387

ARTICLE
Signatures of selection analysis using whole-genome
sequence data reveals novel candidate genes for pony
and light horse types
Siavash Salek Ardestani, Mehdi Aminafshar, Mohammad Bagher Zandi Baghche Maryam,
Mohammad Hossein Banabazi, Mehdi Sargolzaei, and Younes Miar

Abstract: Natural selection and domestication have shaped modern horse populations, resulting in a vast range
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of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally
based on their body type. Understanding the genetic basis of horse type variation and selective pressures related
to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences
were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type
in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we
found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements
including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This
study contributes to a better understanding of the genetic background of differences between pony and light
horse types.
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Key words: fixation index, horse type, nucleotide diversity, signatures of selection, whole-genome sequence.
Résumé : La sélection naturelle et la domestication ont façonné les populations modernes de chevaux, ce qui a
produit une vaste gamme de races distinctes sur le plan phénotypique. Les races de chevaux sont classifiées en trois
types (poney, cheval de selle et cheval de trait) selon leur morphologie. Une compréhension de l’assise génétique
de la variation pour la morphologie et des pressions sélectives liées à la tendance évolutive peut s’avérer impor-
tante pour les stratégies de sélection actuelles. Des séquences génomiques ont été générées pour 14 poneys et
32 chevaux de selle pour étudier les signatures génétiques de la sélection du type chevalin chez les poneys et les
chevaux de selle. Au sein des extrêmes chevauchant pour l’indice de fixation et la diversité nucléotidique, les
auteurs ont trouvé des signatures génomiques inédites de balayages sélectifs à proximité de gènes clés déjà
rapportés comme étant impliqués dans le déterminisme de caractères morphologiques incluant C4ORF33, CRB1,
CPN1, FAM13A et FGF12, lesquels influencent possiblement la variation pour la morphologie corporelle chez les
poneys et les chevaux de selle. Cette étude fournit un éclairage qui contribuera à une meilleure compréhension de
l’assise génétique des différences phénotypiques entre les poneys et les chevaux de selle.
Mots-clés : indice de fixation, type de cheval, diversité nucléotidique, signatures de sélection, séquençage gé-
nomique complet.

Introduction history including agriculture, transportation, and sport

Horse domestication started in Western Asia approxi- (Bowling and Ruvinsky 2000; Jun et al. 2014). Domestica-
mately 5000–6000 years ago (Bowling and Ruvinsky tion, intensive selection, and various environmental con-
2000). Horses have played pivotal roles in the human ditions, as well as horse industry modernization, have

Received 2 January 2020. Accepted 6 May 2020.

S. Salek Ardestani and M. Aminafshar. Department of Animal Science, Science and Research Branch, Islamic Azad University,
Tehran 1477893855, Iran.
M.B. Zandi Baghche Maryam. Department of Animal Science, University of Zanjan, Zanjan 4537138791, Iran.
M.H. Banabazi. Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education &
Extension Organization, Karaj 3146618361, Iran.
M. Sargolzaei. Department of Pathobiology, University of Guelph, Guelph, ON NIG 2W1, Canada; Select Sires Inc., Plain City,
OH 43064, USA.
Y. Miar. Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
Corresponding author: Younes Miar (email: miar@dal.ca).
Copyright remains with the author(s) or their institution(s). This work is licensed under a Creative Commons Attribution 4.0 International
License (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author(s) and source
are credited.

Genome 63: 387–396 (2020) dx.doi.org/10.1139/gen-2020-0001 Published at www.nrcresearchpress.com/gen on 14 May 2020.

 388
shaped the more than 400 horse breeds with different
physiology, behavior, and body measurements (Brooks
et al. 2010; Metzger et al. 2014; Frischknecht et al. 2016).
Based on their type, horse breeds are categorized into
pony, light, and draft (Dall’Olio et al. 2010; Gurgul et al.
2019). Performance and marketability improvement of
horses are significantly related to their types and body
measurements in different fields (Meira et al. 2014). Po-
nies have small skeletal structure and have been used for
child horseback riding (Dall’Olio et al. 2010), and during
the industrial revolution they were used for coal mining
in the UK (Colby 1921). Their height is typically shorter
than 14.2 hands (1.44 m), with a distinctive characteristic
of short legs in relation to the body depth (Draper et al.
2014). In contrast, light horses have long thin muscles
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with longer wither heights and have been used in differ-
ent fields such as sports (show jumping, dressage, and
eventing), endurance, harness racing, and racing. Draft
horses are heavy and extremely muscular with tall stat-
ure; they have been commonly used for meat produc-
tion, working in farms, and pulling carriages (Dall’Olio
et al. 2010; Draper et al. 2014). In general, horse type
classification is based on some phenotypic traits, such as
body shape and specifically body stature (Dall’Olio et al.
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2010; Petersen et al. 2013; Gurgul et al. 2019).
Typically, deciphering the genetic foundation of body
measurements is important for performance improve-
ment of horses (Kader et al. 2015). Today, signatures of
selection studies that identify the genomic regions that
have been subjected to selective pressures have become
feasible in most animal species (Wang et al. 2016; Salek
Ardestani et al. 2020). Signatures of selection and
genome-wide association studies have played key roles
in identifying the genomic regions underlying body mea-
surements in several animal species such as horse (Kader
et al. 2015; Grilz-Seger et al. 2019), cattle (W. Zhang et al.
2016), and swine (Rubin et al. 2012) using sequencing and
genotyping technologies. Several signatures of selection
studies have been able to detect candidate genes associ-
ated with horse type (Gurgul et al. 2019) and body mea-
surements, especially wither height (Petersen et al. 2013;
Kader et al. 2015; Frischknecht et al. 2016; Al Abri et al.
