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RESEARCH ARTICLE OPEN ACCESS
Spanish Journal of Agricultural Research
18 (1), e0403, 11 pages (2020)
eISSN: 2171-9292
https://doi.org/10.5424/sjar/2020181-15459
Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)
Comparison of different selection methods for improving litter size
in sheep using computer simulation
Meysam Latifi (Latifi, M)1, Amir Rashidi (Rashidi, A)1, Rostam Abdollahi-Arpanahi (Abdollahi-Arpanahi, R)2
and Mohammad Razmkabir (Razmkabir, M)1
1 University of Kurdistan, Faculty of Agriculture, Dept. of Animal Science, Sanandaj, Iran 2 University of Tehran, College of Aburaihan,
Dept. of Animal Science, Tehran, Pakdasht, Iran
Abstract
Aim of study: To assess selection methods via introgression to improve litter size in native and synthetic sheep breeds.
Area of study: Sanandaj, Kurdistan, Iran.
Material and methods: Selection approaches were performed using classical, genomic, gene-assisted classical (GasClassical)
and gene-assisted genomic (GasGenomic) selection. Litter size trait with heritability of 0.1 including two chromosomes was simu-
lated. On chromosome 1, a single QTL as the major gene was created to explain 40% of the total additive genetic variance. After
simulation of a historical population, the animals from the last historical population were split into two populations. For the next 7
generations, animals were selected for favorable or unfavorable alleles to create distinct breeds of A or B, respectively. Then from
the last generation, both males and females from breed B were selected to create a native population. On the other hand, males from
breed A and females from breed B were mated to simulate a synthetic population. Finally, intra-population selections were carried
out based on high breeding values during the last five generations.
Main results: The genetic gain in the synthetic breed was higher than that of the native breed under all selection methods. The
frequencies of favorable alleles after five generations in the classical, genomic, GasClassical and GasGenoimc selection approach-
es in the synthetic breed were 0.623, 0.730, 0.850 and 0.848, respectively.
Research highlights: Combining gene-assisted selection with classical or genomic selection has the potential to improve ge-
netic gain and increase the frequencies of favorable allele for litter size in sheep.
Additional key words: major gene; synthetic breed; genomic evaluation
Abbreviations used: CBLUP (conventional or best linear unbiased prediction); GasClassical (gene-assisted classical selection);
GasGenomic (gene-assisted genomic selection); GPBV (prediction of genomic breeding values); LD (linkage disequilibrium); LS
(litter size); MCMC (Monte Carlo Markov Chain); PBV (prediction of breeding value); QTL (quantitative trait loci); SNP (single
nucleotide polymorphisms); TBV (true breeding value)
Authors’ contributions: Designed the study: ML and AR. Analyzed the data: ML. Wrote the paper: ML, AR. and RAA. Supervised
the work: AR. All authors read the paper and approved the final manuscript.
Citation: Latifi, M; Rashidi, A; Abdollahi-Arpanahi, R; Razmkabir, M (2020). Comparison of different selection methods for
improving litter size in sheep using computer simulation. Spanish Journal of Agricultural Research, Volume 18, Issue 1, e0403.
https://doi.org/10.5424/sjar/2020181-15459
Supplementary material (Fig. S1) accompanies the paper on SJAR’s website.
Received: 13 Jul 2019. Accepted: 02 Apr 2020.
Copyright © 2020 INIA. This is an open access article distributed under the terms of the Creative Commons Attribution 4.0
International (CC-by 4.0) License.
Funding: The authors received no specific funding for this work.
Competing interests: The authors have declared that no competing interests exist.
Correspondence should be addressed to Amir Rashidi: arashidi@uok.ac.ir
Introduction
Litter size (LS) is defined as the number of lambs
born per ewe lambing. In sheep, a large variation in
litter size has been observed among and within
breeds. A trait such as LS can be genetically affected
by many genes with small effects as well as major
genes with large effects (Drouilhet et al., 2009). The
major genes frequency is one of the main factors in
improving breeding program efficiency for LS in
sheep (Elsen et al., 1994). Since the heritability of
LS is low (Hanford et al., 2005; Mokhtari et al.,
2010), the selection based on the ewe’s own perfor-
mance might induce a slow genetic gain. In addition,
DNA testing of major genes and learning about in-
heritance patterns shown that major genes could lead
to improvement of ovulation rates and LS in sheep
(Davis, 2005).
