastAgeOldAgeMales for males

                           FirstAgeLastAgeOldAgeFemales for females

                        Default: LastAge must be provided

 

  proportion

                        Definition: Proportion of animals to be randomly culled

                        Type: Real

                        Options:

                           0.0≤proportion≤1.0

                        Default: proportion must be provided

 

  **Relation to other namelists**

    &OBSERVATIONS

    Animals that are randomly culled can have observations realised at culling.

    The observations realised and the age at which culling needs to take place

    for a trait(s) to be realised is specified in &OBSERVATIONS. The exception

    is that animals randomly culled after conception and prior to birth (i.e.,

    age -gestation_length to -1) can never have observations realised. Animals

    must be born to have observations realised.

 

  **Additional information**

  1) RandomCullingGroups is only required when nRandomCullingGroups>0. That is,

     there is no random (involuntary) culling when nRandomCullingGroups=0.

 

  2) Number of lines provided for RandomCullingGroups must equal

     nRandomCullingGroups

 

  3) When a sex-age combination of animals is not specified in

     RandomCullingGroups, the random-culling proportion for this combination is

     set to zero. That is, no random culling takes place for this sex-age

     combination.

 

  4) When a sex-age combination is specified more than once in

     RandomCullingGroups, the random-culling proportion is overwritten each

     time. That is, the last proportion provided for the sex-age combination is

     used.

 

  5) FirstAge and LastAge can range from -gestation_length to OldAge, where

     OldAge is OldAgeMales for males and OldAgeFemales for females. This implies

     that males and females can be randomly culled after they have been

     conceived and prior to birth. This may not make sense biologically.

     However, it can be useful from a simulation view point. It can, in some

     instances, reduce the number of time steps required. For example, when

     gestation_length>0, animals are randomly culled, and the animals do not

     have traits realised or are not selected during early life stages.

 

  6) Animals randomly culled after conception and prior to birth (i.e., age

     -gestation_length to -1) can never have observations realised. Realisation

     of observations for randomly culled animals is specified in namelist

     observations, variable CullingInvoluntary. Animals must be born to have

     observations realised.

 

&BASEPOPULATION

  age_class_base=age_class_base

  max_age_base_males=max_age_base_males

  max_age_base_females=max_age_base_females

  age_class_male=age_class_male

  age_class_female=age_class_female

  sample_base=sample_base

  output_base=output_base

  base_input_path=base_input_path

  base_output_path=base_output_path     /

 

  **Task**

  Input to generate the base population.

 

  **Properties of names**

  age_class_base        Definition: Method used to generate the age structure of

                                    the base population.

                        Type: Character

                        Options:

                           no_structure     All base animals generated have

                                            birth time 0. The numbers of

                                            base males and females generated in

                                            each herd is determined by the size

                                            of the herds. Herd sizes are

                                            generated using information provided

                                            in namelist &SELECTION, variable

                                            selection_scheme.

                           create_structure Age structure generated using

                                            information provided in namelist

                                            &SELECTION, variable

                                            selection_scheme. Birth times for

                                            the base animals range from

                                            1-AgeMales-gestation_length to 0 for

                                            males and

                                            1-AgeFemales-gestation_length to 0

                                            for females, where AgeMales and

                                            AgeFemales are the maximum

                                            reproductive ages for male and

                                            females (see Additional

                                            Information). This method ensures

                                            enough base males and females to

                                            cover reproduction in each time

                                            step.

                           input            Age structure for base males and

                                            females provided in age_class_male

                                            and age_class_female. Birth times of

                                            base animals range from

                                            1-max_age_base_males-

                                            gestation_length to 0 for males and

                                            1-max_age_base_females-

                                            gestation_length to 0 for females

                                            (see Additional Information). Input

                                            provided for max_age_base_males,

                                            max_age_base_females,

                                            age_class_male, and age_class_female

                                            determines if enough base males and

                                            females to cover reproduction in

                                            each time step.

                        Default: no_structure

 

  max_age_base_males    Definition: Oldest age at which males in the base

                                    population breed; measured in time steps.

                                    Used when age_class_base ‘input’.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  max_age_base_females  Definition: Oldest age at which females in the base

                                    population breed; measured in time steps.

                                    Used when age_class_base ‘input’.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  age_class_male        Definition: Matrix specifying the number of base males

                                    in each herd when age_class_base ‘input’.

                        Dimension: (max_age_base_males+gestation_length) x nherd

                        Bounds: 1-gestation_length:max_age_base_males, 1:nherd

                        Type: Integer

 

  age_class_female      Definition: Matrix specifying the number of base males

                                    in each herd when age_class_base ‘input’.

                        Dimension: (max_age_base_females+gestation_length) x

                                    nherd

                        Bounds: 1-gestation_length:max_age_base_females, 1:nherd

                        Type: Integer

 

  sample_base           Definition: Sampling the base population.

                        Type: Character

                        Options:

                           yes Sample the base (new base animals).

                           no  Use the base animals from previous simulation(s).

                               Program doesn’t sample new base animals.

                        Default: yes

 

  output_base           Definition: Store base animals (all base files).

                        Type: Character

                        Options:

                           yes Store the base population from current simulation

                           no  Do not store base population

                        Default: no

 

  base_input_path       Definition: Directory where base population from

                                    previous simulations exists

                        Type: Character

                        Options: Any existing and accessible directory

                        Default: An existing and accessible directory must be

                                 provided

 

  base_output_path      Definition: Directory where base population from

                                    previous simulations is stored

                        Type: Character

                        Options: Any existing and accessible directory

                        Default: An existing and accessible directory must be

                                 provided

 

  **Relation to other namelists**

  &POPPRM, &POPVARIABLES, &SELECTION, and &EVA

  Information from these namelists is used to generate the base population

 

  **Additional information**

  1) age_class_base ‘no_structure’

     (a) Variables max_age_base_males, max_age_base_females, age_class_male and

         age_class_female are not used.

     (b) All base males and females have the same age. They are all born at time

         0. The consequence of this is that, when gestation_length and/or the

         minimum reproductive age of the base animals is greater than 0, there

         will be time steps with no selection candidates available for

         reproduction. This does not cause the program to stop.

     (c) When germ plasm is used for reproduction,

          (i) Germ plasm is stored for all base males if male germ plasm is used

              for reproduction. The number of germ plasm stored is the sum of

              all germ plasm stored for males during a time step. That is, the

              sum of germ plasm stored at each stage of &NAMELIST selection,

              variable selection_scheme with sex_code 1, 3, or 5 and destiny_sel

              2, 12, 26, or 126 and &NAMELIST EVA, variable EvaSelection with

              MaleDestinySel 2, 12, 26, or 126.

         (ii) Germ plasm is stored for all base females if female germ plasm is

              used for reproduction. The number of germ plasm stored is the sum

              of all germ plasm stored for females during a time step. That is,

              the sum of germ plasm stored at each stage of &NAMELIST selection,

              variable selection_scheme with with sex_code 2, 4, or 6 and

              destiny_sel 2, 12, 127, or 147 and &NAMELIST EVA, variable

              EvaSelection with FemaleDestinySel 2, 12, 127, or 147.

 

  2) age_class_base ‘create_structure’

     (a) Variables max_age_base_males, max_age_base_females, age_class_male and

         age_class_female are not used.

     (b) The age structure of base animals in each herd ranges from

         1-gestation_length to AgeMales for males and 1-gestation_length to

         AgeFemales for females, where AgeMales and AgeFemales are the maximum

         reproductive ages for male and females in the herd. This converts to

         birth times that range from 1-AgeMales-gestation_length to 0 for males

         and 1-AgeFemales-gestation_length to 0 for females. The consequence of

         this is that, there should always be sufficient selection candidates

         available for reproduction in each time step.

     (c) When germ plasm is used for reproduction,

          (i) Germ plasm is stored for base males if male germ plasm is used

              for reproduction. All males that are younger than or at the same

              age as the maximum age at which male germ plasm is used have germ

              plasm stored. The number of germ plasm stored is the sum of all

              germ plasm stored for males during a time step, as described for

              age_class_base ‘no_structure’.

         (ii) When the maximum age at which males are used for reproduction is

              greater than OldAgeMales, it is assumed that base males older than

              OldAgeMales are dead and died from old age at time BirthMalei +

              OldAgeMales, where BirthMalei is the birth time of the ith male.

        (iii) 2(b) (i) and (ii) applies to females.

 

  3) age_class_base ‘input’

     (a) Variables max_age_base_males, max_age_base_females, age_class_male and

         age_class_female are used

     (b) Bounds of age_class_male and age_class_female are

         1-gestation_length:max_age_base_males, 1:nherd and

         1-gestation_length:max_age_base_females, 1:nherd. That is, the first

         input datum provided for age_class_male is element 1-gestation_length,1

         (i.e., age 1-gestation_length, herd 1). The program stops when

         insufficient or surplus data is provided.

     (c) The age structure of the base population is user specified. The

         consequence of this is that, if insufficient base animals are

         specified, there will be time steps with insufficient selection

         candidates available for reproduction. This does not cause the program

         to stop.

     (d) When germ plasm is used for reproduction, germ plasm is stored for base

         males, as described for age_class_base ‘create_structure’.

 

  4) When sample_base ‘no’, the base population stored in the directory

     specified by base_input_path is used. When ‘yes’, base_input_path is not

     used.

 

  5) When output_base ‘yes’, the base population is stored in the directory

     specified by base_output_path. When ‘no’, base_output_path is not

     used.

 

&POPVARIABLES

 nherd=nherd

 nfixed=nfixed

 ntbv=ntbv

 nres=nres

 nobs=nobs

 

  **Task**

  Input to generate the population.

 

  **Properties of names**

  nherd                 Definition: Number of herds in each population.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  nfixed                Definition: Number of fixed effects.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  ntbv                  Definition: Number of traits, where a trait is defined

                                    as a characteristic for which a true

                                    breeding value is simulated/estimated.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  nres                  Definition: Number of residual effects.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  nobs                  Definition: Number of observations.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  **Relation to other namelists**

  &MATINGHERDS and &GENERATIONSBACK

  If nherd³1, the namelists &MATINGHERDS and &GENERATIONSBACK are read.

  If nherd=1, these namelists are not read.

 

&SELECTIONPARAMETERS

 selection_groups=selection_groups

 dmu_version=dmu_version      /

 

  **Task**

  Provide basic input for selection.

 

  **Properties of names**

  selection_groups      Definition: Number of selection stages.

                        Type: Integer

                        Options: ³1

                        Default: 1

 

  dmu_version           Definition: DMU version called.

                        Type: character

                        Options:

                           dmu4 DMU4 is called to predict breeding values.

                           dmu5 DMU5 is called to estimate variance components

                                and predict breeding values.

                        Default: dmu4

 

  **Relation to other namelists**

  1) &SELECTION

     This namelist is always read. The number of lines required in the namelist

     &SELECTION is equal to selection_groups.

 

  **Additional information**

 

 

&SELECTION

 selection_scheme=

 sex_code  live_status  population_id  selection_unit  age(1)  age(2)

 herd_id(1)  herd_id(2)  selection_method  selection_criterion  RunBlup  numbers

 related_stage  tag  destiny_sel  TestHerd  destiny_unsel  repro_capacity 

 litter_size  sex_ratio  n_germplasm  SelectionRule    /

 

 NB! Number of lines must equal selection_groups provided in namelist

 &SELECTIONPARAMETERS

 

  **Task**

  Input for selection. Namelist is always read.