2018). A signatures of selection study in Shetland ponies
detected IGF1R and ADAMTS17 genes as selective signals
related to wither height (Frischknecht et al. 2016). Simi-
larly, a study of Debao ponies pointed to candidate genes
such as TBX3 and HMGA2 underlying body size (Kader
et al. 2015). Furthermore, ANKRD1 gene was found to be
associated with wither height using selective sweep anal-
ysis in American Miniature horses (Al Abri et al. 2018).
Gurgul et al. (2019) identified LCORL, NCAPG, TBX3, and
LASP1 genes as selective signals in draft and pony horses.
1Supplementary data are available with the article through the journal Web site at http://nrcresearchpress.com/doi/suppl/10.1139/gen-
2020-0001.
Genome Vol. 63, 2020
Although most studies suggested employing single nu-
cleotide polymorphism (SNP) array data as a useful and
economical tool for identification of selective signatures,
the detection power is limited compared to whole-
genome sequence data, due to their low-density cover-
age. In our former study (Salek Ardestani et al. 2020),
selective signals were identified by utilizing different se-
lection signatures methods in sport (German and Dutch
warmblood) and non-sport horse groups (Arab, Akhal-
Teke, Thoroughbred, Standardbred, draft, and pony
breeds). However, the main objective of our current
study was to identify the genetic signatures of selection
for horse type using whole-genome sequence data of
pony and light horses and different population combina-
tions. This study may help us to better understand the
role of selection during evolutionary process and recent
breeding efforts in light and pony horse types. Moreover,
it may be helpful to optimize horse SNP array panels that
are extensively used for breeding purposes, e.g., horse
genomic evaluation.
Materials and methods
Animals
Whole-genome sequence data of 46 horses with Illu-
mina HiSeq (2000, 2500, and 3000) and NextSeq 500 plat-
forms, including 32 light (11 breeds) and 14 pony horses (6
breeds) (Table S11), were downloaded from the European
Nucleotide Archive (https://www.ebi.ac.uk). The light
group included Akhal-Teke (n = 3), Arabian (n = 2), Baden-
Wurttemberg (n = 1), Dutch warmblood (n = 1), Hanover-
ian (n = 6), Holstein (n = 2), Oldenburg (n = 3),
Standardbred (n = 6), Thoroughbred (n = 5), Trakehner
(n = 1), and Westphalian (n = 2). The pony group included
American Miniature (n = 2), Dülmen (n = 1), Connemara
(n = 4), Jeju pony (n = 2), Shetland pony (n = 4), and Welsh
pony (n = 1) (Table S21).
Alignment and variant calling
After converting the Sequence Read Archives to Fastq
paired-end format using fastq-dump command of SRA
Toolkit (version 2.9, https://github.com/ncbi/sra-tools),
the quality control was performed by FastQC (version 0.11.6,
http://www.bioinformatics.babraham.ac.uk/projects/fastqc)
for each sample. Adaptors and low quality reads were
filtered using Trimmomatic 0.36 (Bolger et al. 2014). The
clean reads were aligned to the reference genome of
equine (EquCab2.0) using Burrows-Wheeler Aligner
0.7.17-r1188 (Li and Durbin 2009) and converted to binary
with SAMtools 1.7 (Li et al. 2009). Picard 2.17.11 (https://
broadinstitute.github.io/picard) was used to remove the
potential PCR duplications as well as avoiding systematic
biases. The base quality score recalibration was per-
Published by NRC Research Press
 Salek Ardestani et al.
formed according to the recommended workflow in Ge-
nome Analysis Toolkit 3.8 (McKenna et al. 2010).
Variant calling was performed by applying “Haplo-
typeCaller”, “stand emit conf 10”, and “stand call conf
30” options to detect insertion/deletions (Indels) and
SNPs in the genomic variant call format file. We sepa-
rated SNPs and Indels through “selectVariant” option in
Genome Analysis Toolkit and discarded the sex chromo-
somes. High-quality SNPs were identified using the fol-
lowing stringent filtration criteria: (1) Phred-scaled
quality score (QUAL) < 40.0, (2) Quality by depth
(QD) < 2.0, (3) Mapping quality (MQ) < 25.0, (4) Phred-
scaled p-value using Fisher’s exact test to detect strand
bias (FS) > 60.0, (5) Mapping quality rank sum test
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(MQRankSum) < −12.50, (6) Read position rank sum test
(ReadPosRankSum) < −8.0. All filtered SNPs were anno-
tated using Variant Effect Predictor (https://www.ensembl.
org/info/docs/tools/vep/). Additionally, SNPs were filtered
using PLINK 2.0 (Purcell et al. 2007) according to the fol-
lowing criteria: minor allele frequency (maf) 0.01, Hardy–
Weinberg p-value (hwe) 0.001, individuals with more
than 10% missing genotypes (mind) 0.1, and missing rate
per SNP (geno) 0.1. Visualization of SNP densities per
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each 100 kb window was performed by utilizing circos
0.69.6 (Krzywinski et al. 2009).
Phylogenetic analysis
The phylogenetic analysis can describe the genetic re-
lationship between different breeds based on genetic di-
versity, and thus, it can be applied as a useful tool for
managing the genetic diversity (Davies et al. 2008). To
decipher the genetic relationship among all individuals,
the phylogenetic tree was constructed for the whole SNP
data using neighbour-joining method in VCF-kit 0.1.6
(Cook and Andersen 2017). FigTree 1.4.3 (http://tree.bio.
ed.ac.uk/software/figtree) was also used to visualize
the phylogenetic network. Additionally, the neighbour-
joining tree was converted to the genetic distance matrix
by employing a python script.