Meysam Latifi, Amir Rashidi, Rostam Abdollahi-Arpanahi and Mohammad Razmkabir
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
2
domly mated for 1000 generations with an effective
population size of 1000 animals (500 males and 500
females). At the second step, two random samples
consisting of 330 animals as founders (30 males and
300 females for each breed) were drawn out of the last
generation of historical population to simulate two dif-
ferent breeds, hereafter called A and B breeds. For the
next 7 generations, using a random mating design,
animals from breed A and B were selected based on
favorable and unfavorable alleles of the major gene,
respectively. Hence, two breeds were generated and
fixed for favorable and unfavorable alleles. After fixa-
tion of favorable and unfavorable alleles, the breeding
values of animals for LS were predicted using a thresh-
old model (Model 2 below). At the third step, 30 males
and 300 females from the last generation of Breed B
were selected based on high breeding values and
treated as founders to generate the native breed. Fur-
thermore, to generate the synthetic breed, 30 males and
300 females from the last generation of breed A and B,
respectively, were selected based on high breeding
values and treated as founders. The founder animals
expanded over five generations and were selected and
mated based on high breeding values and minimizing
inbreeding. In order to have a constant population size
across generations, each dam produced 5 offsprings
with an equal probability of each sex. Replacement
rates for males and females were 40% and 20%, re-
spectively. In generations G1 to G5, the native and the
synthetic breeds were kept at a constant size of 1500
breeding candidates per each breed and 30 males and
300 females were selected in each generation as parents
of the next generation.
Genome structure
The LS trait in sheep was simulated with heritabil-
ity of 0.1. The genome consisted of 2 chromosomes,
each 100 cM in length. For each chromosome, 10000
markers and 100 QTLs were simulated (20000 SNPs
and 200 QTLs in total). Due to the limitation in com-
putational requirements, only two chromosomes were
considered. One of the QTLs at position 25.7 cM on
chromosome 1 was considered as the major gene which
explained 40% of the additive genetic variance for LS
trait. This fraction of genetic variance for the major
gene was similar to that reported in the Lacaune sheep
by Bodin et al. (2014). Other QTLs were randomly
distributed over the chromosomes. The rest of the ad-
ditive genetic variance (60%) was allocated to the re-
maining 199 QTLs. The QTLs effects were sampled
from a gamma distribution with shape of parameter ϒ
= 0.4. Biallelic SNP markers were randomly distrib-
When a major gene with desirable characteristics is
detected in a particular breed, introduction and intro-
gression of this gene into other breeds might be desir-
able. The cross between two or more breeds and sub-
sequent mating among crossbred animals is considered
a synthetic breed. Almost 418 synthetic breeds have
been developed from the combination of two and more
breeds (Rasali et al., 2006). One of the main purposes
of developing synthetic breeds has been to increase
prolificacy and reproduction efficiency (Hulet et al.,
1984; Fahmy, 1990). Hence, crossbreeding between
high and low prolific breeds for increasing favorable
allele frequencies in a synthetic breed appear to be use-
ful for improving LS. Previous studies have shown that
breeding programs for introduction and introgression
of favorable alleles such as the Booroola gene (FecB)
into other sheep breeds is highly successful (Gootwine
et al., 2008; Mishra et al., 2009).
Conventional or best linear unbiased prediction
(CBLUP) selection is based on pedigree and pheno-
typic information (Henderson, 1975). Genomic selec-
tion, described by Meuwissen et al. (2001) is a method
for improving quantitative traits in plant and animal
breeding. This technique relies on the segmentation of
the genome in thousands of intervals bracketed by
contiguous markers and effects of all markers on the
whole genome are estimated (Gaspa et al., 2015).
Several major genes (casual mutations) have been
identified for LS in sheep (Galloway et al., 2000; Souza
et al., 2001; Hanrahan et al., 2004; Martinez-Royo et
al., 2008; Drouilhet et al., 2009). The genomic selec-
tion method (Duchemin et al., 2012) has opened its
way into sheep breeding programs. Combining ge-
nomic or classical selection with gene-assisted selection
could be used for creating a synthetic sheep breed.
Therefore, the objectives of this study were: (1) to
compare classical, genomic, gene-assisted classical
(GasClassical) and gene-assisted genomic (GasGe-
nomic) selection methods in introducing a favorable
gene for the creation of a synthetic breed to improve
LS; and (2) to track genetic gain between a native and
a synthetic sheep breed via classical and genomic selec-
tion over five generations in a sheep population by
simulation.