 

  **Properties of names**

  sex_code              Definition: Type of selection

                        Type: Integer

                        Options:

                           0 Truncation or select-all selection; ignoring sex

                             of the candidates

                           1 Truncation or select-all selection of males

                           2 Truncation or select-all selection of females

                           3 Truncation or select-all selection of males born

                             out of bull-dams

                           4 Truncation or select-all selection among bull

                             dams previously selected in current time step

                           5 Truncation or select-all selection among males

                             previously tagged in current time step; tag

                             specified in by variable tag

                           6 Truncation or select-all selection among females

                             previously tagged in current time step; tag

                             specified in by variable tag

                           7 EVA-selection among males and/or females tagged for

                             EVA-selection.

                        Default: sex_code must be specified.

 

  live_status           Definition: Live status of the candidates

                        Type: Integer

                        Options:

                           0 Animal is candidate for selection if (i) it is

                             alive or (ii) it is not alive and has germplasm

                             stored

                           1 Only live animals are considered for selection.

                        Default: live_status must be specified.

 

  population_id         Definition: Specifies which population is selected.

                        Type: Integer

                        Options: 1≤population_id≤npop

                        Default: population_id must be specified.

 

  selection_unit        Definition: Unit on which selection operates

                        Type: Character

                        Options:

                           across_pop  Across all populations

                           population  Across all herds within the specified

                                       population

                           across_herd Across specified herds

                           within_herd Within specified herds

                           family      Within full-sib families

                        Default: selection_unit must be specified.

 

  age(1)                Definition: Youngest age at which animals are considered

                                    for selection.

                        Type: Integer

                        Options:

                           age(1)≥1 when gestation_length 0

                           age(1)≥0 when gestation_length>0

                        Default: age(1) must be specified.

 

  age(2)                Definition: Oldest age at which animals are considered

                                    for selection.

                        Type: Integer

                        Options:

                           1≤age(2)age(1) when gestation_length 0

                           0≤age(2)age(1) when gestation_length>0

                        Default: age(2) must be specified.

 

  herd_id(1)            Definition: First herd within which animals are

                                    considered for selection.

                        Type: Integer

                        Options: 1≤herd_id(1)herd_id(2)nherd

                        Default: herd_id(1) must be specified.

 

  herd_id(2)            Definition: Last herd within which animals

                                    are considered for selection.

                        Type: Integer

                        Options: 1≤herd_id(2)herd_id(1)

                        Default: herd_id(2) must be specified.

 

  selection_method      Definition: Method of selection

                        Type: Character

                        Options:

                           select_all Selection of all animals that fulfil

                                      specified criteria

                           truncation Truncation selection

                        Default: selection_method must be specified.

 

  selection_criterion   Definition: Criterion on which selection is based

                        Type: Character

                        Options:

                           random Random number, i.e. random selection.

                           pheno  Phenotypic selection

                           blup   Selection on BLUP EBV’s

                           gas    Selection (BLUP EBV + gene effect)

                           mas    Selection on MA-BLUP EBV’s

                        Default: selection_criterion must be specified

 

  RunBlup               Definition: Estimate EBVs when BLUP, GAS, or MAS used

                                    as selection criterion

                        Type: Integer

                        Options:

                           0 EBVs are not estimated

                           1 EBVs are estimated

                        Default: RunBlup must be specified

 

  numbers               Definition: Number of animals to be selected from each

                                    selection_unit

                        Type: Integer

                        Options: ≥1

                        Default: numbers must be specified

 

  related_stage         Definition: The total number of animals selected in the

                                    current stage of selection are included in

                                    the numbers selected in the related_stage

                                    in the same time step

                        Type: Integer

                        Options: 0 No related stages

                                 2≤related_stage≤selection_groups

                        Default: related_stage must be specified.

 

  tag                   Definition: Animals with specified tag are selection

                                    candidates when sex_code 5 or 6

                        Type: Integer

                        Options:

                             90 Selection among candidates tagged to be left

                                alive

                             91 Selection among candidates tagged to reproduce

                                (mate)

                             92 Selection among candidates tagged to have germ

                                plasm stored

                             93 Selection among candidates tagged for genotyping

                             94 Selection among candidates tagged for transfer

                                to another (test) herd

                             96 Selection among candidates tagged to have DYD

                                sampled (only available for males)

                            912 Selection among candidates tagged to reproduce

                                and have germ plasm stored

                            914 Selection among candidates tagged to reproduce

                                after transfer to another (test) herd

                            916 Selection among candidates tagged to reproduce

                                and have DYD sampled (only available for males)

                            917 Selection among candidates tagged to reproduce

                                as bull-dams (only available for females)

                            926 Selection among candidates tagged to have germ

                                plasm stored and DYD sampled (only available for

                                males)

                           9126 Selection among candidates tagged to reproduce,

                                have germ plasm stored, and DYD sampled (only

                                available for males)

                           9127 Selection among candidates tagged to reproduce

                                as bull-dams and have germ plasm stored (only

                                available for females)

                           9147 Selection among candidates tagged to reproduce

                                as bull-dams after transfer to another (test)

                                herd (only available for females)

                        Default: tag must be specified.

 

  destiny_sel           Definition: Defines the destiny of selected animals

                        Type: Integer

                        Options:

                              0 Selected candidates are left alive

                              1 Selected candidates are reproduced (mated)

                              2 Selected candidates have germ plasm stored

                              3 Selected candidates are genotyped or

                                candidates for genotyping

                              4 Selected candidates are transferred to another

                                (test) herd; the herd is specified by TestHerd

                              6 Selected candidates have DYD sampled (only

                                available for males)

                             12 Selected candidates are reproduced and have germ

                                plasm stored

                             14 Selected candidates are reproduced after

                                transfer to another (test) herd; the herd is

                                specified by TestHerd

                             16 Selected candidates are reproduced and have DYD

                                sampled (only available for males)

                             17 Selected candidates are reproduced as bull-dams

                                (only available for females)

                             26 Selected candidates have germ plasm stored and

                                DYD sampled (only available for males)

                            126 Selected candidates are reproduced, have germ

                                plasm stored, and DYD sampled (only available

                                for males)

                            127 Selected candidates are reproduced as bull-dams

                                and have germ plasm stored (only available for

                                females)

                            147 Selected candidates are reproduced as bull-dams

                                after transfer to another (test) herd; the herd

                                is specified by TestHerd (only available for

                                females)

                             90 Selected candidates are tagged as candidates to

                                be left alive

                             91 Selected candidates are tagged as candidates to

                                reproduce (mate)

                             92 Selected candidates are tagged as candidates to

                                have germ plasm stored

                             93 Selected candidates are tagged as candidates for

                                genotyping

                             94 Selected candidates are tagged as candidates for

                                transfer to another (test) herd

                             95 Selected candidates are tagged as candidates for

                                EVA selection

                             96 Selected candidates are tagged as candidates to

                                have DYD sampled (only available for males)

                            912 Selected candidates are tagged as candidates to

                                reproduce and have germ plasm stored

                            914 Selected candidates are tagged as candidates to

                                reproduce after transfer to another (test) herd

                            916 Selected candidates are tagged as candidates to

                                reproduce and have DYD sampled (only available

                                for males)

                            917 Selected candidates are tagged as candidates to

                                reproduce as bull-dams (only available for

                                females)

                            926 Selected candidates are tagged as candidates to

                                have germ plasm stored and DYD sampled (only

                                available for males)

                           9126 Selected candidates are tagged as candidates to

                                reproduce, have germ plasm stored, and DYD

                                sampled (only available for males)

                           9127 Selected candidates are tagged as candidates to

                                reproduce as bull-dams and have germ plasm

                                stored (only available for females)

                           9147 Selected candidates are tagged as candidates to

                                reproduce as bull-dams after transfer to another

                                (test) herd (only available for females)

                        Default: destiny_sel must be specified.

 

  TestHerd              Definition: Test herd to which selected animals are

                                    transferred when destiny_sel 4, 14, or 147

                        Type: Integer

                        Options: 1≤TestHerdnherd

                        Default: TestHerd must be specified.

 

  destiny_unsel         Definition: Destiny of candidates that are not selected

                        Type: Integer

                        Options:

                           0 Animal is culled

                           1 Animal is left alive

                        Default: destiny_unsel must be specified.

 

  repro_capacity        Definition: Reproductive capacity (number of matings)

                                    of selected individuals (biologically

                                    constrained or otherwise).

                        Type: Integer

                        Options: ≥1

                        Default: repro_capacity must be specified.

 

  litter_size           Definition: Number of offspring per mating

                        Type: Integer

                        Options: ≥1

                        Default: litter_size must be specified

 

  sex_ratio             Definition: Probability of an offspring being a female

                        Type: Real

                        Options: 0.0≤sex_ratio≤1.0

                        Default: sex_ratio must be specified.

 

  germ_plasm            Definition: Number of units of germ plasm stored per

                                    selected animal.

                        Type: Integer

                        Options: germ_plasm≥0

                        Default: germ_plasm must be specified.

 

  SelectionRule         Definition: Selection rule number; only valid for

                                    truncation selection.

                        Type: Integer

                        Options:

                            0 No selection rule

                           ≥1 Selection rule. Rule number must correspond to a

                              rule number specified in namelist rules, variable

                              SelectionRules.

                        Default: SelectionRule must be specified.

 

  **Relation to other namelists**

  1) &SELECTIONPARAMETERS

     The number of lines or selection stages required in selection_scheme

     must be equal to selection_groups provided in namelist

     &SELECTIONPARAMETERS.

 

  2) &POPVARIABLES

     herd_id(1) and herd_id(2) must be less than or equal to nherd provided in

     namelist &POPVARIABLES.

 

  3) &BASEPOPULATION

     Information in selection_scheme is used to generate the base population

 

  4) &RULES

     If SelectionRule>0 in any selection stage, the namelist &RULES is read.

 

  5) &EVA

     If sex_code 7 in any selection stage of selection_scheme, the namelist &EVA

     is read. The number of lines or EVA-selection stages provided in &EVA must

     equal the number of selection stages with EVA-selection (i.e., number of

     lines in selection_scheme with sex_code 7).

 

  **Additional information**

  1) All variables in namelist &SELECTION, variable selection_scheme are read

     and, therefore, must be specified. However, there are cases where some

     variables are not used. The most striking case is when sex_code 7 (EVA

     selection). This specifies that EVA selection is to be carried out. The

     information required to carry out EVA selection is not provided in

     selection_scheme, but in namelist &EVA, variable EvaSelection. Another case

     is when selected animals are not destined to be mated. In this case,

     variables, such as repro_capacity, litter_size, and sex_ratio, are read,

     but not used. For variables that are not used, the input provided is

     irrelevant. However, for clarity, we recommend providing 0 for integer

     variables, 0.0 for sex_ratio (the only real), and ‘ ‘ for character

     variables.

 

  2) (a) live_status must be 0 or 1 when sex_code 0:6.

     (b) live_status can only be 0 when

           (i) sex_code 1:4 and destiny_sel 1,

          (ii) sex_code 5 or 6, tag 91, and destiny_sel 1,

         (iii) sex_code 0:4 and destiny_sel 91 or 95.

          (iv) selection_unit not ’family’

     (c) When live_status 0, destiny_sel 1, and a dead animal with stored germ

         plasm is selected for reproduction, the animal’s reproductive capacity

         is defined as follows. If the number of stored germ plasm is greater or

         equal to repro_capacity, the animal’s reproductive capacity is

         repro_capacity. If, however, the number of stored germ plasm is less

         than repro_capacity, the animal’s reproductive capacity is the number

         of stored germ plasm. The consequence of this is that, insufficient

         stored germ plasm can lead to less matings being carried out than

         planned.

 

  3) population_id must be 1 when sex_code 0:6 (at present).