Selective signals and gene ontology
As cross-population and allele-frequency based meth-
ods of signatures of selection, fixation index (FST) (Weir
and Cockerham 1984) and pairwise nucleotide diversity
(␪␲) (Nei and Li 1979) were used to detect selective signals
in pony and light horse breeds. The FST and ␪␲ values
were calculated for pony and light horses using the slid-
ing window approach (100 kb with a step size of 50 kb)
in VCFtools 0.1.15 (Danecek et al. 2011). The formula of
Weir and Cockerham (1984) was used to calculate the
FST values:
关兺 兴
2 5D18-like and 4P4-like genes. ECA 12 is enriched by copy
␴f2 2 wi(f̄i ⫺ f̄)
i⫽1
FST ⫽ ⫽
f̄(1 ⫺ f̄) f̄(1 ⫺ f̄)
389
where f̄ and ␴f2 are the mean and variance of allele fre-
冉
quencies, respectively; wi is the ratio of ni to M wi ⫽
ni
M
冊
in which, ni and M are the number of individuals in ith
population and the total number of individuals in both
populations, respectively.
The ␪␲ values were calculated through
␪␲ ⫽
N
N⫺1 兺p p ␲
ij
i j ij
where N is the total number of individuals in a popula-
tion, ␲ij is the number of different nucleotides per site
between ith and jth sequences, and pi and pj are allele
frequencies in ith and jth sequences, respectively. To nor-
malize the FST values, Z-transformation was performed
using “scale” command in R program. Also, the ␪␲ values
were transformed using log2 function (Yang et al. 2016).
Top 1% windows that overlapped between Z(FST) and
冉 冊
␪␲共pony兲
log2 values were defined as strong selective sig-
␪␲共light兲
nals in pony and light groups (Yang et al. 2016; Li et al.
2017). These windows were mapped to genes using
“biomaRt” package (https://bioconductor.org/packages/
biomaRt). To reveal the functional enrichment of
genomic regions underlying selection pressures, gene
ontology analysis was executed according to biological
processes using gprofiler (https://biit.cs.ut.ee/gprofiler)
and Benjamini–Hochberg FDR correction.
Results and discussion
Genomic variants
The whole-genome sequences of pony and light horses
(1786 Gb) were aligned to 94.59%–99.84% of the equine
genome reference assembly at 14.7× average depth. After
removing the marked PCR duplicates,and performing
base quality score recalibration as well as variant calling,
we detected 16 075 591 SNPs (Table S31). The annotation
of SNPs distribution for all samples is shown in Table S41.
We calculated SNP densities per each 100 kb window in
which the highest density of SNPs was located on horse
chromosome (ECA) 20: 32.7–32.8 Mb with 3343 SNPs
(Fig. S11). This genomic region contains MHC class II DQ-
alpha chain and MHC class II DR-beta chain genes (Fig. S11).
The group of MHC genes, known as high polymorphic
and recombinative genomic regions (Gaudieri et al. 2000), is
associated with disease resistance (Van Oosterhout 2009).
The highest nucleotide diversities for light and pony
groups in 100 kb windows were located on ECA 2: 107.85–
107.95 Mb and ECA 12: 13.05–13.15 Mb, respectively
(Fig. S11). ECA 12: 13.05–13.15 Mb includes olfactory receptor
number of variants (CNV) due to the existence of major
clusters of olfactory receptor genes (Ghosh et al. 2014).
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 390
Fig. 1. Neighbour-joining tree for light and pony breeds.
The light breeds are Akhal-Teke (AKT), Dutch warmblood
(KW), Baden-Wurttemberg (BW), Hanoverian (HAN),
Holstein (HOL), Oldenburg (OLD), Trakehner (TRA),
Westphalian (WF), Arabian (AR), Standardbred (ST), and
Thoroughbred (TH). The Pony breeds are Welsh pony (WP),
Shetland pony (SHP), American Miniature (AMP), Dülmen
(DUP), Connemara (CONP), and Jeju pony (JEP).
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Phylogenetic analysis
In this study, the phylogenetic neighbour-joining tree
divided pony and light groups into two separate clusters
(Fig. 1). In the light cluster, similar to the study by
Petersen et al. (2013), there were three main branches
including Arabian–Akhal-Teke, Standardbred, and
German warmblood–Thoroughbred. All German
warmblood breeds including Dutch warmblood, Baden-
Wurttemberg, Hanoverian, Holstein, Oldenburg,
Trakehner, and Westphalian were classified in one
branch, indicating the genetic similarity and probable
sharing of founder lines. Our phylogenetic results
showed two Westphalians (WF1, WF2) in separate sub-
branches; a Hanoverian (HAN6) was located near WF2,
which might be due to hybridization among German
warmblood breeds. In the pony cluster, two main
branches were illustrated, one of which belongs to Con-
nemara, and the other consists of Dülmen, Welsh pony,
Jeju pony, Shetland pony, and American Miniature. Sim-
ilar to the study by Petersen et al. (2013), there was a close
genetic distance between Shetland pony and American
Miniature breeds (Table S51). It should be noted that in
the phylogenetic analysis the interpretation of the re-
sults related to the breeds with one individual, such
as Baden-Wurttemberg, Dutch warmblood, Trakehner,
Dülmen, and Welsh pony can still be reliable due to the
large number of SNPs used in this study similar to previ-
Genome Vol. 63, 2020
ous studies (C. Zhang et al. 2018; Asadollahpour Nanaei
et al. 2019).
Genome-wide signatures of selection analysis
Previous studies have indicated that signatures of se-
lection analyses are particularly helpful for detecting
genes related to body measurements and specifically
wither height in horse (Kader et al. 2015; Frischknecht
et al. 2016; Al Abri et al. 2018). A lot of qualitative evi-
dence has proved that there are several effective genetic
factors in body morphology variation, such as wither
height which is controlled by lots of minor effect genes
in naturally evolving species, whereas in domesticated
animals it is controlled by a few major effect genes
(Kader et al. 2015). Therefore, regarding the conservative
role of genes in body morphology regulation, signatures
of selection analyses can potentially provide an opportu-
nity to detect genomic regions associated with horse
type. To identify genomic regions under putative selec-
tion, several statistical methods based on allele fre-
quency variation have been developed such as FST (Weir
and Cockerham 1984) and ␪␲ (Nei and Li 1979).