Material and methods
Simulation
Simulations were performed (Fig. 1) based on the
forward-in-time process using the QMSim software
(Sargolzaei & Schenkel, 2009). The first step involved
the historical population being generated and ran-
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
3
Introduction of a major gene to improve litter size in sheep population
trait such as LS. All parameters used for the simulation
are summarized in Table 1.
Selection
Two selection strategies were used from G0 to G5.
The first was creation of the synthetic breed to intro-
duce a favorable allele by classical, genomic, GasClas-
sical and GasGenomic selection and the second was
the selection of superior animals in the native breed
based on classical and genomic selection.
Prediction of breeding values
―Classical selection. The Bayesian method was
used for prediction of breeding values (PBVs) based
on pedigree and phenotypic information. For Bayesian
method, the MCMCglmm R package developed by
uted along the two chromosomes. The mutation rate
for both markers and QTL was assumed 2.5×10-4 per
locus per generation (Esfandyari et al., 2015). The true
breeding value (TBV) for an individual was calculated
by multiplying the genotype codes by the QTL ef-
fects. Finally, the phenotypic value of each individual
i (yi), was created by adding a normally distributed
residual
e
i
~
N
0,
σ
e
2
( )
to the sum over QTLs of ge-
netic values as shown below:
y
i
=
k
=1
m
∑
x
ik
α
k
+
e
i
(1)
Above, xik (i=1, …, n; k=1,…, m) is an element of
the incidence marker matrix for additive genetic effects
(αk) and ei is a random residual [ e ~
N
0,
Iσ
e
2
( )
], where
σ
e
2is the residual variance. To convert a continuous
trait into a threshold trait in each generation, 20% of
the high-level phenotypes were considered to be 2, and
the rest were considered as 1 to simulate a categorical
19
1
Figure 1. Structure of the simulation schemes. 2
(500 males and 500 females)
Generation = 1000
After fixation of favorable
and unfavorable alleles in
Breed A and B, respectively,
the breeding values of the
animals were predicted
Breed B (30 males and 300 females)
7 generations
Selection based on unfavorable allele
Breed A (30 males and 300 females)
7 generations
Selection based on favorable allele
Native Breed
Selection based on high breeding
values for 5 generations
Synthetic Breed
Selection based on high breeding
values for 5 generations
Figure 1. Structure of the simulation schemes.
Meysam Latifi, Amir Rashidi, Rostam Abdollahi-Arpanahi and Mohammad Razmkabir
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
4
Hadfield (2010) was applied to analyze classical selec-
tion using BLUP methodology. The following animal
model was used:
l = 1μ + Za + e (2)
where l is the vector of underlying latent variable for trait
(one threshold and two categories of response), μ is the
overall mean, 1 is a vector of ones, Z is the incidence
matrix relating phenotypic records to the animals, a is a
vector of random additive genetic effects with distribution
a~ N(0, A
σ
a
2
)
and e is a vector of random residuals with
e~ N(0, I
σ
e
2)
, where
σ
a
2 and
σ
e
2are additive genetic and
residual variances, respectively. A and I are the additive
genetic relationship and the identity matrices, respec-
tively. A total of 300,000 rounds of Gibbs sampler were
considered and the first 30,000 rounds were discarded as
a burn-in period. The thinning interval was set to 100
cycles. In each generation, pedigree and phenotypic re-
cords of new generation were added to the recent pedi-
gree and data file. Therefore, PBVs for every round of
selection were re-calculated and the predicted breeding
values were used for selection.
―Genomic selection. The Bayes B method was used
to estimate marker effects with Monte Carlo Markov
Chain (MCMC). In Bayes B, it is assumed that each
SNP has either an effect of zero or non-zero with prob-
abilities of π and 1-π, respectively, and for those with
non-zero effect, it is assumed that each SNP has a dif-
ferent variance. The BGLR (Bayesian Generalized
Linear Regression) package of R software (Perez &
Campos, 2014) was used for prediction of genomic
breeding values (GPBVs). The Gibbs sampler was run
for 30,000 rounds with a 3,000 burn-in period. The
thinning interval was set to 10 cycles. The following
model was used to estimate the genomic breeding values:
l =
µ
+
j=1
n
∑xijmj+e
(3)
where l is the vector of underlying latent variable for
trait (one threshold and two categories of response), μ
is the overall mean, 1 is a vector of ones, xij is an inci-
dence matrix for marker j and individual i, mj is a
random effect for marker j and e is the random resid-
ual error with distribution of e~ N(0, I
σ
e
2). In each
generation, the effects of markers were estimated using
female phenotypes. GPBVs for male and females were
calculated as the sum of all marker effects according
to their marker genotypes:
GPBVi=
j=1
n
∑xijmj
!