 

  4) (a) selection_unit must be ‘across_pop’, ‘population’, ‘across_herd’,

        ‘within_herd’, or ‘family’ when sex_code 0:6.

     (b) When selection_unit ‘across_herd’, ‘within_herd’, or ‘family’,

         herd_id(1) and herd_id(2) are required. Otherwise, herd_id(1) and

         herd_id(2) are not used.

     (c) selection_unit cannot be ‘family’ with sex_code 3:4, selection_method

         ‘select_all’, and live_status 0.

     (d) Selection within full-sib families (selection_unit ‘family’) implies

         selection within all full-sib families in herds herd_id(1) and

         herd_id(2) with individuals from ages age(1) to age(2). The number of

         full-sib families is not specified explicitly at the ‘within-family’

         selection stage. The number is determined at other selection stages

         where selection of animals for mating occurs.

 

  5) (a) age(1)>0 and age(2)age(1) when sex_code 0:6.

     (b) age(2)OldAgeMales when sex_code 1, 3, or 5 and live_status 1.

     (c) age(2)OldAgeFemales when sex_code 2, 4, or 6 and live_status 1.

     (d) age(2)≤max(OldAgeMales,OldAgeFemales) when sex_code 0 and

         live_status 1.

 

  6) 1≤herd_id(1)nherd and 1≤herd_id(2)nherd when sex_code 0:6 and

     selection_unit ‘across_herd’, ‘within_herd’, or ‘family’.

 

  7) (a) selection_method must be ‘select_all’ or ‘truncation’ when sex_code

         0:6.

     (b) When selection_method ‘select_all’, the destiny of the selected

         candidates cannot include reproduction. That is, destiny_sel cannot be

         1, 12, 14, 16, 17, 126, 127, or 147. Furthermore, selection_criterion,

         numbers, destiny_unsel, repro_capacity, litter_size, and sex_ratio are

         not used. related_stage is also not used, but must be set to 0 (at

         present).

 

  8) selection_criterion must be ‘random’, ‘pheno’, ‘blup’, ‘gas’, or ‘mas’ when

     sex_code 0:6 and selection_method ‘truncation’.

 

  9) (a) RunBlup must be 0:1 when sex_code 0:6, selection_method ‘truncation’,

         and selection_criterion ‘blup’, ‘gas’, or ‘mas’.

     (b) RunBlup is not used when sex_code 7, selection_method ‘select_all,

         and selection_criterion ‘random’ or ‘pheno’. It is set to 0.

     (c) RunBlup must be 1 in the first selection stage(s) where

         selection_criterion ‘blup’, ‘gas’, or ‘mas’. The first selection

         stage(s) can be a EVA-selection stage(s).

     (d) When RunBlup 1, sex_code 0:6, selection_method ‘truncation’,

         selection_criterion ‘blup’, ‘gas’, or ‘mas’, and selection stage not

         the first selection stage where selection_criterion ‘blup’, ‘gas’, or

        ‘mas’, EBVs are only estimated if new information has been gathered

         since the previous EBV estimation. At present, this new information is

         genotyping of animals.

 

 10) (a) numbers>0 when sex_code 0:6 and selection_method ‘truncation’.

     (b) When selection_unit ‘across_pop’, ‘population’, or ‘across-herd’,

         numbers refers to the total number of animals to be selected. When

         selection_unit ‘within_herd’ or ‘family’, numbers refers to the number

         of animals to be selected from each herd or full-sib family.

 

 11) (a) related_stage≥0 and related_stageselection_groups when sex_code 1:6

         and selection_method ‘truncation’.

     (b) Possible to have multiple related stages. That is, several selection

         stages can have the same related_stage. All animals selected in each of

         these stages are included in the number of animals selected at the

         related stage. That is, selection stage related_stage.

     (c) related_stage must be greater than selection stage. This implies that

         the minimum related selection stage is 2 (i.e., stage specified by

         related_stage in selection stage) in selection stage 1.

     (d) related_stage is not used at selection stage selection_groups (i.e.,

         the last selection stage). It is set to 0.

     (e) related_stage cannot be used when sex_code 0 or selection_method

         ‘select_all’ in either the selection stage or related selection stage.

         In both cases, related_stage must be set to 0 (at present).

     (f) Related selection stage cannot have selection_criterion ‘family’.

     (g) related_stage cannot be used in combination with EVA selection (at

         present).

     (h) When sex_code 1 or 5 in selection stage, the related selection stage

         must have sex_code 1 or 5.

         When sex_code 2 or 6 in selection stage, the related selection stage

         must have sex_code 2 or 6.

         When sex_code 3 in selection stage, the related selection stage

         must have sex_code 1, 3, or 5.

         When sex_code 4 in selection stage, the related selection stage

         must have sex_code 2, 4, or 6.

 

 12) (a) Tag must be specified when sex_code 5:6.

     (b) Tag must be 91 and destiny_sel 1 when live_status 0.

     (c) Tag must correspond to destiny_sel. That is, when tag 90, destiny_sel

         must be 0, tag 91 destiny_sel 1, tag 92 destiny_sel 2, tag 93

         destiny_sel 3, and so on.

     (d) Tagged animals cannot be re-tagged. That is, destiny_sel cannot be

         90:9147 when sex_code 5:6.

 

 13) (a) destiny_sel must be specified when sex_code 0:6.

     (b) destiny_sel cannot include reproduction or storage of germ plasm when

         sex_code 0. That is, destiny_sel cannot be 1, 2, 12, 14, 16, 17, 26,

         126, 127, or 147.

     (c) destiny_sel cannot include reproduction when selection_unit ‘family’.

         That is, destiny_sel cannot be 1, 12, 14, 16, 17, 126, 127, or 147.

     (d) Females cannot have DYD sampled. That is, destiny_sel cannot be 6, 16,

         26, 126, 96, 916, 926, or 9126 when sex_code 0, 2, 4, or 6.

     (e) Males cannot be bull-dams. That is, destiny_sel cannot be 17, 127, 147,

         917, 9127, or 9147 when sex_code 0, 1, 3, or 5.

     (f) There is only a limited number of valid destinies for selected bull

         dams. They are destiny_sel 0, 1, 2, 3, 12, or 95 when sex_code 4.

     (g) Tagging can be carried out over several selection stages. Tagging is

         carried out with two intentions:

          (i) Animals are tagged with a view to selection with sex_code 5 or 6

              at a subsequent selection stage during the same time step. This

              form for tagging is specified with sex_code 0:4 and destiny_sel

              90, 91, 92, 93, 94, 96, 912, 914, 916, 917, 926, 9126, 9127, or

              9147; exceptions specified in 12) (d)-(f). Animals remain tagged

              until they are candidates for selection in a selection stage with

              sex_code 5 or 6. That is, they fulfil the criteria specified in a

              selection stage with sex_code 5 or 6. Following the selection

              stage, the candidates, whether selected or unselected, lose the

              tag specified by Tag. Other tags are not removed.

         (ii) Animals are tagged for EVA selection at a subsequent selection

              stage during the same time step with sex_code 0:6 and destiny_sel

              95. The one restriction (at present) is that, when tagging

              females, both normal females or bull dams can be tagged together.

              That is, females selected for EVA selection cannot be both normal

              females (sex_code 2 or 6) and bull dams (sex_code 4). All animals

              tagged for EVA selection lose their tag following a stage of EVA

              selection. That is, when sex_code 7.

 

 14) (a) TestHerd must be specified when destiny_sel includes transfer to

         another (test) herd. That is, destiny_sel 4, 14, or 147.

     (b) 1≤TestHerdnherd when specified.

 

 15) destiny_unsel must be 0:1 when sex_code 0:6 and selection_method

     ‘truncation’.

 

 16) repro_capacity>0 when sex_code 2, 4, or 6, selection_method ‘truncation’,

     and destiny_sel 1, 12, 14, 17, 127, or 147. Otherwise, it is set to 0.

 

 17) litter_size>0 when sex_code 2, 4, or 6, selection_method ‘truncation’,

     and destiny_sel 1, 12, 14, 17, 127, or 147. Otherwise, it is set to 0.

 

 18) 0.0≤sex_ratio≤1.0 when sex_code 2, 4, or 6, selection_method ‘truncation’,

     and destiny_sel 1, 12, 14, 17, 127, or 147. Otherwise, it is set to 0.0.

 

 19) (a) germ_plasm>0 when sex_code 1:6 and destiny_sel 2, 12, 26, 126, or 127.

     (b) If an animal is reselected to have germ plasm stored within a time step

         or during a subsequent time step, the new number of germ plasm is added

         to the number currently stored for the animal. The exception is males

         and females in the base population.

 

 20) SelectionRule is only valid when sex_code 0:6 and selection_method

    ‘truncation’. When selection_method ‘select_all’, SelectionRule is ignored.

 

&RULES

 SelectionRules=

 rule  SireTimeTotal  DamTimeTotal  FamilyTimeTotal  SireMatingsTimeTotal 

 DamMatingsTimeTotal  SireTotal  DamTotal  FamilyTotal  SireMatingsTotal 

 DamMatingsTotal

 

 SireTimeTotals=SireTimeTotals

 DamTimeTotals=DamTimeTotals

 FamilyTimeTotals=FamilyTimeTotals

 SireMatingsTimeTotals=SireMatingsTimeTotals

 DamMatingsTimeTotals=DamMatingsTimeTotals

 SireTotals=SireTotals

 DamTotals=DamTotals

 FamilyTotals=FamilyTotals

 SireMatingsTotals=SireMatingsTotals

 DamMatingsTotals=DamMatingsTotals     /

 

 NB! Number of lines must equal the number of different rules provided in

 SelectionRule in namelist &SELECTION, variable selection_scheme.

 

  **Task**

  Specify selection rule(s) for truncation selection.

 

  **Properties of names**

  rule                  Definition: Selection-rule number; must correspond to

                                    a selection rule in namelist &SELECTION,

                                    variable SelectionRule

                        Type: Integer

                        Options: ≥1

                        Default: rule must be specified

 

  SireTimeTotal         Definition: Specifies which element of SireTimeTotals

                                    contains the maximum number of offspring

                                    that can be selected from each sire during

                                    each time step

                        Type: Integer

                        Options:

                            ≥1 Element of SireTimeTotals that contains the

                               maximum number of offspring that can be selected

                               from each sire during each time step

                            -9 Maximum number of offspring not applicable

                        Default: SireTimeTotal must be specified

 

  DamTimeTotal          Definition: Specifies which element of DamTimeTotals

                                    contains the maximum number of offspring

                                    that can be selected from each dam during

                                    each time step

                        Type: Integer

                        Options:

                            ≥1 Element of DamTimeTotals that contains the

                               maximum number of offspring that can be selected

                               from each dam during each time step

                            -9 Maximum number of offspring not applicable

                        Default: DamTimeTotal must be specified

 

  FamilyTimeTotal       Definition: Specifies which element of FamilyTimeTotals

                                    contains the maximum number of offspring

                                    that can be selected from each full-sib

                                    family during each time step

                        Type: Integer

                        Options:

                            ≥1 Element of FamilyTimeTotals that contains the

                               maximum number of offspring that can be selected

                               from each full-sib family during each time step

                            -9 Maximum number of offspring not applicable

                        Default: FamilyTimeTotal must be specified

 

  SireMatingsTimeTotal  Definition: Specifies which element of

                                    SireMatingsTimeTotals contains the maximum

                                    number of matings for each sire during

                                    each time step

                        Type: Integer

                        Options:

                            ≥1 Element of SireMatingsTimeTotals that contains

                               the maximum number of matings for each sire

                               during each time step

                            -9 Maximum number of matings not applicable

                        Default: SireMatingsTimeTotals must be specified

 