In this study, we calculated the mean of FST(pony-light)
for each window of 100 kb with a step size of 50 kb. After
FST Z-transformation, the Z(FST) values followed a normal
distribution that is presented in Fig. 2. A total number of
446 windows including 377 genes were detected in the
top 1% of Z(FST) values, ranged from 3.20 to 10.44
(Table S61). The highest Z(FST) value was located at 51.25–
51.35 Mb of ECA 7. This region consists of the putative
gustatory receptor clone (LOC100061702) gene and a novel
identified gene in horse (ENSECAG00000002851) with hu-
man ortholog of L1TD1. In human, L1TD1 gene is related to
bone mineral density (Chesi et al. 2017) and lip morphol-
ogy (Cha et al. 2018). Furthermore, we could identify
13 genes in the top 1% of Z(FST) values that had been
previously reported as candidate genes for body mea-
surements (Fig. 3) in human (N=Diaye et al. 2011;
Cousminer et al. 2013; Wood et al. 2014; Bae et al. 2016)
and other species such as horse (Makvandi-Nejad et al.
2012; Metzger et al. 2013; Staiger et al. 2016), cattle
(W. Zhang et al. 2016; Han et al. 2017), and swine (Rubin
et al. 2012). These candidate genes are LCORL, NCAPG,
DCAF16, FAM189A1, C4ORF33, BMP2, CRB1, IGFBP3, OPCML,
FGF12, DDX55, FAM13A, and CPN1.
Identifying processes governing diversity of genome
has played an effective role in evolutionary genetics
(Ellegren and Galtier 2016) and is a spotlight for selective
sweep studies (Moon et al. 2015; Yang et al. 2016; Li et al.
2017; Z. Zhang et al. 2018). Approaches based on nucleo-
tide diversity such as pairwise nucleotide diversity have
been used to detect selective signals for animal species
such as sheep (Yang et al. 2016), goat (Li et al. 2017), duck
(Z. Zhang et al. 2018b), and horse (Moon et al. 2015). In this
study, the transformed ␪␲ values log2 冉 冉 ␪␲共pony兲
␪␲共light兲冊冊 were
calculated for each window of 100 kb with a step size of
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 Salek Ardestani et al. 391

Fig. 2. The distribution of (A) Z-transformed fixation index or Z(FST) and (B) logarithm of transformed nucleotide diversity or
log2 冉
␪␲共pony兲
␪␲共light兲 冊
values in 100 kb windows with sliding windows of 50 kb.
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Fig. 3. The distribution of Z-transformed fixation index (Z(FST)) values in horse autosomes. Data points above the blue
horizontal line are the top 1% of Z(FST) values. The NCAPG, LCORL, and DCAF16 genes were not overrepresented in the top 1% of
log2 冉
␪␲共pony兲
␪␲共light兲 冊
values.

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 392
冉 冉
Fig. 4. The distribution of transformed nucleotide diversity log2
␪␲共pony兲
␪␲共light兲
冉
blue horizontal line are the top 1% of log2
values.
冊
␪␲共pony兲
␪␲共light兲
values. The HMGA2 gene was not overrepresented in the top 1% of Z(FST)
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50 kb (Fig. 4). These values followed a normal distribu-
tion (Fig. 2). A total number of 446 windows including
366 genes were identified in the top 1% of transformed ␪␲
values, ranged from 0.91 to 2.64 (Table S61). To identify
more reliable selective signals, we determined the over-
lapped windows between the top 1% of Z(FST) and trans-
formed ␪␲ values by the cut-off ratio (Fig. 5).
We detected 139 overlapped genes as selective signals
in the pony and light groups (Table S61), 10 of which
including BMP2, CPN1, IGFBP3, OPCML, DDX55, FGF12,
FAM13A, FAM189A1, C4ORF33, and CRB1 genes have been
detected to be related to body measurements (Table 1) in
human (N=Diaye et al. 2011; Cousminer et al. 2013; Wood
et al. 2014; Bae et al. 2016) and animals (Fang et al. 2010;
Fan et al. 2011; Olivieri et al. 2016; Xia et al. 2017). The
LCORL, DCAF16, and NCAPG genes were not overrepre-
sented by transformed ␪␲ approach, conversely, HMGA2
gene was only screened in the top 1% of transformed ␪␲
values; however, these genes were detected as functional
candidate genes for body measurements in previous
genome-wide association studies (Makvandi-Nejad et al.
2012; Kader et al. 2015; W. Zhang et al. 2016; Sevane et al.
2017).
Genes associated with wither height
The genetic background of horse wither height varia-
tion has been studied by Makvandi-Nejad et al. (2012),
who reported one locus near LCORL and NCAPG genes
Genome Vol. 63, 2020
冊冊
values in horse autosomes. Data points above the
with three other loci located near HMGA2, ZFAT, and
LASP1 genes explaining approximately 83% of wither
height variation. On the other hand, Signer-Hasler et al.
