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
Description of individual namelists:
&RULES
&EVA
&OBSERVATIONS
Description of individual output files:
age_distribution_individual_selected.res
age_distribution_sires_selected.res
Mendelian_selection_differential.res
Program that simulates selective breeding schemes for animals. The program is
written in FORTRAN.
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)
Complete list of input parameters (namelists).
&EVA
&OBSERVATIONS
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
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.
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.
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:
FirstAge≤LastAge≤OldAgeMales for males
FirstAge≤LastAge≤OldAgeFemales 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.
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.
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.
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_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
**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≤TestHerd≤nherd
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**
The number of lines or selection stages required in selection_scheme
must be equal to selection_groups provided in namelist
&SELECTIONPARAMETERS.
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_stage≤selection_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≤TestHerd≤nherd 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**
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≤stage≤selection_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≤MaleTestHerd≤nherd
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≤FemaleTestHerd≤nherd
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**
(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≤MaleTestHerd≤nherd and 0≤FemaleTestHerd≤nherd 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.
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
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**
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.
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**
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≤obs≤nobs
Default: obs must be specified
FirstHerd Definition: First herd within which animals are
candidates to have observation obs realised
Type: Integer
Options:
1≤FirstHerd≤nherd 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≤LastHerd≤nherd 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≤age≤OldAgeMales when gestation_length 0
0≤age≤OldAgeMales when gestation_length>0
Females
1≤age≤OldAgeFemales when gestation_length 0
0≤age≤OldAgeFemales 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≤selection≤OldAgeMales when gestation_length 0
0≤selection≤OldAgeMales when gestation_length>0
Females
1≤selection≤OldAgeFemales when gestation_length 0
0≤selection≤OldAgeFemales 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≤CullingUnselected≤OldAgeMales when gestation_length 0
0≤CullingUnselected≤OldAgeMales when gestation_length>0
Females
1≤CullingUnselected≤OldAgeFemales when gestation_length 0
0≤CullingUnselected≤OldAgeFemales 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≤CullingInvoluntary≤OldAgeMales when gestation_length 0
0≤CullingInvoluntary≤OldAgeMales when gestation_length>0
Females
1≤CullingInvoluntary≤OldAgeFemales when gestation_length 0
0≤CullingInvoluntary≤OldAgeFemales 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≤TimeLag≤ntime
Default: TimeLag must be specified.
AgeMates Definition: Age of mates when offspring are born.
Type: Integer
Options: 1≤AgeMates≤ntime, where 1 means that mates
are one time step older than offspring.
Default: AgeMates must be specified.
**Relation to other namelists**
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)
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: ????
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
set_qtl_parameters=set_qtl_parameters
set_marker_parameters=set_marker_parameters
use_marker_template=use_marker_template /
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**
&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.
If set_marker_parameters=2 the namelist &SAMPLE_MARKER_PARAMETERS is read.
IF LD_method≠’no’ the namelist &LD is read.
If use_marker_template=2, the namelist &TEMPLATE_PARAMETERS is read.
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**
&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]
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**
&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]
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**
&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
/
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**
&SAMPLE_MARKER_PARAMETERS is only read if set_marker_parameters=2 in namelist
&CONTROL_GENOME.
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**
&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]
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**
&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
/
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**
&SAMPLE_QTL_PARAMETERS is only read if set_qtl_parameters=2 in namelist
&CONTROL_GENOME.
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**
&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.
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_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**
&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_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 is read if ibd_method=‘link&ld’ or ‘ld’.
&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
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
Options: ³1
n_eff Definition: Effective size of population
Options: ³1
n_window Definition: Number of markers to the left and right
Options: ³1
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.
Options: 0.0 <= c_prob < 1.0
**Relation to other namelists**
Namelist &IBD_PARAMETERS is only read if ibd_method=link&ld or ld in namelist
&IBD.
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
**Relation to other namelists**
Namelist &SELECTIVE_GENOTYPING is only read if selective_genotyping=‘yes’ in
namelist &IBD.
gas_weight=gas_weight
start_gas=start_gas /
**Task**
Parameters used in gene assisted selection.
**Properties of names**
gas_weight Definition: Weight placed on known gene effect; the
weight is relative to polygenic effects.
Type: Real
Options: ³0.0
Default: 1.0 (i.e., gene and polygenic effects are
equally weighted)
start_gas Definition: Determines in which time step GAS should
begin
Type: integer
Options: 1 <= start_gas <= ntime
Default: 1
**Relation to other namelists**
&POPPRM and &SELECTION
&GAS_PARAMETERS is only read if (1) nchrom>0 in namelist &POPPRM and
(2) selection_criterion=‘gas’ in any selection stage of selection_scheme in
namelist &SELECTION.
template_density=template_density
founder_representation=founder_representation
print_genotypes=print_genotypes /
**Task**
Parameters used to specify the use of a marker template. The marker template
is a dense marker map that provides unique genotypes for all base individuals.