  DamMatingsTimeTotal   Definition: Specifies which element of

                                    DamMatingsTimeTotals contains the maximum

                                    number of matings for each dam during each

                                    time step

                        Type: Integer

                        Options:

                            ≥1 Element of DamMatingsTimeTotals that contains

                               the maximum number of matings for each dam during

                               each time step

                            -9 Maximum number of matings not applicable

                        Default: DamMatingsTimeTotals must be specified

 

  SireTotal             Definition: Specifies which element of SireTotals

                                    contains the maximum number of offspring

                                    that can be selected from each sire across

                                    time steps

                        Type: Integer

                        Options:

                            ≥1 Element of SireTotals that contains the

                               maximum number of offspring that can be selected

                               from each sire

                            -9 Maximum number of offspring not applicable

                        Default: SireTotal must be specified

 

  DamTotal              Definition: Specifies which element of DamTotals

                                    contains the maximum number of offspring

                                    that can be selected from each dam across

                                    time steps

                        Type: Integer

                        Options:

                            ≥1 Element of DamTotals that contains the

                               maximum number of offspring that can be selected

                               from each dam

                            -9 Maximum number of offspring not applicable

                        Default: DamTotal must be specified

 

  FamilyTotal           Definition: Specifies which element of FamilyTotals

                                    contains the maximum number of offspring

                                    that can be selected from each full-sib

                                    family across time steps

                        Type: Integer

                        Options:

                            ≥1 Element of FamilyTotals that contains the

                               maximum number of offspring that can be selected

                               from each full-sib family

                            -9 Maximum number of offspring not applicable

                        Default: FamilyTotal must be specified

 

  SireMatingsTotal      Definition: Specifies which element of SireMatingsTotals

                                    contains the maximum number of matings for

                                    each sire across time steps

                        Type: Integer

                        Options:

                            ≥1 Element of SireMatingsTotals that contains

                               the maximum number of matings for each sire

                            -9 Maximum number of matings not applicable

                        Default: SireMatingsTotals must be specified

 

  DamMatingsTotal       Definition: Specifies which element of DamMatingsTotals

                                    contains the maximum number of matings for

                                    each dam across time steps

                        Type: Integer

                        Options:

                            ≥1 Element of DamMatingsTotals that contains

                               the maximum number of matings for each dam

                            -9 Maximum number of matings not applicable

                        Default: DamMatingsTotals must be specified

 

  SireTimeTotals        Definition: Array that contains the maximum number(s) of

                                    offspring that can be selected from each

                                    sire during each time step

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   SireTimeTotal across rules

                        Options:

                            ≥1 For each element specified in SireTimeTotal

                             0 For each element not specified in SireTimeTotal

                        Default: SireTimeTotals must be specified when

                                 SireTimeTotal≥1 for any rule

 

  DamTimeTotals         Definition: Array that contains the maximum number(s) of

                                    offspring that can be selected from each

                                    dam during each time step

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   DamTimeTotal across rules

                        Options:

                            ≥1 For each element specified in DamTimeTotal

                             0 For each element not specified in DamTimeTotal

                        Default: DamTimeTotals must be specified when

                                 DamTimeTotal≥1 for any rule

 

  FamilyTimeTotals      Definition: Array that contains the maximum number(s) of

                                    offspring that can be selected from each

                                    full-sib family during each time step

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   FamilyTimeTotal across rules

                        Options:

                            ≥1 For each element specified in FamilyTimeTotal

                             0 For each element not specified in FamilyTimeTotal

                        Default: FamilyTimeTotals must be specified when

                                 FamilyTimeTotal≥1 for any rule

 

  SireMatingsTimeTotals Definition: Array that contains the maximum number(s) of

                                    matings for each sire during each time step

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   SireMatingsTimeTotal across rules

                        Options:

                            ≥1 For each element specified in

                               SireMatingsTimeTotal

                             0 For each element not specified in

                               SireMatingsTimeTotal

                        Default: SireMatingsTimeTotals must be specified when

                                 SireMatingsTimeTotal≥1 for any rule

 

  DamMatingsTimeTotals  Definition: Array that contains the maximum number(s) of

                                    matings for each dam during each time step

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   DamMatingsTimeTotal across rules

                        Options:

                            ≥1 For each element specified in

                               DamMatingsTimeTotal

                             0 For each element not specified in

                               DamMatingsTimeTotal

                        Default: DamMatingsTimeTotals must be specified when

                                 DamMatingsTimeTotal≥1 for any rule

 

  SireTotals            Definition: Array that contains the maximum number(s) of

                                    offspring that can be selected from each

                                    sire across time steps

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   SireTotal across rules

                        Options:

                            ≥1 For each element specified in SireTotal

                             0 For each element not specified in SireTotal

                        Default: SireTotals must be specified when

                                 SireTotal≥1 for any rule

 

  DamTotals             Definition: Array that contains the maximum number(s) of

                                    offspring that can be selected from each

                                    dam across time steps

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   DamTotal across rules

                        Options:

                            ≥1 For each element specified in DamTotal

                             0 For each element not specified in DamTotal

                        Default: DamTotals must be specified when

                                 DamTotal≥1 for any rule

 

  FamilyTotals          Definition: Array that contains the maximum number(s) of

                                    offspring that can be selected from each

                                    full-sib family across time steps

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   FamilyTotal across rules

                        Options:

                            ≥1 For each element specified in FamilyTotal

                             0 For each element not specified in FamilyTotal

                        Default: FamilyTotals must be specified when

                                 FamilyTotal≥1 for any rule

 

  SireMatingsTotals     Definition: Array that contains the maximum number(s) of

                                    matings for each sire across time steps

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   SireMatingsTotal across rules

                        Options:

                            ≥1 For each element specified in SireMatingsTotal

                             0 For each element not specified in

                               SireMatingsTotal

                        Default: SireMatingsTotals must be specified when

                                 SireMatingsTotal≥1 for any rule

 

  DamMatingsTotals      Definition: Array that contains the maximum number(s) of

                                    matings for each dam across time steps

                        Type: Integer

                        Dimension: 1 x maximum number specified for

                                   DamMatingsTotal across rules

                        Options:

                            ≥1 For each element specified in DamMatingsTotal

                             0 For each element not specified in DamMatingsTotal

                        Default: DamMatingsTotals must be specified when

                                 DamMatingsTotal≥1 for any rule

 

  **Relation to other namelists**

  &SELECTION

  Namelist rules is read when sex_code 0:6 and selection_method ‘truncation’ in

  any selection stage of namelist &SELECTION, variable selection_scheme.

 

  **Additional information**

 

 

 

 

&EVA

 EvaSelection=

 stage  MaleSelCrit  MaleRunBlup  MaleDestinySel  MaleTestHerd  MaleDestinyUnsel 

 MalePedigree  MaleMaxMatings  MaleGermplasm  FemaleSelCrit  FemaleRunBlup 

 FemaleDestinySel  FemaleTestHerd  FemaleDestinyUnsel  FemalePedigree 

 FemaleMaxMatings  FemaleGermplasm  FutMaleBreeders  FutFemaleBreeders  nMatings 

 LitterSize  SexRatio  EvaParamterFile      /

 

  **Task**

  Input for EVA-selection. Namelist is read when sex_code 7 in any selection

  stage of namelist &SELECTION, variable selection_scheme.

 

  **Properties of names**

  stage                 Definition: Stage of selection; must correspond to

                                    a selection stage in namelist &SELECTION,

                                    variable selection_scheme with sex_code 7.

                        Type: Integer

                        Options: 2≤stageselection_groups

                        Default: stage must be specified

 

  MaleSelCrit           Definition: Criterion used to select males

                        Type: Character

                        Options:

                           pheno Phenotypic selection

                           blup  Selection on BLUP EBV's

                           gas   Selection on (gene effect + BLUP EBV's)

                           mas   Selection on MA-BLUP EBV's

                        Default: MaleSelCrit must be specified

 

  MaleRunBlup           Definition: Estimates EBVs when BLUP, GAS, or MAS used

                                    as selection criterion for males

                        Type: Integer

                        Options:

                           0 EBVs are not estimated

                           1 EBVs are estimated

                        Default: MaleRunBlup must be specified

 

  MaleDestinySel        Definition: Defines the destiny of selected males

                        Type: Integer

                        Options:

                              0 Selected males are left alive

                              1 Selected males are reproduced (mated)

                              2 Selected males have germ plasm stored

                              3 Selected males are genotyped or candidates for

                                genotyping

                              4 Selected males are transferred to another

                                (test) herd; the herd is specified by

                                MaleTestHerd

                              6 Selected males have DYD sampled

                             12 Selected males are reproduced and have germ

                                plasm stored

                             14 Selected males are reproduced after

                                transfer to another (test) herd; the herd is

                                specified by MaleTestHerd

                             16 Selected males are reproduced and have DYD

                                sampled

                             26 Selected males have germ plasm stored and

                                DYD sampled

                            126 Selected males are reproduced, have germ

                                plasm stored, and DYD sampled

                             90 Selected males are tagged as candidates to

                                be left alive

                             91 Selected males are tagged as candidates to

                                reproduce (mate)

                             92 Selected males are tagged as candidates to

                                have germ plasm stored

                             93 Selected males are tagged as candidates for

                                genotyping

                             94 Selected males are tagged as candidates for

                                transfer to another (test) herd

                             96 Selected males are tagged as candidates to

                                have DYD sampled

                            912 Selected males are tagged as candidates to

                                reproduce and have germ plasm stored

                            914 Selected males are tagged as candidates to

                                reproduce after transfer to another (test) herd

                            916 Selected males are tagged as candidates to

                                reproduce and have DYD sampled

                            926 Selected males are tagged as candidates to

                                have germ plasm stored and DYD sampled

                           9126 Selected males are tagged as candidates to

                                reproduce, have germ plasm stored, and DYD

                                sampled

                        Default: MaleDestinySel must be specified

 

  MaleTestHerd          Definition: Test herd to which selected males are

                                    transferred

                        Type: Integer

                        Options: 1≤MaleTestHerdnherd

                        Default: MaleTestHerd must be specified

 

  MaleDestinyUnsel      Definition: Destiny of unselected males

                        Type: Integer

                        Options:

                           0 Males are culled

                           1 Males are left alive

                        Default: MaleDestinyUnsel must be specified

 

  MalePedigree          Definition: Male pedigree used in EVA-selection

                        Type: Character

                        Options:

                           yes Pedigree information used

                           no  Pedigree information not used

                        Default: MalePedigree must be specified

 

  MaleMaxMatings        Definition: Maximum number of matings allocated to

                                    selected males. Male reproductive capacity

                        Type: Integer

                        Options: ≥1

                        Default: MaleMaxMatings must be specified

 

  MaleGermplasm         Definition: Number of units of germplasm stored for

                                    selected males

                        Type: Integer

                        Options: ≥1

                        Default: MaleGermplasm must be specified

 

  FemaleSelCrit         Definition: Criterion used to select females

                        Type: Character

                        Options:

                           pheno Phenotypic selection

                           blup  Selection on BLUP EBV's

                           gas   Selection on (gene effect + BLUP EBV's)

                           mas   Selection on MA-BLUP EBV's

                        Default: FemaleSelCrit must be specified

 

  FemaleRunBlup         Definition: Estimates EBVs when BLUP, GAS, or MAS used

                                    as selection criterion for females

                        Type: Integer

                        Options:

                           0 EBVs are not estimated

                           1 EBVs are estimated

                        Default: FemaleRunBlup must be specified

 