(2012) indicated a quantitative trait loci (QTL) on ECA 3
near LCORL gene and another QTL on ECA 9, together
explaining 18.2% of de-regressed estimated breeding val-
ues for horse wither height (Signer-Hasler et al. 2012). A
majority of former studies (Makvandi-Nejad et al. 2012;
Kader et al. 2015; Metzger et al. 2018) illuminated the
effective role of LCORL gene in controlling horse wither
height variation. Sevane et al. (2017) also revealed a
strong association between one SNP on LCORL gene and
several other body measurements such as hock circum-
ference, knee perimeter, hind cannon circumference,
and fore cannon circumference. In contrast to the
HMGA2, LCORL, and NCAPG genes, the CPN1 and DDX55
genes were identified in the top 1% of both Z(FST) and
transformed ␪␲ values. These genes have significant as-
sociations with human height (Allen et al. 2010) and
pubertal height growth (Cousminer et al. 2013). Addition-
ally, DDX55 gene was also detected as a selective signal in
German warmbloods (Nolte et al. 2019).
Genes associated with skeletal confirmation and growth
BMP2, FGF12, and IGFBP3 are known as candidate genes
for growth and skeletal development. The insulin-like
growth factor (IGF) axis is known as a conserved evolu-
tionarily system (Teumer et al. 2016) and some genes in
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 Salek Ardestani et al. 393

Fig. 5. (A) Overrepresented windows of the top 1% of transformed ␪␲ and Z(FST) values. Data points located in the right side of
the vertical line (the top 1% of transformed ␪␲ values, where transformed ␪␲ value is 0.91) and above the horizontal line (the
top 1% of Z(FST) values, where Z(FST) value is 3.20) were detected as selective signals. (B) The venn diagram for the number of
overlapped genes between the top 1% of transformed ␪␲ and Z(FST) values.
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Table 1. Overrepresented horse type candidate genes between Z(FST) and transformed ␪␲ values.
Candidate Transformed
gene Chromosome Window (Mbp) Z(FST) ␪␲ values Associated phenotype Study
DDX55 8 23.47–23.49 6.83 1.32 Pubertal height growth in human Cousminer et al. 2013
CRB1 30 24.99–25.19 4.36 1.27 Body mass index in broiler chickens Akiyama et al. 2017
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BMP2 22 16.42–16.70 4.21 1.05 Growth and skeletal development in human Huang et al. 2002
FGF12 19 29.30–29.53 4.01 1.18 Skeletal growth in human Zhang et al. 2016a
C4ORF33 2 100.09–100.18 4.04 1.31 Body mass index in human Locke et al. 2015
CPN1 1 29.69–29.71 3.67 0.97 Height in human Allen et al. 2010
OPCML 7 40.70–40.90 4.20 1.52 Body mass index in human Huckins et al. 2018
IGFBP3 4 16.29–16.30 4.71 1.94 Skeletal development in human Chan et al. 2015
FAM189A1 1 107.65–107.75 5.35 1.00 Body mass index in human Frischknecht et al. 2016
FAM13A 3 48.99–49.26 3.36 0.95 Bone weight and fiber muscles size in cattle Xia et al. 2017

this family group are associated with cellular growth
regulators (Cheng et al. 2007), such as IGFBP3 that is re-
lated to skeletal development (Chan et al. 2015). The
BMP2 gene plays a key role in shaping bones, growth, and
skeletal development (Huang et al. 2002). This gene was
found to be associated with body trunk in goat (Fang
et al. 2010), and body depth, length, and width in swine
(Fan et al. 2011). Both BMP2 and IGFBP3 genes were previ-
ously confirmed as selective signals in German warm-
bloods (Nolte et al. 2019). The fibroblast growth factor
family consists of 22 members and genes, such as FGF12
that plays a pivotal role in growth and formation of
bones (F. Zhang et al. 2016). FAM189A1, CRB1, OPCML, and
C4ORF33 are known as candidate genes for body mass
index in human (Frischknecht et al. 2015; Locke et al.
2015; Akiyama et al. 2017; Huckins et al. 2018). Moreover,
the OPCML gene was found to be associated with body
weight and growth rate in broiler chickens (Gu et al.
2011). This gene was confirmed by Gurgul et al. (2019) as a
selective signal between draft and light horse breeds that
might have potentially contributed to developing differ-
ent types of horse. Frischknecht et al. (2016) detected
FAM189A1 as a selective signal for body mass index in
Shetland ponies (Frischknecht et al. 2016). Also, in a
genome-wide association study, Xia et al. (2017) demon-
strated the relation of FAM13A with bone weight, size,
and number of muscle fibers in skeletal muscles of Sim-
mental cattle.
Our selection signatures analysis between pony and
light horses allowed the detection of 10 genes including
BMP2, CPN1, IGFBP3, OPCML, DDX55, FGF12, FAM13A,
FAM189A1, C4ORF33, and CRB1 as direct selective signals.
These genes were found to be associated with body mea-
surements in some species, and thus they might poten-
tially be related to pony and light horse type variation. To
the best of our knowledge, except for DDX55, BMP2,
IGFBP3, OPCML, and FAM189A1 genes, the other five iden-
tified selective signals have not been previously detected
for horse type variation.
Gene ontology of selective signal
To further detect biological function of selective signal
candidate genes, we classified the significant biological
processes of 139 genes underlying selection pressures in
pony and light horses. These significant biological pro-
cesses (Table S71) include insulin-like growth factor re-

Published by NRC Research Press

 394
ceptor signaling pathway (GO:0048009, p-value = 0.01),
regulation of insulin-like growth factor receptor signal-
ing pathway (GO:0043567, p-value = 0.04), positive regu-
lation of presynaptic cytosolic calcium concentration
(GO:0099533, p-value = 0.04), and induction of synaptic
vesicle exocytosis by positive regulation of presynaptic
cytosolic calcium ion concentration (GO:0099703,
p-value = 0.04). A former study revealed the effective role
of insulin-like growth factor receptor signaling pathway
in head circumference and development of the nervous
system (Yang et al. 2019). The selective pressures for this
biological pathway can be reasonable considering the
differences in head dimensions between light and pony
horses. The cytosolic calcium concentration can be effec-
tive in skeletal muscle kinetics (Cho et al. 2017). It can be
Genome Downloaded from cdnsciencepub.com by 181.67.2.57 on 12/30/20
associated with positive regulation of presynaptic cyto-
solic calcium concentration and induction of synaptic
vesicle exocytosis by positive regulation of presynaptic
cytosolic calcium ion concentration pathways. These two
biological pathways could be under selective pressures
particularly in light breeds considering their athletic us-
ages such as racing, endurance, and sports.