(4)
where xij is the genotype of animal i at locus j, and mj
!
is the estimated substitution effect of marker j.
Table 1. Parameters of the simulation process.
Historical and current populations
No. of generations (effective population size) 1000 (1000)
Breed A B Native Synthetic
No. of founder sires (dams) 30 (300) 30 (300) 30 (300) 30 (300)
Criteria for selection/culling Favorable allele/
age
Unfavorable
allele/age
High breeding
value/age
High breeding
value/age
No. of generations for each breed 7 7 5 5
Mating system Random Random Minimizes
inbreeding
Minimizes
inbreeding
No. of offspring per dam 5
Replacement ratio for males (females) 0.4 (0.2)
Sex probability for offspring 0.5
Genome
No. of chromosomes 2
Total length of chromosome (M) 2
Position of markers and QTLs Random
No. of QTL 200
No. of markers 20000
Marker and QTL mutation rate 2.5 × 10–4
Heritability 0.1
Variance of QTL as the major gene (%) 40
Position of major gene (cM) 25.7
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
5
Introduction of a major gene to improve litter size in sheep population
where D = freq(AB) – (freq(A) × freq(B)); freq(AB)
is frequency of observed haplotype; and freq(A) and
freq(B) are frequencies of alleles A and B, respec-
tively.
Evaluation of scenarios
The genetic gain, frequency of favorable allele and
mean of inbreeding coefficient were monitored across
generations for all selection schemes. The genetic gain
per generation was computed as the average TBV over
time. In addition, the accuracy of prediction for both
classical and genomic selection methods was obtained
as the Pearson correlation between the TBVs and (G)
PBVs in each generation. A total of 10 replicates were
produced for each scenario and selection method. The
10 replicates were simulated separately, but the initial
generation (G0) was identical for all scenarios within
each replicate.
Results
Native breed
The results obtained using simulations performed
for the native breed are summarized in Table 2. The
results obtained under classical and genomic selection
methods showed that the trend of true breeding values
increased across generations. The mean of true breed-
ing values for both methods were -0.22 at G0 and in-
creased to 0.264 and 0.621 at G5 for classical and
genomic selection, respectively. Furthermore, the mean
of true breeding values obtained under genomic selec-
Combining gene-assisted selection with
classical and genomic selection
In the present study, selection and culling of animals
in each generation was based on (G)PBVs and age, re-
spectively. For combining gene-assisted selection with
classical and genomic selection (GasClassical and
GasGenomic), we developed an alternative approach that
allows selection of animals with favorable allele and the
highest (G)PBVs as the parents of the next generation.
According to this approach: 1) the PBV or GPBV for
each animal was predicted using model 2 and 3, respec-
tively; 2) homozygosity or heterozygosity of each animal
was determined based on the favorable allele, and 3)
based on the equation below, the weighted predicted
breeding value of each animal was obtained:
G
( )
PBVW=G
( )
PBVp+NFA (5)
where G
( )
PBVW
=G
( )
PBVp+NFA
is the weighted PBV or GPBV,
G
( )
PBVW=
G
( )
PBVp
+NFA
is the predicted PBV or GPBV for each ani-
mal based on model 2 and 3, respectively, and NFA is
number of favorable alleles in each animal. If an animal
had 2, 1 or zero copies of the favorable allele, NFA was
2, 1 and 0, respectively (Fig. S1 [suppl.]).
Linkage disequilibrium (LD)
The LD in the native and the synthetic breeds from
G0 to G5 was assessed by r2 among all pairs of markers
using QMSim software (Sargolzaei & Schenkel, 2009):
r2=D2
fre(A) ×freq(a) ×freq(B) ×freq(b) (6)
Table 2. Mean of true breeding values, accuracy of prediction (r) and mean of inbreeding coefcient (F) in each generation
based on classical and genomic selection in the native breed.