  FemaleDestinySel      Definition: Defines the destiny of selected females

                        Type: Integer

                        Options:

                              0 Selected females are left alive

                              1 Selected females are reproduced (mated)

                              2 Selected females have germ plasm stored

                              3 Selected females are genotyped or candidates

                                for genotyping

                              4 Selected females are transferred to another

                                (test) herd; the herd is specified by

                                FemaleTestHerd

                             12 Selected females are reproduced and have germ

                                plasm stored

                             14 Selected females are reproduced after

                                transfer to another (test) herd; the herd is

                                specified by FemaleTestHerd

                             17 Selected females are reproduced as bull-dams

                            127 Selected candidates are reproduced as bull-dams

                                and have germ plasm stored

                            147 Selected females are reproduced as bull-dams

                                after transfer to another (test) herd; the herd

                                is specified by FemaleTestHerd

                             90 Selected females are tagged as candidates to

                                be left alive

                             91 Selected females are tagged as candidates to

                                reproduce (mate)

                             92 Selected females are tagged as candidates to

                                have germ plasm stored

                             93 Selected females are tagged as candidates for

                                genotyping

                             94 Selected females are tagged as candidates for

                                transfer to another (test) herd

                            912 Selected females are tagged as candidates to

                                reproduce and have germ plasm stored

                            914 Selected females are tagged as candidates to

                                reproduce after transfer to another (test) herd

                            917 Selected females are tagged as candidates to

                                reproduce as bull-dams

                           9127 Selected females are tagged as candidates to

                                reproduce as bull-dams and have germ plasm

                                stored

                           9147 Selected females are tagged as candidates to

                                reproduce as bull-dams after transfer to another

                                (test) herd

                        Default: FemaleDestinySel must be specified

 

  FemaleTestHerd        Definition: Test herd to which selected females are

                                    transferred

                        Type: Integer

                        Options: 1≤FemaleTestHerdnherd

                        Default: FemaleTestHerd must be specified

 

  FemaleDestinyUnsel    Definition: Destiny of unselected females

                        Type: Integer

                        Options:

                           0 Females are culled

                           1 Females are left alive

                        Default: FemaleDestinyUnsel must be specified.

 

  FemalePedigree        Definition: Female pedigree used in EVA-selection

                        Type: Character

                        Options:

                           yes Pedigree information used

                            no Pedigree information not used

                        Default: FemalePedigree must be specified.

 

  FemaleMaxMatings      Definition: Maximum number of matings allocated to

                                    selected females. Female reproductive

                                    capacity.

                        Type: Integer

                        Options: ≥1

                        Default: FemaleMaxMatings must be specified.

 

  FemaleGermplasm       Definition: Number of units of germplasm stored for

                                    selected females

                        Type: Integer

                        Options: ≥1

                        Default: FemaleGermplasm must be specified.

 

  FutMaleBreeders       Definition: Non-candidate males, but potential breeders

                                    at later selection stage or time step, used

                                    to establish relationship matrix. Males

                                    younger than the maximum reproductive age of

                                    living males are used.

                        Type: Character

                        Options:

                           none       Non-candidate males not used

                           herd       Only non-candidate males from same herd(s)

                                      as candidates used

                           population All non-candidate males used

                        Default: FutMaleBreeders must be specified

 

  FutFemaleBreeders     Definition: Non-candidate females, but potential

                                    breeders at later selection stage or time

                                    step, used to establish relationship matrix.

                                    Females younger than the maximum

                                    reproductive age of living males are used.

                        Type: Character

                        Options:

                           none       Non-candidate females not used

                           herd       Only non-candidate females from same

                                      herd(s) as candidates used

                           population All non-candidate females used

                        Default: FutMaleBreeders must be specified

 

  nMatings              Definition: Total number of matings

                        Type: Integer

                        Options: ≥1

                        Default: nMating must be specified

 

  LitterSize            Definition: Number of offspring per mating

                        Type: Integer

                        Options: ≥1

                        Default: LitterSize must be specified

 

  SexRatio              Definition: Probability of an offspring being a female

                        Type: Real

                        Options: 0.0≤ SexRatio ≤1.0

                        Default: SexRatio must be specified

 

  EvaParameterFile      Definition: File with input to EVA

                        Type: Character(len≤50)

                        Options: Any character string; file must exist in

                                 directory specified in namelist &DESTINR,

                                 variable reportR.

                        Default: EvaParameterFile must be specified

 

  **Relation to other namelists**

  &SELECTION

  (a) Namelist &EVA is read when sex_code 7 in any selection stage of

      namelist &SELECTION, variable selection_scheme.

  (b) Number of EVA-selection stages in namelist &EVA, variable EvaSelection

      must equal the number of selection stages in namelist &SELECTION,

      variable selection_scheme with EVA-selection (i.e., sex_code 7).

 

  &BASEPOPULATION

     Information in EvaSelection is used to generate the base population.

 

  **Additional information**

  1) All variables in namelist &EVA, variable EvaSelection are read

     and, therefore, must be specified. However, there are cases where some

     variables are not used. The most striking case is when MalePedigree or

     FemalePedigree set to ‘no’. Other cases are when selected animals are not

     destined to be mated. In these cases, variables, such as Littersize and

     SexRatio are not used. For variables that are not used, the input provided

     is irrelevant. However, for clarity, we recommend providing 0 for integer

     variables and 0.0 for SexRatio (the only real).

 

  2) Only animals tagged for EVA-selection are selection candidates. That is,

     animals tagged in selection stages prior to the EVA-selection stage and

     after the previous EVA-selection stage, if there is more than one EVA-

     selection stage. Animals are tagged for EVA selection in namelist

     selection, variable selection_scheme.

 

  3) EVA-selection tags are removed from all animals following a stage of EVA

     selection.

 

  4) stage must correspond to a selection stage in namelist &SELECTION, variable

     selection_scheme with sex_code 7.

 

  5) Either MalePedigree or FemalePedigree, or both, must be ‘yes’. That is, EVA

     selection is not carried out when both MalePedigree and FemalePedigree

     are ‘no’. In this case, the program stops.

 

  6) (a) When MalePedigree ‘yes’, MaleSelCrit, MaleRunBlup, MaleDestinySel,

         MaleDestinyUnsel, and MaleMaxMatings must be specified. These variables

         are not used when MalePedigree ‘no’. In this case, MaleSelCrit is set

         to ‘ ‘ and the other (integer) variables to 0.

     (b) When FemalePedigree ‘yes’, FemaleSelCrit, FemaleRunBlup,

         FemaleDestinySel, FemaleDestinyUnSel, and FemaleMaxMatings must be

         specified. These variables are not used when FemalePedigree ‘no’. In

         this case, FemaleSelCrit is set to ‘ ‘ and the other (integer)

         variables to 0.

 

  7) (a) MaleRunBlup must be 0:1 when MaleSelCrit ‘blup’, ‘gas’, or ‘mas’;

         FemaleRunBlup must be 0:1 when FemaleSelCrit ‘blup’, ‘gas’, or ‘mas’.

     (b) MaleRunBlup is not used when MaleSelCrit ‘pheno’; FemaleRunBlup is not

         used when FemaleSelCrit ‘pheno’. In these cases, MaleRunBlup and

         FemaleRunBlup are set to 0.

     (c) MaleRunBlup and/or FemaleRunBlup must be 1 if the EVA-selection stage

         is the first selection stage where selection_criterion ‘blup’, ‘gas’,

         or ‘mas’. The first selection stage(s) can be a truncation-selection

         stage(s).

     (d) When MaleRunBlup and/or FemaleRunBlup 1, selection_criterion ‘blup’,

         ‘gas’, or ‘mas’, and selection stage not the first selection stage

         where selection_criterion ‘blup’, ‘gas’, or  ‘mas’, EBVs are only

         estimated if new information has been gathered since the previous EBV

         estimation. At present, this new information is genotyping of animals.

 

  8) (a) When males that are not alive are amongst those males tagged for EVA

         selection (i.e., live_status 0 in namelist &SELECTION, variable

         selection_scheme),

          (i) MaleDestinySel must be 1 or 91,

         (ii) When MaleDestinySel 1, and a dead animal with stored germ plasm is

              selected for reproduction, the animal’s reproductive capacity

              is defined as follows. If the number of stored germ plasm is

              greater or equal to MaleMaxMatings, the animal’s reproductive

              capacity is MaleMaxMatings. If, however, the number of stored germ

              plasm is less than MaleMaxMatings, the animal’s reproductive

              capacity is the number of stored germ plasm. The consequence of

              this is that, insufficient stored germ plasm can lead to less

              matings being carried out than planned.

     (b) 8)(a) applies to females

 

  9) Females tagged for EVA selection can be either normal females or bull dams.

     That is, both normal females (sex_code 2 or 6 in namelist &SELECTION,

     variable selection_scheme) and bull dams (sex_code 4) cannot be selected

     for EVA selection.

 

 10) (a) Animals can be tagged with a view to selection with sex_code 5 or 6 at

         a subsequent selection stage during the same time step. That is,

         MaleDestinySel can be 90, 91, 92, 93, 94, 96, 912, 914, 916, 926, or

         9126 and FemaleDestinySel 91, 92, 93, 94, 912, 914, 917, 9127, or 9147.

     (b) Animals cannot be tagged for EVA selection. That is, MaleDestinySel and

         FemaleDestinySel cannot be 95.

 

 11) (a) MaleTestHerd must be specified when MaleDestinySel includes transfer to

         another (test) herd. That is, MaleDestinySel 4 or 14.

     (b) FemaleTestHerd must be specified when FemaleDestinySel includes

         transfer to another (test) herd. That is, FemaleDestinySel 4, 14, or

         147.

     (c) 0≤MaleTestHerdnherd and 0≤FemaleTestHerdnherd when specified.

 

 12) (a) MaleMaxMatings>0 when MalePedigree ‘yes’.

     (b) FemaleMaxMatings>0 when FemalePedigree ‘yes’.

 

 13) (a) MaleGermplasm>0 when MaleDestinySel 2, 12, 26, or 126.

     (b) FemaleGermplasm>0 when FemaleDestinySel 2, 12, or 127.

     (c) If an animal is reselected to have germ plasm stored within a time step

         or during a subsequent time step, the new number of germ plasm is added

         to the number currently stored for the animal. The exception is males

         and females in the base population.

 

 14) LitterSize>0 and 0.0≤SexRatio≤1.0 when the destiny for selected females

     includes reproduction. That is, FemalePedigree ‘yes’ and FemaleDestinySel

     1, 2, 14, 17, 127, or 147.

 

 15) EvaParameterFile must be specified and the file must exist.

 

&MATINGDESIGN

 mating_design=mating_design      /

 

  **Task**

  Specify method to mate selected animals.

 

  **Properties of names**

  mating_design         Definition: Method to mate selected animals.

                        Type: Character

                        Options:

                           random_mating Parents mated randomly.

                           mc_mating     Minimum-coancestry mating.

                           mcac_mating   Mating by minimising covariance of

                                         ancestral genetic contributions.

                        Default: random_mating

 

&MATINGHERDS

 male_mating=male_mating

 female_mating=female_mating      /

 

  **Task**

  Mates males and females across or within herds when more than one herd.

 

  **Properties of names**

  male_mating           Definition: Mate males across or within herds.

                        Type: Character

                        Options:

                           across_herds Males mated across herds.

                           within_herd  Males mated within_herds.

                        Default: across_herds

 

  female_mating         Definition: Mate females across or within herds.

                        Type: Character

                        Options:

                           across_herds Females mated across herds.

                           within_herd  Females mated within_herds.