It is sampled for all offspring according to Mendelian sampling terms allowing
for recombination. The markers are not available for selection purposes but
serves only as a monitoring tool, e.g. providing a high resolution measure of
IBD.
**Properties of names**
template_density Definition: Number of markers per cM
Type: Real
Options: ³0.0
Default: 2.0
print_genotypes Definition: Controls whether the template genotype for
all animals in timestep # is outputted in
the file ‘template_info#.res’.
Type: Integer
Options:
1: Yes, output
2: No, no output
Default: 1
founder_representation Definition: Specify if founder representation should be
calculated. For each time step the representation of
each base animal in specific loci are given. These
loci includes all QTL and a number of template loci
specified in &FOUNDER_PARAMETERS
Type: Integer
Options:
1: No, founder representation is not calculated.
2: Yes, founder representation is calculated.
Default: 1
**Relation to other namelists**
&TEMPLATE_PARAMETERS is only read if use_marker_template=2 in namelist
&CONTROL_GENOME.
pos_founderloci=pos_founderloci
n_founderloci=n_founderloci /
**Task**
Specifies for which loci founder representation should be determined.
**Properties of names**
n_founderloci Definition: Number of template loci in which founder
representation should be determined
Type: Integer
Options: ³0
Default: 0
pos_founderloci Definition: Positions of template loci in which founder
representation should be determined
Type: Real
Options: ³0.0
Default: 0.0
**Relation to other namelists**
&TEMPLATE_PARAMETERS
&FOUNDER_PARAMETERS is only read if founder_representation=2 in namelist
&TEMPLATE_PARAMETERS.
Twenty sires and 120 dams are selected each generation. Each sire is mated to
six dams, resulting in 120 full-sib families. Each dam produces 10 offspring and
1200 offspring are produced each generation. Marker information is not used.
&DESTINR
reportr='/hag/UncleFester/adam/' / [Output written to /hag/UncleFester/adam/]
&RANDOM_NUMBER_SEED
ran_seed=1 / [Clock generates seed for random number generator]
&POPPRM
npop=1 [One population]
gestation_length=0 [Gestation length 0 time steps]
nchrom=0 [Polygenic effects considered; no marker information]
OldAgeMales=1 [Age at which males are culled for old age]
OldAgeFemales=1 / [Age at which females are culled for old age]
&CONTROLPARAMETERS
ntime=20 [Simulation run for 20 generations]
nrep=100 [Simulation replicated 100 times]
start_rep=1 [First replicate simulated is replicate 1]
cull_males=0 [All males are stored in memory]
print_replicate=0 [Simulated data sets are not stored]
time_steps_season=1.0 [One time step per season]
time_steps_year=1 / [One time step per season]
&BASEPOPULATION
age_class_base=no_structure [All base animals born time step 0]
sample_base=yes [Base population is re-sampled in each replicate]
output_base=no / [Base population is not stored]
&POPVARIABLES
nherd=1 [One herd in the population]
nfixed=1 [One fixed effect]
ntbv=1 [Selection for a single trait]
nres=1 [One residual effect]
nobs=1 / [One observation recorded for each animal]
&SELECTIONPARAMETERS
selection_groups=2 [Two selection groups]
breeding_structure=conventional [Offspring generated by traditional methods]
dmu_version=dmu4 / [Breeding values estimated by BLUP using DMU4]
&SELECTION
selection_scheme=
1 1 1 'population' 1 1 1 1 'truncation' 'blup' 60 0 0 1 0 0 2 10 0.50 0
2 1 1 'population' 1 1 1 1 'truncation' 'blup' 120 0 0 1 0 0 1 10 0.50 0 /
[Selection stage 1
1 Selection of males
1 Live males selected
1 Males in first population selected
‘population’ Selection of males within the first population
1 Males from one time step of age considered for selection
1 Males older than one time step of age not considered for selection
1 First herd where selection carried out
1 Last herd where selection carried out
'truncation' Truncation selection
‘blup’ Selection based on breeding values estimated by BLUP
60 Sixty males selected in each round of selection
0 No related selection stages
0 No tag
1 Males selected to reproduce
0 Males not selected are culled
0 No test herd
2 Each male mated twice
10 Ten offspring produced by each male mating (this is ignored for
males)
0.50 Probability of offspring being female (this is not ignored for
males)
0 No germ plasm from selected males is stored
Selection stage 2
1 Selection of females
1 Live females selected
1 Females in first population selected
‘population’ Selection of females within the first population