Selection method Gen MeanTBV r(PBV,TBV) F
Classical 0 -0.220 ± 0.155 0.253 ± 0.056 0.000 ± 0.000
1 -0.146 ± 0.154 0.309 ± 0.064 0.000 ± 0.000
2 -0.064 ± 0.168 0.374 ± 0.066 0.000 ± 0.000
3 0.042 ± 0.187 0.370 ± 0.102 0.000 ± 0.000
4 0.146 ± 0.206 0.375 ± 0.055 0.004 ± 0.004
5 0.264 ± 0.226 0.358 ± 0.075 0.016 ± 0.007
Genomic 0 -0.220 ± 0.155 0.669 ± 0.077 0.000 ± 0.000
1 -0.145 ± 0.155 0.696 ± 0.067 0.000 ± 0.000
2 0.017 ± 0.170 0.722 ± 0.061 0.000 ± 0.000
3 0.209 ± 0.197 0.763 ± 0.047 0.000 ± 0.000
4 0.416 ± 0.215 0.779 ± 0.047 0.000 ± 0.000
5 0.621 ± 0.228 0.738 ± 0.046 0.002 ± 0.001
Meysam Latifi, Amir Rashidi, Rostam Abdollahi-Arpanahi and Mohammad Razmkabir
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
6
tion was 74% higher than that of the classical selection.
Thus, the accuracy of prediction using genomic selec-
tion was higher compared to the classical selection.
The highest accuracies for classical and genomic selec-
tion was obtained in G4 and afterwards, decreased in
G5 (Table 2). At G5, the mean of inbreeding coeffi-
cients for the native breed under classical and genom-
ic selection were 0.016 and 0.002, respectively.
Synthetic breed
The results obtained using simulations performed
for the synthetic breed are summarized in Table 3. As
expected, regardless of selection methods, mean of true
breeding values increased across generations. Genetic
gain obtained under GasGenomic (1.347) was higher
than that of obtained using the GasClassical selection
(1.007), and the value of 1.319 obtained for Genomic
selection was higher than that of obtained for the clas-
sical selection method (0.884). Combining gene assist-
ed-selection with classical and genomic selection led
to higher genetic gain. Consequently, genetic gain
obtained by GasGenomic and GasClassical selection
methods was greater than those of genomic and clas-
sical selection (2% and 16% higher genetic gain from
G0 to G5, respectively). As shown in Table 3, genom-
ic and GasGenomic selection resulted in better accura-
cies of PBV prediction in comparison with classical
and GasClassical selection methods. The highest ac-
curacy for classical, genomic, GasClassical and
GasGenomic selection in the synthetic breed were
obtained at G4 which decreased slightly at G5 (Table
3). For the synthetic breed, a similar pattern to that of
the native breed was observed for the mean of inbreed-
ing coefficient. At G5, mean of inbreeding coefficients
were 0.011, 0.002, 0.008 and 0.002 for classical,
genomic, GasClassical and GasGenomic genomic se-
lection, respectively. The mean of inbreeding coeffi-
cient in classical and GasClassical selection varied
more compared to genomic and GasGenomic selection.
The frequency of the favorable allele in each gen-
eration under classical, genomic, GasClassical and
GasGenomic selection in the synthetic breed for 10
replicates is shown in Fig. 2. The frequency of the fa-
vorable allele started with an initial value of 0.091 at
G0 and reached to 0.623, 0.730, 0.850 and 0.848 at G5
for classical, genomic, GasClassical and GasGenomic
selection methods, respectively (Table 3). The fre-
quency of favorable allele under classical and genomic
Table 3. Mean of true breeding values, accuracy of prediction (r) and mean of inbreeding coefcient (F) in each generation
based on classical, genomic, GasClassical and GasGenomic selection methods in the synthetic breed.