                        Default: across_herds

 

  **Relation to other namelists**

  &POPVARIABLES

  If nherd>1, namelist &MATINGHERDS is read.

  If nherd=1, namelist &MATINGHERDS is not read.

 

  **Additional information**

  Two steps are carried out when the population is made up of more than one

  herd.

  (1) The program checks that there is the appropriate number of breeding

      animals in each herd. If not, animals are transferred across herds. A

      typical example where animals are transferred is when selection is carried

      out across herds and selected animals are mated within herds; there is no

      guarantee that there are enough animals for mating within each herd.

  (2) The animals are mated.

 

  The manner by which these two steps are carried out is determined by input to

  (i) male_mating and female_mating, and (ii) mating_design. There are four

  Possibilities:

 

  1) male_matings=across_herds, female_matings=across_herds

     (a) Randomly transfers females across herds. Females are removed from

         their current herds and randomly transferred to another herd. They

         can also be 'transferred' back to the current herd.

     (b) Males are mated to the females across herds. The offspring are

         allocated the herd of their dam. Males retain their original herd.

  2) male_matings=across_herds, female_matings=within_herd

     (a) Transfers surplus females across herds when the available number of

         females does not equal the number required for mating. Females with the

         lowest selection criteria are transferred; when a herd has too many

         females for mating, those females with the lowest selection criteria

         are transferred to herds with too few females.

     (b) Males are mated to females across herds. The offspring are allocated

         the herd of their dam.

  3) male_matings=within_herd, female_matings=across_herds

     (a) Transfers surplus males across herds when the available number of

         males does not equal the number required for mating. Males with the

         lowest selection criteria are transferred; when a herd has too many

         males for mating, those males with the lowest selection criteria

         are transferred to herds with too few males.

     (b) Females are mated to males across herds. The offspring are allocated

         the herd of their sire.

  4) male_matings=within_herd, female_matings=within_herd

     (a) Transfers surplus males and/or females across herds when the available

         number of males and/or females does not equal the number required for

         mating. Males and/or females with the lowest selection criteria are

         transferred; when a herd has too many males and/or females for mating,

         those males and/or females with the lowest selection criteria are

         transferred to herds with too few males and/or females.

     (b) Males and females are mated within herds. The offspring are

         allocated the herd of their parents.

 

&GENERATIONSBACK

 ngenerations=ngenerations      /

 

  **Task**

  Specify the ancestors used when mating by minimum-coancestry-covariance.

 

  **Properties of names**

  ngenerations          Definition: Number of generations ancestors of selected

                                    animals are traced back when using minimum-

                                    coancestry-covariance mating.

                        Type: Integer

                        Options: ≥0

                        Default: 5

 

  **Relation to other namelists**

  &MATINGDESIGN

  If mating_design=mcac_mating, ngenerations is read.

  If mating_design=random_mating or mc_mating, ngenerations is not read.

 

&OBSERVATIONS

 nMaleObs=nMaleObs

 nFemaleObs=nFemaleObs

 nDydObs=nDydObs

 

 MaleObservations=

 obs  FirstHerd  LastHerd  age  alive  selection  CullingUnselected 

 CullingOldAge  CullingInvoluntary  genotyping

 

 FemaleObservations=

 obs  FirstHerd  LastHerd  age  alive  selection  CullingUnselected 

 CullingOldAge  CullingInvoluntary  genotyping

 

 DydObservations=

 Obs  nOffspring  TimeLag  AgeMates      /

 

NB! Number of lines for MaleObservations, FemaleObservations, and DydObservations must equal nMaleObs, nFemaleObs, and nDydObs.

 

  **Task**

  Input for realising observations. Namelist is always read.

 

  **Properties of names**

  nMaleObs              Definition: Number of observations recorded for males

                        Type: Integer

                        Options: ³0

                        Default: 0

 

  nFemaleObs            Definition: Number of observations recorded for females

                        Type: Integer

                        Options: ³0

                        Default: 0

 

  nDydObs               Definition: Number of DYD observations for males

                        Type: Integer

                        Options: ³0

                        Default: 0

 

  obs                   Definition: Observation number

                        Type: Integer

                        Options: 1≤obsnobs

                        Default: obs must be specified

 

  FirstHerd             Definition: First herd within which animals are

                                    candidates to have observation obs realised

                        Type: Integer

                        Options:

                          1≤FirstHerdnherd First herd number

                                         -9 Herd not considered

                        Default: FirstHerd must be specified

 

  LastHerd              Definition: Last herd within which animals are

                                    candidates to have observation obs realised

                        Type: Integer

                        Options:

                           1≤LastHerdnherd Last herd number

                                         -9 Herd not considered

                        Default: LastHerd must be specified

 

  age                   Definition: Age which animals are candidates to have

                                    observation obs realised

                        Type: Integer

                        Options:

                           Males

                             1≤ageOldAgeMales when gestation_length 0

                             0≤ageOldAgeMales when gestation_length>0

                           Females

                             1≤ageOldAgeFemales when gestation_length 0

                             0≤ageOldAgeFemales when gestation_length>0

                           -9 Age not considered

                        Default: age must be specified

 

  alive                 Definition: Live status of candidates to have

                                    observation obs realised

                        Type: Integer

                        Options:

                            1 Animal needs to be alive

                           -9 Live status not considered

                        Default: alive must be specified

 

  selection             Definition: Age at which an animal needs to be

                                    selected to produce offspring and produce

                                    offspring for observation obs to be realised

                                    at age age

                        Type: Integer

                        Options:

                           Males

                             1≤selectionOldAgeMales when gestation_length 0

                             0≤selectionOldAgeMales when gestation_length>0

                           Females

                             1≤selectionOldAgeFemales when gestation_length 0

                             0≤selectionOldAgeFemales when gestation_length>0

                           -9 Selection not considered

                        Default: selection must be specified

 

  CullingUnselected     Definition: Age at which an animal needs to be

                                    culled because it was not selected to have

                                    observation obs realised

                        Type: Integer

                        Options:

                     Males

                       1≤CullingUnselectedOldAgeMales when gestation_length 0

                       0≤CullingUnselectedOldAgeMales when gestation_length>0

                     Females

                       1≤CullingUnselectedOldAgeFemales when gestation_length 0

                       0≤CullingUnselectedOldAgeFemales when gestation_length>0

                     -1 Observation obs realised at culling regardless of age

                     -9 Culling not considered

                        Default: CullingUnselected must be specified

 

  CullingOldAge         Definition: Animal has observation obs realised when

                                    culled for old age

                        Type: Integer

                        Options:

                           1 Observation realised when culled for old age

                          -9 Culling not considered

                        Default: CullingOldAge must be specified

 

  CullingInvoluntary    Definition: Age at which an animal needs to be

                                    culled involuntary to have observation

                                    obs realised

                        Type: Integer

                        Options:

                    Males

                      1≤CullingInvoluntaryOldAgeMales when gestation_length 0

                      0≤CullingInvoluntaryOldAgeMales when gestation_length>0

                    Females

                      1≤CullingInvoluntaryOldAgeFemales when gestation_length 0

                      0≤CullingInvoluntaryOldAgeFemales when gestation_length>0

                    -1 Observation obs realised at culling regardless of age

                    -9 Culling not considered

                        Default: CullingInvoluntary must be specified

 

  genotyping            Definition: Animal has observation obs realised when

                                    genotyped

                        Type: Integer

                        Options:

                            1 Animal needs to be genotyped

                           -9 Genotyping not considered

                        Default: genotyping must be specified

 

  nOffspring            Definition: Number of offspring in progeny group.

                        Type: Integer

                        Options: ≥1

                        Default: noffspring must be specified.

 

  TimeLag               Definition: Time lag (in time steps) from selection

                                    until the DYD is realised

                        Type: Integer

                        Options: 0≤TimeLagntime

                        Default: TimeLag must be specified.

 

  AgeMates             Definition: Age of mates when offspring are born.

                        Type: Integer

                        Options: 1≤AgeMatesntime, where 1 means that mates

                                 are one time step older than offspring.

                        Default: AgeMates must be specified.

 

  **Relation to other namelists**

   &POPPRM

   Restrictions on age, selection, CullingUnselected, CullingOldAge, and

   CullingInvoluntary depend on gestation_length

 

  **Additional information**

  1) At least one of nMaleObs, nMaleObs, or nDydObs must be greater than zero

 

  2) (a) When FirstHerd -9, LastHerd must be -9

     (b) When LastHerd -9, FirstHerd must be -9

 

  3) When selection≠-9, age must be greater than selection

 

  4) When selection≥0, alive is not used

 

  5) When CullingUnselected≠-9, age must be -9

 

  6) When CullingOldAge≠-9, age must be -9

 

  7) When CullingInvoluntary≠-9, age must be -9

 

  8) When genotyping 1, age must be -9

 

  9) DYD’s cannot be sampled for traits influenced by maternal effects (whether

     genetic or environmental) (at present)

 

&MATRICES

 g_matrix=g_matrix

 r_matrix=r_matrix

 g_means=g_means     /

 

  **Task**

  Provide G and R matrices and trait means.

 

  **Properties of names**

  g_matrix              Definition: Elements of G matrix, additive genetic

                           (co)variances. Elements are read in as

   (row 1,column 1), (1,2), ... (1,column n), (2,1),

   (2,2) ...

                        Dimension: ntbv*ntbv

                        Type: Real

                        Default: ????

 

  r_matrix              Definition: Elements of R matrix, residual

                           (co)variances. Elements are read in as

   (row 1,column 1), (1,2), ... (1,column n), (2,1),

   (2,2) ...

                        Dimension: nres*nres

                        Type: Real

                        Default: ????

 

  g_means               Definition: Vector of means of traits.

                        Dimension: ntbv*1

                        Type: Real

                        Default: ???? 

 

&DESIGN_MATRICES

 sex_difference=sex_difference

 x_mean=x_mean

 z_breeding_value=z_breeding_value

 w_residual=w_residual

 z_maternal_genetic=z_maternal_genetic

 w_maternal_residual=w_maternal_residual

 economic_weight=economic_weight

 phen_select_weight=phen_select_weight

 ebv_observation=ebv_observation     /

 

  **Task**

  Provides matrices …

 

  **Properties of names**

 

  sex_difference        Definition: Vector of deviations of females from males.

                        Dimension: nfixed*1

                        Type: Real

                        Default: 0.0

 

  x_mean                Definition: Design matrix relating g_means to

observations.

                        Dimension: nobs*nfixed

                        Type: Integer

                        Default: Matrix of 0’s

 

  z_breeding_value      Definition: Design matrix relating breeding values to

observations.

                        Dimension: nobs*ntbv

                        Type: Integer

                        Default: Matrix of 0’s

 

  w_residual            Definition: Design matrix relating residuals to

observations.

                        Dimension: nobs*nres

                        Type: Integer

                        Default: Matrix of 0’s

 

  z_maternal_genetic    Definition: Design matrix relating breeding values of

the dam to observations.

                        Dimension: nobs*ntbv

                        Type: Integer

                        Default: Matrix of 0’s

 

  w_maternal_residual   Definition: Design matrix relating residuals of dams to

observations.

                        Dimension: nobs*nres

                        Type: Integer

                        Default: Matrix of 0’s

 

  economic_weight       Definition: Vector with relative economic weights of

true breeding values.

                        Dimension: ntbv*1

                        Type: Real

                        Default: 0.0

 

  phen_select_weight    Definition: Vector with weighting factors of

observations for phenotypic selection.

                        Dimension: nobs*1

                        Type: Real

                        Default: 0.0

 

  ebv_observation       Definition: Matrix relating observations to predicted

                                    breeding values.