1 Females from one time step of age considered for selection
1 Females older than one time step of age not considered for
selection
1 First herd where selection carried out
1 Last herd where selection carried out
'truncation' Truncation selection
‘blup’ Selection based on breeding values estimated by BLUP
120 120 females selected in each round of selection
0 No related selection stages
0 No tag
1 Females selected to reproduce
0 Females not selected are culled
0 No test herd
2 Each female mated twice
10 Ten offspring produced by each female mating
0.50 Probability of offspring being female
0 No germ plasm from selected females is stored]
&MATINGDESIGN
mating_design=mcac_mating / [Selected animals mated by minimum coancestry
covariance mating]
&GENERATIONSBACK
ngenerations=6 / [Ancestors traced six generations back when using
minimum coancestry covariance mating]
&OBSERVATIONS
nMaleObs=1
nFemaleObs=1
nDydObs=0
MaleObservations=
1 -9 -9 1 1 -9 -9 -9 -9 -9
FemaleObservations=
1 -9 -9 1 1 -9 -9 -9 -9 -9 /
&MATRICES
g_matrix=
0.25 [Additive genetic variance 0.25 of selected trait]
r_matrix=
0.75 [Residual variance 0.75 of selected trait]
g_means=
0.0 / [(Genetic) mean of selected trait in base population]
&DESIGN_MATRICES
sex_difference=
0 [No sex difference for the selected trait]
x_mean=
1 [Design matrix relating means to observations]
z_breeding_value=
1 [Design matrix relating breeding values to
observations]
w_residual=
1 [Design matrix relating residuals to observations]
z_maternal_genetic=
0 [Design matrix relating breeding values of dams to
observations]
w_maternal_residual=
0 [Design matrix relating residuals of dams to
observations]
economic_weight=
1 [Relative economic value of the selected trait]
ebv_observation=
1 / [Design matrix relating observations to predicted
breeding values]
Dairy cattle example where 200 young bulls and 1000 bull dams are selected each
generation using marker-assisted selection for a single QTL and a single trait.
Young bulls are tested using DYDs sampled outside the simulated populations.
&DESTINR
REPORTR ='/hag/popgen/acs/genotyp/ld_sel/' /
[Output written to /hag/popgen/acs/genotyp/ld_sel/]
&random_number_seed
ran_seed=1 [Clock generates seed for random number generator]
/
&POPPRM
npop=1
gestation_length=1
nchrom=1
OldAgeMales=8
OldAgeFemales=8 /
&CONTROLPARAMETERS ntime=25
nrep=50
start_rep=1
cull_males=1
print_replicate=0
PRINT_AGE_DISTRIBUTION_INDIVIDUAL_SELECTED = yes,
PRINT_AGE_DISTRIBUTION_SIRES_SELECTED = yes,
PRINT_SELECTION_DIFFERENTIAL = yes,
PRINT_ACCURACY = yes,
PRINT_NUMBER_GENOTYPED = yes
/
&BASEPOPULATION age_class_base=create_structure
sample_base=yes
output_base=no
/
&POPVARIABLES nherd=45
nfixed=1
ntbv=1
nres=1
nobs=1
/
&SELECTIONPARAMETERS
selection_groups=6,
dmu_version=dmu4 /
&selection
selection_scheme=
3 1 1 'population' 1 1 1 1 'truncation' 'blup' 400 0 0 3 0 0 0 0 0 0
2 1 1 'population' 1 5 1 1 'truncation' 'blup' 800 0 0 3 0 1 0 0 0 0
3 1 1 'population' 1 1 1 1 'truncation' 'mas' 200 0 0 26 0 0 0 0 0 2000
1 0 1 'population' 5 30 1 1 'truncation' 'blup' 10 0 0 1 0 0 450 0 0 0
2 1 1 'population' 1 5 1 1 'truncation' 'mas' 1000 6 0 17 0 1 1 1 0.5 0
2 1 1 'herd' 1 5 1 45 'truncation' 'blup' 100 0 0 1 0 0 1 1 0.5 0
/
&matingdesign
mating_design='random_mating'
/
&matingherds
male_matings='across_herd',
female_matings='within_herd'
/
&OBSERVATIONS
/
&MATRICES
g_matrix=
0.03
r_matrix=
0.96
g_means=
0.0
/
&DESIGN_MATRICES
sex_difference=
0
x_mean=
1
z_breeding_value=
1
w_residual=
1
z_maternal_genetic=
0
w_maternal_residual=
0
economic_weight=
1
ebv_observation=
1
/
&control_genome set_qtl_parameters=1,
set_marker_parameters = 1
use_marker_template = 1
LD_method='Meu'
/
&marker_numbers
markers=
4
lengths=
100
/
&marker_parameters
m_positions=
50 51.5 53.5 54
m_alleles=
5 5 5 5
/
&marker_allele_frequencies
m_al_freq=
0.2 0.2 0.2 0.2 0.2
0.2 0.2 0.2 0.2 0.2
0.2 0.2 0.2 0.2 0.2
0.2 0.2 0.2 0.2 0.2
/
&qtl_parameters
qtls=
1
q_positions=
52.5
q_alleles=
2
/
&qtl_effects_frequencies
q_effects=
0.236 0.0
q_al_freq=
0.1 0.9
/
&LD LD_ngen=100
LD_npat=100
LD_nmat=100
cri_val_qtl=0.01 /
&IBD ibd_method='link&ld'
start_mas=3
use_selective_genotyping='yes' /
&IBD_PARAMETERS
/
&SELECTIVE_GENOTYPING
genotyping_method='combine'
prop_male=1.0
prop_female=0.4
/
Complete list of output files (some optional):
accuracy.res (optional)
age_distribution_individual_selected.res (optional)
age_distribution_sires_selected.res (optional)
animal#.res (optional)