Conclusions
For personal use only.
In conclusion, the comprehensive comparison of
whole-genome sequences of pony and light horses iden-
tified genomic regions and biological processes underly-
ing selective pressures for light and pony horse types. In
pony and light groups, 139 genes were detected as signa-
tures of selection that are enriched for four significant
biological pathways. We detected five under-selective-
pressure novel genes including CPN1, FGF12, FAM13A,
C4ORF33, and CRB1 that might possibly be related to body
measurement differences between light and pony types,
such as wither height, skeletal confirmation, and
growth. Moreover, these results can provide a better ge-
netic perspective of phenotypic differences among pony
and light groups. Obviously, there might have been some
limitation due to the small number of horses in this
study, and therefore, further investigation and valida-
tion using genome-wide association and signatures of
selection studies are required with larger populations
and multiple horse breeds.
Author contributions
S.S.A., M.A., Y.M., and M.B.Z.M. conceived and de-
signed this experiment. S.S.A. wrote the first draft of the
manuscript and analyzed data under Y.M.’s supervision.
S.S.A., M.A., Y.M., M.S., M.H.B., and M.B.Z.M. discussed
the results and contributed to the final manuscript. S.S.A
and Y.M. wrote the final manuscript. All authors re-
viewed and approved the final manuscript.
Funding statement
Select Sires Inc. provided support in the form of sala-
ries for author M.S., but they did not have any additional
role in the study design, data collection and analysis,
Genome Vol. 63, 2020
decision to publish, or preparation of the manuscript.
The specific roles of this author are articulated in the
author contributions section.
Competing interests
Author M.S. is employed at Select Sires Inc. This orga-
nization did not play any role in the study design, data
collection and analysis, decision to publish, or prepara-
tion of the manuscript and only provided financial sup-
port in the form of M.S.‘s salary. This does not alter our
adherence to Genome journal policies on sharing data and
materials. Other authors have declared that no compet-
ing interests exist.
References
Akiyama, M., Okada, Y., Kanai, M., Takahashi, A.,
Momozawa, Y., Ikeda, M., et al. 2017. Genome-wide associa-
tion study identifies 112 new loci for body mass index in the
Japanese population. Nat. Genet. 49(10): 1458–1467. doi:10.
1038/ng.3951. PMID:28892062.
Al Abri, M.A., Posbergh, C., Palermo, K., Sutter, N.B., Eberth, J.,
Hoffman, G.E., and Brooks, S.A. 2018. Genome-wide scans
reveal a quantitative trait locus for withers height in horses
near the ANKRD1 gene. J. Equine Vet. Sci. 60: 67–73.e61. doi:
10.1016/j.jevs.2017.05.008.
Allen, H.L., Estrada, K., Lettre, G., Berndt, S.I., Weedon, M.N.,
Rivadeneira, F., et al. 2010. Hundreds of variants clustered in
genomic loci and biological pathways affect human height.
Nature, 467(7317): 832–838. doi:10.1038/nature09410. PMID:
20881960.
Asadollahpour Nanaei, H., Ayatollahi Mehrgardi, A., and
Esmailizadeh, A. 2019. Comparative population genomics
unveils candidate genes for athletic performance in Ha-
noverians. Genome, 62(4): 279–285. doi:10.1139/gen-2018-
0151. PMID:30779599.
Bae, S., Choi, S., Kim, S.M., and Park, T. 2016. Prediction of
quantitative traits using common genetic variants: applica-
tion to body mass index. Genomics Inform. 14(4): 149–159.
doi:10.5808/GI.2016.14.4.149. PMID:28154505.
Bolger, A.M., Lohse, M., and Usadel, B. 2014. Trimmomatic: a
flexible trimmer for Illumina sequence data. Bioinformatics,
30(15): 2114–2120. doi:10.1093/bioinformatics/btu170. PMID:
24695404.
Bowling, A.T., and Ruvinsky, A. (Editors). 2000. The genetics of
the horse. CABI. 26 pp.
Brooks, S., Makvandi-Nejad, S., Chu, E., Allen, J., Streeter, C.,
Gu, E., et al. 2010. Morphological variation in the horse: de-
fining complex traits of body size and shape. Anim. Genet.
41(s2): 159–165. doi:10.1111/j.1365-2052.2010.02127.x. PMID:
21070291.
Cha, S., Lim, J.E., Park, A.Y., Do, J.-H., Lee, S.W., Shin, C., et al.
2018. Identification of five novel genetic loci related to facial
morphology by genome-wide association studies. BMC
Genomics, 19(1): 481. doi:10.1186/s12864-018-4865-9. PMID:
29921221.
Chan, Y., Salem, R.M., Hsu, Y.-H.H., McMahon, G., Pers, T.H.,
Vedantam, S., et al. 2015. Genome-wide analysis of body pro-
portion classifies height-associated variants by mechanism
of action and implicates genes important for skeletal devel-
opment. Am. J. Hum. Genet. 96(5): 695–708. doi:10.1016/j.ajhg.
2015.02.018. PMID:25865494.
Cheng, I., DeLellis Henderson, K., Haiman, C.A., Kolonel, L.N.,
Henderson, B.E., Freedman, M.L., and Le Marchand, L.C. 2007.