                        Dimension: nobs*ntbv

                        Type: Integer

                        Default: Matrix of 0’s

 

  **Relation to other namelists**

  The size of the matrices are determined by information provided in namelists

  &POPVARIABLES.

 

&CONTROL_GENOME

  set_qtl_parameters=set_qtl_parameters

  set_marker_parameters=set_marker_parameters

  LD_method=LD_method

  use_marker_template=use_marker_template     /

 

  **Task**

  Specify the methods used to simulate QTL and genetic markers; if (1) the

  parameters of the QTL and markers are provided on input or sampled, (2)

  linkage disequilibrium is established between the QTL and marker in the base

  population, and (3) a marker template is sampled.

 

  **Properties of names**

  set_qtl_parameters    Definition: QTL parameters are (1) provided in the

                                    namelists QTL_PARAMETERS and

                                    QTL_EFFECTS_FREQUENCIES, or (2) sampled.

                        Type: Integer

                        Options:

                           1 QTL parameters are provided

                           2 QTL parameters are sampled

                        Default: 1

 

  set_marker_parameters Definition: Marker parameters are (1) provided in the

                                    namelists MARKER_PARAMETERS and

                                    MARKER_ALLELE_FREQUENCIES, or (2) sampled.

                        Type: Integer

                        Options

                           1 Marker parameters are provided

                           2 Marker parameters are sampled

                        Default: 1

 

  LD_method             Definition: Specify if linkage disequilibrium (LD) is

                                    established between QTL and marker alleles

                                    in the base population.

                        Options:

                           No  LD is not established; QTL and marker alleles are

                               in linkage equilibrium.

                           Meu LD is established using the method of

                               Meuwissen (2000, 2001)

                        Type: Character

                        Default: Meu

 

  use_marker_template   Definition: Specify if a marker template map is sampled;

the marker template is a dense marker map

that provides unique genotypes for all

individuals. The markers are not available

for selection purposes but serves only as a

monitoring tool, e.g. providing a

highresolution measure of IBD.

                        Type: Integer

                        Options:

                           1 Template is not sampled

                           2 Template is sampled

                        Default: 1

 

  **Relation to other namelists**

  &POPPRM

  &CONTROL_GENOME is only read if nchrom>0 in namelist &POPPRM.

 

  &QTL_PARAMETERS and &QTL_EFFECTS_FREQUENCIES

  If set_qtl_parameters=1 the namelists &QTL_PARAMETERS and

  &QTL_EFFECTS_FREQUENCIES are read.

 

  &SAMPLE_QTL_PARAMETERS and &SAMPLE_QTL_NUMBERS

  If set_qtl_parameters=2 the namelists &SAMPLE_QTL_PARAMETERS and

  &SAMPLE_QTL_NUMBERS are read.

 

  &MARKER_PARAMETERS and &MARKER_ALLELE_FREQUENCIES

  If set_marker_parameters=1 the namelists &MARKER_PARAMETERS and

  &MARKER_ALLELE_FREQUENCIES are read.

 

  &SAMPLE_MARKER_PARAMETERS

  If set_marker_parameters=2 the namelist &SAMPLE_MARKER_PARAMETERS is read.

 

  &LD

  IF LD_method≠’no’ the namelist &LD is read.

 

  &TEMPLATE_PARAMETERS

  If use_marker_template=2, the namelist &TEMPLATE_PARAMETERS is read.

 

&MARKER_NUMBERS

 lengths=lengths

 markers=markers     /

 

  **Task**

  Provide the lengths and number of markers on each chromosome.

 

  **Properties of names**

  lengths               Definition: Length (cM) of each chromosome

                        Type: Integer

                        Dimension: nchrom*1

     Integer required for each chromosome; the

                                   number of chromosomes, nchrom, is provided in

                                   namelist &POPPRM.

                        Options: ³0

                        Default: 0

 

  markers               Definition: Number of markers on each chromosome

                        Type: Integer

                        Dimension: nchrom*1

     Integer required for each chromosome; the

                                   number of chromosomes, nchrom, is provided in

                                   namelist &POPPRM.

                        Options: ³0

                        Default: 0

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &MARKER_NUMBERS is read when nchrom>0 in &CONTROL_GENOME.

 

  **Additional information**

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, seven markers are located on two chromosomes (nchrom=2, namelist

  &POPPRM); four markers are located on the first chromosome, three markers are

  on the second.

 

  &MARKER_NUMBERS

  lengths=

   110.2

 

    97.6        [Two chromosomes; the first is 110.2cM, the second 97.6cM]

 

  markers=

       4

 

       3     /  [The first chromosome has four markers, the second three]

 

&MARKER_PARAMETERS

 m_positions=m_positions

 m_alleles=m_alleles     /

 

  **Task**

  Provide positions of the marker loci and the number of alleles at each locus.

 

  **Properties of names**

  m_positions           Definition: Position (cM) of the markers on each

                                    chromosome

                        Type: Real

                        Dimension: Real required for each marker; the number of

                                   markers is the sum of the number of markers

                                   on each chromosome (markers, namelist

                                   &MARKER_NUMBERS).

                        Options: ³0

                        Default: 0.0

 

  m_alleles             Definition: Number of alleles at each marker locus

                        Type: Integer

                        Dimension: Integer required for each marker; the number

                                   of markers is the sum of the number of

                                   markers on each chromosome (markers, namelist

                                   &MARKER_NUMBERS).

                        Options: ³0

                        Default: 0

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &MARKER_PARAMETERS is only read if set_marker_parameters=1 in namelist

  &CONTROL_GENOME.

 

  **Additional information**

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, seven markers are on located two chromosomes (nchrom=2, namelist

  &POPPRM; markers=4 3, namelist &MARKER_NUMBERS); four markers are located on

  the first chromosome, three markers are on the second.

 

  &MARKER_PARAMETERS

  m_positions=

   13.2

   17.6

   45.1

   47.3      [Positions (cM) of the four marker loci on the first chromosome]

 

   67.1

   71.7

   77.4      [Positions of the three markers loci on the second chromosome]

 

  m_alleles=

      4

      3

      2      [Four, three, two, and two alleles are at the four marker loci

      2       located on the first chromosome]

 

      2

      3      [Two, three and two alleles are at the three marker loci located on

      2     / the second chromosome]

 

&MARKER_ALLELE_FREQUENCIES

 m_al_freq=m_al_freq     /

 

  **Task**

  Provide frequencies of each marker allele.

 

  **Properties of names**

  m_al_freq             Definition: Frequencies of marker alleles

                        Type: Real

                        Dimension: Real required for each marker allele; the

                                   number of marker alleles is the sum of the

                                   number of alleles at each marker locus

                                   (m_alleles, namelist &MARKER_PARAMETERS).

                        Options: ³0.0

                        Default: 0.0

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &MARKER_ALLELE_FREQUENCIES is only read if set_marker_parameters=1 in

  namelist &CONTROL_GENOME.

 

  **Additional information**

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, seven marker loci are located on two chromosomes (nchrom=2, namelist

  &POPPRM; markers=4 3, namelist &MARKER_NUMBERS); four markers are located on

  the first chromosome, three markers are on the second. The numbers of

  alleles at the four marker loci on the first chromosome are four, three, two,

  and two; the numbers at the three loci located on the second chromosome are

  two, three, and two (m_alleles, namelist &MARKER_PARAMETERS).

 

  &MARKER_ALLELE_FREQUENCIES

  m_al_freq=

   0.86 0.07 0.05 0.02 [Frequencies of the four alleles at the first marker

locus located on the first chromosome]

   0.65 0.30 0.05      [Frequencies of the three alleles at the second marker

locus located on the first chromosome]

   0.50 0.50

   0.70 0.30

 

   0.55 0.45           [Frequencies of the two alleles at the first marker locus

located on the second chromosome]

   0.40 0.30 0.30

   0.90 0.10

    /

 

&SAMPLE_MARKER_PARAMETERS

 marker_type=marker_type

 marker_coverage=marker_coverage

 msat_density=msat_density

 snp_density=snp_density

 marker_spacing=marker_spacing      /

 

  **Task**

  Provides parameters to sample marker loci; type, number, density, and

  distribution of the loci.

 

  **Properties of names**

  marker_type           Definition: Type of markers sampled

                        Type: Character

                        Options:

                           msat  Microsatellites

                           snps  SNPs

                           both  Both SNPs and microsatellites

                        Default: snps

 

  marker_coverage       Definition: Number of markers sampled

                        Type: Integer

                        Options:

                           1 Number is provided in namelist &MARKER_PARAMETERS

                           2 Number is a function of marker density, where

                             marker density is provided as msat_density or

                             snp_density in namelist &SAMPLE_MARKER_PARAMETERS.

                        Default: 1

 

  msat_density          Definition: Number of microsatellite markers per cM.

                        Type: Real

                        Options: ³0.0

                        Default: 0.1

 

  snp_density           Definition: Number of SNPs markers per cM.

                        Type: Real

                        Options: ³0.0

                        Default: 1.0

 

  marker_spacing        Definition: Spacing of markers along the genome

                        Type: Integer

                        Options:

                           1 Markers evenly spaced across the genome

                           2 Markers randomly spaced across the genome

                        Default: 2

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &SAMPLE_MARKER_PARAMETERS is only read if set_marker_parameters=2 in namelist

  &CONTROL_GENOME.

 

&QTL_PARAMETERS

 qtls=qtls

 q_positions=q_positions

 q_alleles=q_alleles  /

 

  **Task**

  Number and position of QTLs, the number of alleles at each QTL, and the

  weight of each QTL.

 

  **Properties of names**

  qtls                  Definition: Number of QTLs on each chromosome

                        Type: Integer

                        Dimension: Integer required for each chromosome; the

                                   number of chromosomes, nchrom, is provided in

                                   namelist &POPPRM.

                        Options: ³0

                        Default: 0

 

  q_positions           Definition: Position (cM) of each QTL on each chromosome

                        Type: Real

                        Dimension: Real required for each QTL; the number of

                                   QTLs is the sum of the number of QTLS on each

                                   chromosome (qtls, namelist &QTL_PARAMETERS).

                        Options: ³0.0

                        Default: 0.0

 

  q_alleles             Definition: Number of alleles at each QTL

                        Type: Integer

                        Dimension: Integer required for each QTL; the number of

                                   QTLs is the sum of the number of QTLS on each

                                   chromosome (qtls, namelist &QTL_PARAMETERS).

                        Options: ³0

                        Default: 0

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &QTL_PARAMETERS is only read if set_qtl_parameters=1 in namelist

  &CONTROL_GENOME.

 

  **Additional information**

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, five QTLs are located on two chromosomes (nchrom=2, namelist

  &POPPRM); three QTLs are located on the first chromosome, two QTLs on the

  second.

 

  &QTL_PARAMETERS

  qtls=

      3

             [Two chromosomes; three QTLs are located on the first chromosome,

      2      two are located on the second]

 

  q_positions=

    3.2

    7.6

   15.1      [Positions (cM) of the three QTLs on the first chromosome]

 

   17.1

   54.7      [Positions of the two QTLs on the second chromosome]

 

  q_alleles=

      3

      2      [Three, two, and two alleles are at the three QTL loci located on

      2       the first chromosome]

 

      3      [Three and two alleles are at the two QTL loci located on the

      2 /     second chromosome]

 

&QTL_EFFECTS_FREQUENCIES

 q_effects=q_effects

 q_al_freq=q_al_freq     /

 

  **Task**

  Provide effects and frequencies of each QTL allele.

 

  **Properties of names**

  q_effects             Definition: Effect of each QTL allele

                        Type: Real

                        Dimension: Real required for each QTL allele; the

                                   number of QTL alleles is the sum of the

                                   number of alleles at each QTL (q_alleles,

                                   namelist &QTL_PARAMETERS).