Selection
method Gen MeanTBV r(PBV,TBV) Frequency1F
Classical 0 -0.142 ± 0.151 0.263 ± 0.034 0.091 ± 0.000 0.000 ± 0.000
1 0.282 ± 0.154 0.298 ± 0.066 0.500 ± 0.000 0.000 ± 0.000
2 0.332 ± 0.149 0.361± 0.095 0.451 ± 0.005 0.000 ± 0.000
3 0.384 ± 0.163 0.506 ± 0.057 0.429 ± 0.024 0.000 ± 0.000
4 0.530 ± 0.168 0.514 ± 0.059 0.491 ± 0.051 0.002 ± 0.003
5 0.742 ± 0.176 0.462 ± 0.086 0.623 ± 0.072 0.011 ± 0.004
Genomic 0 -0.142 ± 0.151 0.581 ± 0.089 0.091 ± 0.000 0.000 ± 0.000
1 0.281 ± 0.153 0.646 ± 0.056 0.500 ± 0.000 0.000 ± 0.000
2 0.399 ± 0.144 0.720 ± 0.052 0.449 ± 0.003 0.000 ± 0.000
3 0.579 ± 0.177 0.799 ± 0.043 0.442 ± 0.003 0.000 ± 0.000
4 0.852 ± 0.198 0.834 ± 0.045 0.537 ± 0.004 0.001 ± 0.001
5 1.177 ± 0.207 0.820 ± 0.048 0.730 ± 0.003 0.002 ± 0.003
GasClassical 0 -0.142 ± 0.151 0.251 ± 0.044 0.091 ± 0.000 0.000 ± 0.000
1 0.279 ± 0.152 0.303 ± 0.084 0.500 ± 0.000 0.000 ± 0.000
2 0.304 ± 0.168 0.386 ± 0.053 0.449 ± 0.005 0.000 ± 0.000
3 0.460 ± 0.184 0.510 ± 0.060 0.550 ± 0.033 0.000 ± 0.000
4 0.666 ± 0.220 0.516 ± 0.049 0.700 ± 0.053 0.002 ± 0.003
5 0.883 ± 0.251 0.482 ± 0.065 0.850 ± 0.043 0.008 ± 0.005
GasGenomic 0 -0.142 ± 0.151 0.635 ± 0.089 0.091 ± 0.000 0.000 ± 0.000
1 0.281 ± 0.151 0.672 ± 0.068 0.500 ± 0.000 0.000 ± 0.000
2 0.407 ± 0.145 0.741 ± 0.052 0.449 ± 0.004 0.000 ± 0.000
3 0.637 ± 0.150 0.784 ± 0.050 0.538 ± 0.027 0.000 ± 0.000
4 0.915 ± 0.159 0.805 ± 0.041 0.698 ± 0.003 0.001 ± 0.000
5 1.205 ± 0.184 0.793 ± 0.052 0.848 ± 0.005 0.002 ± 0.003
1Frequencies of favorable allele
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
7
Introduction of a major gene to improve litter size in sheep population
selection. Moreover, genetic gain in the synthetic breed
under GasGenomic (60%) and Genomic (57%) selec-
tion methods was higher than that obtained for the
native breed using the genomic selection method.
Linkage disequilibrium in the native and the
synthetic breeds
The average LD decay obtained using genomic se-
lection method for all possible pairs of markers in the
native and the synthetic breeds are shown in Fig. 4. As
illustrated, the maximum average of r2 for the native
and the synthetic breeds (genomic and GasGenomic
selection) at distance 0.0 to 50 kb at G0 were 0.19 and
0.18, respectively. However, the minimum average of
r2 at a distance of 400 to 500 kb for the native and the
selection (Figs. 2a and 2c) showed high fluctuations
whereas when applying GasClassical and GasGenomic
selections, no fluctuation was observed over 10 repli-
cates (Figs. 2b and 2d).
Comparison between the native
and the synthetic breeds
Mean of true breeding values for the native and the
synthetic breeds obtained using different methods are
shown in Fig. 3. As illustrated, genetic gains for LS in
the synthetic breed under classical or genomic selec-
tions were higher than selections in the native breed.
Genetic gain in the synthetic breed with GasClassical
(117%) and classical (82%) selection methods was
greater than that in the native breed under classical
Figure 2. Pattern of allele frequencies of the favorable allele for the synthetic breed under a) Classical b) Gene-assisted classical
(GasClassical), c) Genomic and d) Gene-assisted genomic (GasGenomic) selection across 10 replicates (the black line is the mean
of 10 replicates).