Genetic determinants of circulating insulin-like growth fac-
tor (IGF)-I, IGF binding protein (BP)-1, and IGFBP-3 levels in a
Published by NRC Research Press
 Salek Ardestani et al.
multiethnic population. J. Clin. Endocrinol. Metab. 92(9):
3660–3666. doi:10.1210/jc.2007-0790. PMID:17566087.
Chesi, A., Mitchell, J.A., Kalkwarf, H.J., Bradfield, J.P.,
Lappe, J.M., Cousminer, D.L., et al. 2017. A genomewide asso-
ciation study identifies two sex-specific loci, at SPTB and
IZUMO3, influencing pediatric bone mineral density at mul-
tiple skeletal sites. J. Bone Miner. Res. 32(6): 1274–1281. doi:
10.1002/jbmr.3097. PMID:28181694.
Cho, C.-H., Woo, J.S., Perez, C.F., and Lee, E.H. 2017. A focus on
extracellular Ca2+ entry into skeletal muscle. Exp. Mol. Med.
49(9): e378. doi:10.1038/emm.2017.208. PMID:28912570.
Colby, F.M. 1921. New International Yearbook: A Compendium
of the World’s Progress for the Year 1920. Dodd, Mead & Co.,
New York. 171 pp.
Cook, D.E., and Andersen, E.C. 2017. VCF-kit: assorted utilities
for the variant call format. Bioinformatics, 33(10): 1581–1582.
doi:10.1093/bioinformatics/btx011. PMID:28093408.
Cousminer, D.L., Berry, D.J., Timpson, N.J., Ang, W., Thiering, E.,
Genome Downloaded from cdnsciencepub.com by 181.67.2.57 on 12/30/20
Byrne, E.M., et al. 2013. Genome-wide association and longi-
tudinal analyses reveal genetic loci linking pubertal height
growth, pubertal timing and childhood adiposity. Hum. Mol.
Genet. 22(13): 2735–2747. doi:10.1093/hmg/ddt104. PMID:
23449627.
Dall’Olio, S., Fontanesi, L., Nanni Costa, L., Tassinari, M.,
Minieri, L., and Falaschini, A. 2010. Analysis of horse myosta-
tin gene and identification of single nucleotide polymor-
phisms in breeds of different morphological types. J. BioMed.
Biotechnol. 2010: 542945. doi:10.1155/2010/542945. PMID:
20706663.
For personal use only.
Danecek, P., Auton, A., Abecasis, G., Albers, C.A., Banks, E.,
DePristo, M.A., et al. 2011. The variant call format and
VCFtools. Bioinformatics, 27(15): 2156–2158. doi:10.1093/
bioinformatics/btr330. PMID:21653522.
Davies, T.J., Fritz, S.A., Grenyer, R., Orme, C.D.L., Bielby, J.,
Bininda-Emonds, O.R., et al. 2008. Phylogenetic trees and the
future of mammalian biodiversity. Proc. Natl. Acad. Sci.
U.S.A. 105(Suppl. 1): 11556–11563. doi:10.1073/pnas.0801917105.
PMID:18695230.
Draper, J., Sly, D., and Muir, S. 2014. The ultimate book of the
horse and rider. Lorenz Books.
Ellegren, H., and Galtier, N. 2016. Determinants of genetic di-
versity. Nat. Rev. Genet. 17(7): 422–433. doi:10.1038/nrg.2016.
58. PMID:27265362.
Fan, B., Onteru, S.K., Du, Z.-Q., Garrick, D.J., Stalder, K.J., and
Rothschild, M.F. 2011. Genome-wide association study identi-
fies loci for body composition and structural soundness traits
in pigs. PLoS ONE, 6(2): e14726. doi:10.1371/journal.pone.
0014726. PMID:21383979.
Fang, X., Xu, H., Zhang, C., Zhang, J., Lan, X., Gu, C., and Hong, C.
2010. Polymorphisms in BMP-2 gene and their associations
with growth traits in goats. Genes Genomics, 32(1): 29–35.
doi:10.1007/s13258-010-0762-6.
Frischknecht, M., Jagannathan, V., Plattet, P., Neuditschko, M.,
Signer-Hasler, H., Bachmann, I., et al. 2015. A non-
synonymous HMGA2 variant decreases height in Shetland
ponies and other small horses. PLoS ONE, 10(10): e0140749.
doi:10.1371/journal.pone.0140749. PMID:26474182.
Frischknecht, M., Flury, C., Leeb, T., Rieder, S., and
Neuditschko, M. 2016. Selection signatures in Shetland
ponies. Anim. Genet. 47(3): 370–372. doi:10.1111/age.12416.
PMID:26857482.
Gaudieri, S., Dawkins, R.L., Habara, K., Kulski, J.K., and
Gojobori, T. 2000. SNP profile within the human major his-
tocompatibility complex reveals an extreme and interrupted
level of nucleotide diversity. Genome Res. 10(10): 1579–1586.
doi:10.1101/gr.127200. PMID:11042155.
Ghosh, S., Qu, Z., Das, P.J., Fang, E., Juras, R., Cothran, E.G., et al.
2014. Copy number variation in the horse genome. PLoS
395
Genet. 10(10): e1004712. doi:10.1371/journal.pgen.1004712.
PMID:25340504.
Grilz-Seger, G., Druml, T., Neuditschko, M., Mesarič, M.,
Cotman, M., and Brem, G. 2019. Analysis of ROH patterns in
the Noriker horse breed reveals signatures of selection for
coat color and body size. Anim. Genet. 50(4): 334–346. doi:10.
1111/age.12797. PMID:31199540.
Gu, X., Feng, C., Ma, L., Song, C., Wang, Y., Da, Y., et al. 2011.
Genome-wide association study of body weight in chicken F2
resource population. PLoS ONE, 6(7): e21872. doi:10.1371/
journal.pone.0021872. PMID:21779344.