                                   The block of input is repeated for each true

                                   breeding value simulated.

                        Options: ³0.0

                        Default: 0.0

 

  q_al_freq             Definition: Frequencies of QTL alleles

                        Type: Real

                        Dimension: Real required for each QTL allele; the

                                   number of QTL alleles is the sum of the

                                   number of alleles at each QTL (q_alleles,

                                   namelist &QTL_PARAMETERS).

                        Options: ³0.0

                        Default: 0.0

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &QTL_EFFECTS_FREQUENCIES is only read if set_qtl_parameters=1 in namelist

  &CONTROL_GENOME.

 

  **Additional information**

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, QTLs are located on two chromosomes (nchrom=2, namelist &POPPRM);

  three QTLs are located on the first chromosome, two QTLs on the second. The

  numbers of alleles at the three QTLs on the first chromosome are three, two,

  and two; the numbers at the two loci on the second chromosome are two and

  three (q_alleles, namelist &MARKER_PARAMETERS).

 

  &QTL_EFFECTS_FREQUENCIES

  q_effects=

   10.7 -3.0 -7.7      [Effects of the three alleles at the first QTL located

on the first chromosome]

    2.2 -2.2           [Effects of the two alleles at the second QTL located on

the first chromosome]

    5.1 -5.1

 

    1.9 -1.9           [Effects of the two alleles at the first QTL located on

the second chromosome]

    5.2  2.0 -7.2

 

  q_al_freq=

   0.07 0.23 0.70      [Frequencies of the three alleles at the first QTL

located on the first chromosome]

   0.05 0.95           [Frequencies of the two alleles at the second QTL located

on the first chromosome]

   0.50 0.50

 

   0.75 0.25           [Frequencies of the two alleles at the first QTL located

on the second chromosome]

   0.20 0.30 0.50

     /

 

&SAMPLE_QTL_PARAMETERS

 qtl_effect_input=qtl_effect_input

 gene_distribution=gene_distribution

 gamma_scale=gamma_scale

 gamma_shape=gamma_shape      /

 

  **Task**

  Provide parameters to sample QTLs; sample QTLs by number or QTL variance,

  distribution of QTL across the genome, and distribution of QTL effects.

 

  **Properties of names**

  qtl_effect_input      Definition: Specifies whether a (1) given number of QTL,

                                    (2) given amount of variance explained by

                                    QTL, or (3) given number of QTL explaining a

                                    given amount of variance is sampled

                        Type: Integer

                        Options: 1 Number of QTL sampled

                                 2 Amount of variance explained by QTL is

                                   sampled

                                 3 Number of QTL explaining given amount of

                                   variance is sampled

                        Default: 1

 

  gene_distribution     Definition: QTL are uniformly or multinomially

                                    distributed across the genome

                        Type: Integer

                        Options: 1 Uniform distribution

                                 2 Multinomial distribution

                        Default: 1

 

  gamma_scale           Definition: Scale parameter of gamma distribution; QTL

                                    effects assumed to follow a gamma

                                    distribution

                        Type: Real

                        Options: ³0.0

                        Default: 5.4

 

  gamma_shape           Definition: Shape parameter of gamma distribution; QTL

                                    effects assumed to follow a gamma

                                    distribution

                        Type: Real

                        Options: ³0.0

                        Default: 0.42

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &SAMPLE_QTL_PARAMETERS is only read if set_qtl_parameters=2 in namelist

  &CONTROL_GENOME.

 

&SAMPLE_QTL_NUMBERS

 n_qtl_trait=n_qtl_trait

 var_qtl_trait=var_qtl_trait     /

 

  **Task**

  Provide parameters to sample QTLs; number of QTLs affecting each trait and the

  variance of the traits explained by the QTLs.

 

  **Properties of names**

  n_qtl_trait           Definition: Number of QTL affecting each trait

                        Type: Integer

                        Dimension: Integer required for each trait; where the

                                   number of traits, ntbv, is provided in

                                   namelist &POPVARIABLES.

                        Options: ³0

                        Default: 0

 

  var_qtl_trait         Definition: Variance of each trait explained by QTL

                        Type: Real

                        Dimension: Real required for each trait; where the

                                   number of traits, ntbv, is provided in

                                   namelist &POPVARIABLES.

                        Options: ³0.0

                        Default: 0.0

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &SAMPLE_QTL_NUMBERS is only read if set_qtl_parameters=2 in namelist

  &CONTROL_GENOME.

 

  **Additional information**

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, two traits (ntbv=2, namelist &POPVARIABLES) are affected by 2 and 4

  QTLS.

 

  &SAMPLE_QTL_NUMBERS

  n_qtl_trait=

      2

      4       [Two traits affected by two and four QTLs]

 

  var_qtl_trait=

    0.2

  100.0    /  [QTL variance 0.2 for the first trait, 100.0 for the second trait]

 

&LD

 LD_ngen=ngen

 LD_npat=npat

 LD_nmat=nmat

 cri_val_qtl=cri_val_qtl     /

 

  **Task**

  Parameters to generate linkage disequilibrium (LD) between QTL and marker

  alleles in the base population.

 

  **Properties of names**

  ngen                  Definition: Number of generations simulated to

                                    generation LD in the base population.

                        Type: Integer

                        Options: ³1

                        Default: 100

 

  npat                  Definition: Number of paternal founders in each

                                    generation.

                        Type: Integer

                        Options: ³1

                        Default: 100

 

  nmat                  Definition: Number of maternal founders in each

                                    generation.

                        Type: Integer

                        Options: ³1

                        Default: 100

 

  cri_val_qtl           Definition: Value use as proportional sensitivity, when

determining the QTL frequency. E.g.

cri_val_qtl=0.2 means a 20% difference is

accepted between the sampled and the

specified QTL frequency.

                        Type: Real

                        Options: 0.0<cri_val_qtl£1.00

                        Default: 0.20

 

  **Relation to other namelists**

  &CONTROL_GENOME

  &LD is only read if LD_method=‘Meu’ in namelist &CONTROL_GENOME.

 

  **Additional information**

  Small cri_val_qtl values will cause the program to run slowly.

 

&IBD

 ibd_task=ibd_task

 ibd_method=ibd_method

 inbreeding=inbreeding

 use_selective_genotyping=use_selective_genotyping

 update_var_qtl=update_var_qtl

 start_ma_blup=start_ma_blup

 genotype_sire_base=genotype_sire_base

 qtl_wt=qtl_wt        /

 

  **Task**

  Parameters to compute IBD matrix or inverse of the IBD matrix

 

  **Properties of names**

  ibd_task                Definition: Specifies if the IBD matrix or inverse of

                                      the IBD matrix is computed

                          Type: Character

                          Options:

                             ibd     IBD matrix is computed (only works with

                                     ibd_method = linkage so far)

                             inv_ibd Inverse of the IBD matrix is computed

                          Default: inv_ibd

 

  ibd_method              Definition: Information used to derive the inverse of

                                      the IBD matrix

                          Type: Character

                          Options:

                             Linkage  Uses only family information

                             link&ld  Uses bot family and linkage disequilibrium

                                      information

                             ld       Uses only linkage disequilibrium

                                      information

                          Default: linkage

 

  inbreeding              Definition: Include inbreeding in IBD matrix

                          Type: Character

                          Options:

                             yes

                             no

                          Default: no

 

  use_selective_genotyping Definition: Proportion of the selection candidates

                                       are genotyped

                          Type: character

                          Options:

                             yes Proportion of selection candidates are

                                 genotyped

                             no  All selection candidates are genotyped

                          Default: no

 

  update_var_qtl          Definition: Update QTL variance used in MA-BLUP after

  each round of selection to take account of

  changes in allele frequencies

                          Type: character

                          Options:

                             yes

                             no

                          Default: no

 

  start_mas               Definition: Determines in which timestep to start

  MAS

                          Type: integer

                          Options: 1 <= start_mas <= ntime

                          Default: 1

 

  genotype_sire_base      Definition: Determines whether base males with

                                      offspring are genotyped.

                          Type: character

                          Options:

                             yes

                             no

                          Default: yes

 

  qtl_wt                  Definition: Weight placed one each QTL during

  selection; the weight is relative to

  polygenic effects.

                          Type: Real

                          Dimension: Real required for each QTL; the number of

                                     QTLs is the sum of the number of QTLS on

 each chromosome (qtls, namelist

 &QTL_PARAMETERS).

                          Options: qtl_qt ³ 0.0

                          Default: 1.0

 

  **Relation to other namelists**

  &POPPRM and &SELECTION

  &IBD is only read if (1) nchrom>0 in namelist &POPPRM and (2)

  selection_criterion=‘mas’ in any selection stage of selection_scheme in

  namelist &SELECTION.

 

  &IBD_PARAMETERS

  &IBD_PARAMETERS is read if ibd_method=‘link&ld’ or ‘ld’.

 

  &SELECTIVE_GENOTYPING

  &SELECTIVE_GENOTYPING is read if use_selective_genotyping=‘yes’.

 

  **Additional information**

  Option ibd_task=‘ibd’ is currently not available.

 

  Option update_var_qtl=‘yes’ only available for one QTL and one trait.

 

  **Example**

  The following illustrates how the input for this namelist is provided. In the

  example, five QTLs are located on two chromosomes (nchrom=2, namelist

  &POPPRM); three QTLs are located on the first chromosome, two QTLs on the

  second.

 

  &IBD

 

  qtl_wt=

    1.0      [Equal weight given to the first QTL on the first chromosome and

              polygenic effects]

    0.9      [Less weight given to the second QTL]

    1.7      [More weight given to the second QTL]

 

    2.2      [More weight given to the first QTL on the second chromosome]

    0.5

 

&IBD_PARAMETERS

 n_t=n_t

 n_eff=n_eff

 n_window=n_window

 c_prob=c_prob /

 

  **Task**

  Parameters used to compute the inverse of the IBD matrix.

 

  **Properties of names**

  n_t                     Definition: Number of generations

                          Type: Integer

                          Options: ³1

                          Default: 100

 

  n_eff                   Definition: Effective size of population

                          Type: integer

                          Options: ³1

                          Default: 100

 

  n_window                Definition: Number of markers to the left and right

                                      side of the QTL position

                          Type: integer

                          Options: ³1

                          Default: 2

 

  c_prob                  Definition: Level of probability for clustering. If

                                      IBD probability larger than c_prob for two

                                      haplotypes, they are clustered. If not,

                                      they remain separate and the IBD

                                      probability is set to 0.

                          Type: real

                          Options: 0.0 <= c_prob < 1.0

                          Default: 0.90

 

  **Relation to other namelists**

  &IBD

  Namelist &IBD_PARAMETERS is only read if ibd_method=link&ld or ld in namelist

  &IBD.

 

&SELECTIVE_GENOTYPING

 genotyping_method=genotyping_method

 prop_male=prop_male

 prop_female=prop_female     /

 

  **Task**

  Specify which selection candidates are genotyped.

 

  **Properties of names**

  genotyping_method        Definition: Criterion used to identify candidates to

                                       be genotyped

                          Type: Character

                          Options:

                             random

                             ave_ebv

                             combine

                          Default: random

 

  prop_male                Definition: Proportion of male candidates to be

                                       genotyped

                          Type: Real

                          Options: 0.0£prop_male£1.0

                          Default: 0.2

 

  prop_female              Definition: Proportion of female candidates to be

                                       genotyped

                          Type: Real

                          Options: 0.0£prop_female£1.0

                          Default: 0.2

 

  **Rel