20
1
2
3
Figure 2. Pattern of allele frequencies of the favorable allele for the synthetic breed under a) 4
Classical b) Gene-assisted classical (GasClassical), c) Genomic and d) Gene-assisted 5
genomic (GasGenomic) selection over 10 replicates (the black line is the mean of 10 6
replicates). 7
8
0
0,2
0,4
0,6
0,8
1
012345
Frequency
Generation
Classical
a
0
0,2
0,4
0,6
0,8
1
012345
Frequency
Generation
GasClassical
b
0
0,2
0,4
0,6
0,8
1
012345
Frequency
Generation
Genomic
c
0
0,2
0,4
0,6
0,8
1
012345
Frequency
Generation
GasGenomic
d
Meysam Latifi, Amir Rashidi, Rostam Abdollahi-Arpanahi and Mohammad Razmkabir
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
8
synthetic breeds (genomic and GasGenomic selection)
at G0 were 0.11 and 0.10, respectively. For the native
and the synthetic breeds (genomic and GasGenomic
selection) at G5, the average maximum values of r2 for
distance of 0.0 to 50 kb were 0.30 and 0.26, respec-
tively. In addition, the average minimum values of r2
for the native and the synthetic breeds (genomic and
GasGenomic selection) from 400 to 500 kb at G5 were
0.23 and 0.18, respectively. For the native and the
synthetic breeds, by increasing marker pair distance,
the values of r2 decreased at G0 and G5 (Fig. 4). The
native breed showed higher levels of LD in comparison
with the synthetic breed at G0 and G5.
Discussion
The results of this study showed that employing
genomic and GasGenomic selection methods rather
than Classical and GasClassical selection lead to in-
crease in genetic gain in the native and the synthetic
breeds. Meuwissen et al. (2001) showed that using
genomic selection method resulted in an increased ac-
curacy of selection for traits with low heritability and
female sex-limited such as LS. A reason for the high
accuracy of prediction in genomic selection could be
due to use of the marker information to capture the
Mendelian sampling terms (Daetwyler et al., 2007).
The results reported by other researchers indicated that
the accuracy of prediction depends on the extent of
linkage disequilibrium, the density of markers, statisti-
cal methods, heritability of trait and selection design
(Wang et al., 2013; Gowane et al., 2018; Karimi et al.,
2019). Using simulated data, higher accuracies were
reported for genomic selection compared to classical
selection in dairy cattle (Gaspa et al., 2015), swine
(Putz et al., 2018) and American mink (Karimi et al.,
2019). In the current study, the accuracies in all selec-
tion methods increased from G0 to G4. Afterward, a
decrease was observed in G5, because individuals in
this generation did not have any recorded offspring.
When the combination of gene-assisted selection with
classical and genomic selection was carried out for
improvement of a trait by introducing a major gene,
genetic gain was higher than when classical and ge-
nomic selection were used alone. These findings indi-
cate that if the major gene is controlling a large propor-
tion of genetic variance in a population, the combination
of classical and genomic selection with gene-assisted
selection leads to an increase in genetic gain. Pedersen
et al. (2009) indicated that using genotype information
increased within-family selection and lead to an increase
in genetic gain as the accuracy of breeding values in-
creased. Generally, this result was obtained using clas-
sical and genomic selection methods in the synthetic
breed which resulted in higher genetic gain compared
to the native breed. High genetic gain for the synthetic
breed led to an increase of heterozygosity at the QTL
level and accuracy of selection method (Ødegard et al.,
2009b). Our results indicated that two breeds (A and B)
Figure 3. Mean of breeding values for the native and the synthetic breeds with Genomic and Clas-
sic selection methods across 10 replicates.
21
1
2
3
4
Figure 3. Mean of breeding values for the native and the synthetic breeds with Genomic and 5
Classic selection methods over 10 replicates. 6
7
-0,4
-0,2
0
0,2
0,4
0,6
0,8
1
1,2
1,4
012345
Mean of true breeding value
Generation
Classical-Native Breed
Classical-Synthetic Breed
GasClassical-Native Breed
Genomic-Native Breed
Genomic-Synthetic Breed
GasGenomic-Synthteic Breed
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
9
Introduction of a major gene to improve litter size in sheep population
GasClassical selection method (31%). These results are
in agreement with Ødegard et al. (2009a), who stated
that combining genomic selection with gene-assisted
selection for the target QTL acted as an additional ac-
tion against decline of the target QTL and gave surpass
genetic gain.