marker#.res (optional)
mean_timesteps.res
mean_timesteps_replicate.res
number_genotyped.res (optional)
obs#.res (optional)
qtl#.res (optional)
selection_differential.res (optional)
sire_contribution.res (optional)
Mendelian_selection_differential.res (optional)
template#.res
template_info#.res (optional)
mean_template#.res (optional)
mean_founder#.res (optional)
(Optional: Only printed if print_accuracy in namelist &CONTROLPARAMETERS has
value yes)
File includes the accuracy (correlation between true and estimated breeding
value) for each group of candidates for selection, so for each replicate,
time step, and stage of selection. If selection is on BLUP EBV’s only the
accuracy of the overall EBV is calculated. If selection is on
markerassisted BLUP EBV’s then both polygenic, QTL, and overall accuracies
are calculated. If selection is on gene-assisted selection, accuracies are
calculated for the polygenic component as well as overall EBV’s.
(Optional: Only printed if print_age_distribution_individual_selected in
Namelist &CONTROLPARAMETERS has value yes)
File includes distribution selected animals over age groups (in time steps)
for each replicate and time step. Distribution is only calculated where
selection from more than one age group is possible
(Optional: Only printed if print_age_distribution_sires_selected in
Namelist &CONTROLPARAMETERS has value yes)
File includes distribution of age of sire (in time steps) at the birth of
selected individuals for each replicate, time step, and stage of selection.
(Optional: Only printed if print_replicate in namelist &CONTROLPARAMETERS
has value yes)
File includes information on each individual animal including sire, dam,
sex, birth, death, herd, true and estimated breeding values etc.
(Optional: Only printed if founder_representation=2 in namelist
TEMPLATE_PARAMETERS)
For all QTL and a specified number of template loci the representation of
each founder (base animal) is given for each time step in replicate #. The
representation is given as the number of each founder allele and the number
of homozygotes for these alleles that the founder has contributed to the
population in the given time step.
(Optional: Only printed if print_replicate in namelist &CONTROLPARAMETERS
has value yes)
File includes marker genotypes for all individuals.
-all of the above output files are to be replaced by the following two files:
(Optional: Only printed if print_Mendelian_selection_differential in
Namelist &CONTROLPARAMETERS has value yes)
File includes mean Mendelian sampling term of QTL for candidates and
selected individuals for each replicate, time step, and stage of selection.
Means are given for both the breeding goal and each trait simulated.
(Optional: Only printed if print_number_genotyped in namelist
&CONTROLPARAMETERS has value yes)
File includes number of males and females genotyped for each replicate and
time step.
(Optional: Only printed if print_replicate in namelist &CONTROLPARAMETERS
has value yes)
File includes realised phenotype, weight (ratio of residual variance to
variance of phenotype given breeding value), time of recording and herd-
year-season class associated with the recording for each observation for
each animal.
(Optional: Only printed if print_replicate in namelist &CONTROLPARAMETERS
has value yes)
File includes QTL genotypes for all individuals.
(Optional: Only printed if print_selection_differential in Namelist
&CONTROLPARAMETERS has value yes)
File includes number of candidates and selected animals, their average true
breeding value, and their average estimated breeding value for each
replicate, time step, and stage of selection. Means are given for both the
breeding goal and each trait simulated.
(Optional: Only printed if print_sire_contribution in Namelist
&CONTROLPARAMETERS has value yes)
File includes number of sires of selected individuals and variance of
progeny group sizes for each replicate, time step, and stage of selection.
(Optional: Only printed if use_marker_template=2 in Namelist
&CONTROL_GENOME)
File includes average number of animals that are IBD in each of the marker
template loci for each time step in replicate #.
(Optional: Only printed if use_marker_template=2 in Namelist
&CONTROL_GENOME)
File includes IBD information based on marker template for all individuals
in each time step for replicate #. If print_genotypes=1 in Namelist
&TEMPLATE_PARAMETERS marker template genotypes for all individuals are
printed as well.