The study presented here about the extent of the LD
can be used to interpret the difference observed among
the breeds. Observed LD is a function of the recombi-
nation rate between loci within a breed and the selec-
tion performed for specific quantitative or qualitative
traits of interest (Prieur et al., 2017). Each of the breeds
showed the decrease in r2 with increased distance be-
tween markers. In the present study, the levels of LD
for the native and the synthetic breeds at a distance
from 0.0 to 50 kb at G0 and G5 was in agreement with
the results reported by Kijas et al. (2014) at a distance
of 10 kb. For the native and synthetic breeds under
selection, the level of LD increased over the genera-
tions. The high level of LD showed a high level of
selection intensity over generations for these breeds.
The extent of LD could be increased by several factors,
including inbreeding, population structure, and bottle-
necks (Pritchard & Przeworski, 2001). In this study,
the extent of LD was found to be remarkably different
between the native and the synthetic breeds (Fig. 4).
This could be due to the creation of the synthetic breed
from two cross-breeds (Breed A and B). Toosi et al.
(2010) mentioned that individual animals are less re-
lated to each other in a crossbreed population; there-
fore, LD haplotypes in crossbred populations are nar-
rower than in a purebred. Results of the current study
showed that the LD decay was different between
breeds, and similar results in sheep were reported by
Al-Mamun et al. (2015).
were separated based on the frequencies of the major
gene after 7 generations. If the two breeds were consid-
erably divergent, the relative advantage of crossing
could be higher.
In both the native and the synthetic breeds, the rate
of increase of inbreeding coefficient was lower in ge-
nomic selection compared to classical selection. Dae-
twyler et al. (2007) stated that the low inbreeding rate
in genomic selection compared to the classical selection
method is due to an increase in prediction accuracy of
the Mendelian sampling. In our simulation, the mating
system was based on optimized mating design. Thus,
pairs of mates were chosen based on minimizing ge-
netic relationship to create the next generation (Sargol-
zaei & Schenkel, 2009). Hence, the rate of inbreeding
coefficient in both genomic and classical selection was
lower than the results reported in previous research
(Ødegard et al., 2009b; Gaspa et al., 2015).
The frequency of favorable allele after five genera-
tions in classical, genomic, GasClassical and GasGe-
nomic selection methods in the synthetic breed were
0.62, 0.73, 0.85 and 0.85, respectively (Table 3). Re-
sults obtained in our study showed that the frequency
of favorable allele in genomic selection increased by
more than 20% compared to the classical selection.
These findings indicate that genomic selection is more
effective in increasing the frequency of favorable allele
than the classical selection without any knowledge of
the major gene’s position. Under GasClassical and
GasGenomic selection methods, the frequency of the
favorable allele was never declined in comparison with
classical and genomic selections (Fig. 2). The fre-
quency of the favorable allele was the same in the
GasClassical and GasGenomic, but the rate of genetic
gain in the GasGenomic was higher than that of the
Figure 4. The average LD decay for the native and the synthetic breeds (genomic and GasGenomic selection) at generation zero
(G0) and ve (G5) across 10 replicates.
22
1
2
Figure 4. The average LD decay for the native and the synthetic breeds (genomic and 3
GasGenomic selection) at generation zero (G0) and five (G5) across 10 replicates. 4
0
0,05
0,1
0,15
0,2
0,25
0,3
0,35
Average LD (r2)
Distance Range (kb)
G0
Genomic-Native Breed Genomic-Synthetic Breed GasGenomic-Synthetic Breed
0
0,05
0,1
0,15
0,2
0,25
0,3
0,35
Average LD (r2)
Distance Range (kb)
G5
Genomic-Native Breed Genomic-Synthetic Breed GasGenomic-Synthetic Breed
Meysam Latifi, Amir Rashidi, Rostam Abdollahi-Arpanahi and Mohammad Razmkabir
Spanish Journal of Agricultural Research March 2020 • Volume 18 • Issue 1 • e0403
10
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The results of this study confirmed that reproduction
and sex-limited traits such as LS in sheep can be im-
proved by using genomic selection methods. The results
also demonstrated that inclusion of information about
known causal mutations into genomic and classical
selection methods can lead to increase in frequency of
favorable allele and subsequently resulted in higher
genetic gain in the synthetic breed.
Acknowledgments
The authors are sincerely grateful to the Dr. M Hos-
sein Yazdi (Head of Technical Analysis Division,
Akvaforsk Genetics Center AS, N-6600 Sunndalsøra,
Norway) and Dr. Mehdi Bohlouli and Carsten Scheper
(Institute of Animal Breeding and Genetics, Justus-
Liebig-University Gießen, 35390 Gießen, Germany)
for the valuable discussions.
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