Gurgul, A., Jasielczuk, I., Semik-Gurgul, E., Pawlina-Tyszko, K.,
Stefaniuk-Szmukier, M., Szmatoła, T., et al. 2019. A genome-
wide scan for diversifying selection signatures in selected
horse breeds. PLoS ONE, 14(1): e0210751. doi:10.1371/journal.
pone.0210751. PMID:30699152.
Han, Y., Chen, Y., Liu, Y., and Liu, X. 2017. Sequence variants of
the LCORL gene and its association with growth and carcass
traits in Qinchuan cattle in China. J. Genet. 96(1): 9–17. doi:
10.1007/s12041-016-0732-0. PMID:28360384.
Huang, W., Rudkin, G.H., Carlsen, B., Ishida, K., Ghasri, P.,
Anvar, B., et al. 2002. Overexpression of BMP-2 modulates
morphology, growth, and gene expression in osteoblastic
cells. Exp. Cell Res. 274(2): 226–234. doi:10.1006/excr.2002.
5483. PMID:11900483.
Huckins, L., Hatzikotoulas, K., Southam, L., Thornton, L.,
Steinberg, J., Aguilera-McKay, F., et al. 2018. Investigation of
common, low-frequency and rare genome-wide variation in
anorexia nervosa. Mol. Psychiatry, 23(5): 1169–1180. doi:10.
1038/mp.2017.88. PMID:29155802.
Jun, J., Cho, Y.S., Hu, H., Kim, H.-M., Jho, S., Gadhvi, P., et al.
2014. Whole genome sequence and analysis of the Marwari
horse breed and its genetic origin. BMC Genomics, 15(Suppl. 9):
S4. doi:10.1186/1471-2164-15-S9-S4. PMID:25521865.
Kader, A., Li, Y., Dong, K., Irwin, D.M., Zhao, Q., He, X., et al.
2015. Population variation reveals independent selection to-
ward small body size in Chinese Debao pony. Genome Biol.
Evol. 8(1): 42–50. doi:10.1093/gbe/evv245. PMID:26637467.
Krzywinski, M.I., Schein, J.E., Birol, I., Connors, J., Gascoyne, R.,
Horsman, D., et al. 2009. Circos: an information aesthetic for
comparative genomics. Genome Res. 19(9): 1639–1645. doi:10.
1101/gr.092759.109. PMID:19541911.
Li, H., and Durbin, R. 2009. Fast and accurate short read align-
ment with Burrows–Wheeler transform. Bioinformatics,
25(14): 1754–1760. doi:10.1093/bioinformatics/btp324. PMID:
19451168.
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J.,
Homer, N., et al. 2009. The sequence alignment/map format
and SAMtools. Bioinformatics, 25(16): 2078–2079. doi:10.1093/
bioinformatics/btp352. PMID:19505943.
Li, X., Su, R., Wan, W., Zhang, W., Jiang, H., Qiao, X., et al. 2017.
Identification of selection signals by large-scale whole-
genome resequencing of cashmere goats. Sci. Rep. 7(1): 15142.
doi:10.1038/s41598-017-15516-0. PMID:29123196.
Locke, A.E., Kahali, B., Berndt, S.I., Justice, A.E., Pers, T.H.,
Day, F.R., et al. 2015. Genetic studies of body mass index yield
new insights for obesity biology. Nature, 518(7538): 197–206.
doi:10.1038/nature14177. PMID:25673413.
Makvandi-Nejad, S., Hoffman, G.E., Allen, J.J., Chu, E., Gu, E.,
Chandler, A.M., et al. 2012. Four loci explain 83% of size vari-
ation in the horse. PLoS ONE, 7(7): e39929. doi:10.1371/journal.
pone.0039929. PMID:22808074.
McKenna, A., Hanna, M., Banks, E., Sivachenko, A.,
Cibulskis, K., Kernytsky, A., et al. 2010. The Genome Analysis
Toolkit: a MapReduce framework for analyzing next-
generation DNA sequencing data. Genome Res. 20(9): 1297–
1303. doi:10.1101/gr.107524.110. PMID:20644199.
Meira, C.T., Farah, M.M., Fortes, M.R., Moore, S.S., Pereira, G.L.,
Published by NRC Research Press
 396
Silva, J.A.I.V., et al. 2014. A genome-wide association study for
morphometric traits in quarter horse. J. Equine Vet. Sci.
34(8): 1028–1031. doi:10.1016/j.jevs.2014.05.011.
Metzger, J., Schrimpf, R., Philipp, U., and Distl, O. 2013. Expres-
sion levels of LCORL are associated with body size in horses.
PLoS ONE, 8(2): e56497. doi:10.1371/journal.pone.0056497.
PMID:23418579.
Metzger, J., Tonda, R., Beltran, S., Águeda, L., Gut, M., and
Distl, O. 2014. Next generation sequencing gives an insight
into the characteristics of highly selected breeds versus non-
breed horses in the course of domestication. BMC Genomics,
15(1): 562. doi:10.1186/1471-2164-15-562. PMID:24996778.
Metzger, J., Rau, J., Naccache, F., Conn, L.B., Lindgren, G., and
Distl, O. 2018. Genome data uncover four synergistic key reg-
ulators for extremely small body size in horses. BMC Genom-
ics, 19(1): 492. doi:10.1186/s12864-018-4877-5. PMID:29940849.
Moon, S., Lee, J.W., Shin, D., Shin, K.-Y., Kim, J., Choi, I.-Y., et al.
2015. A genome-wide scan for selective sweeps in racing
Genome Downloaded from cdnsciencepub.com by 181.67.2.57 on 12/30/20
horses. Asian-Australas J. Anim. Sci. 28(11): 1525–1531. doi:10.
5713/ajas.14.0696. PMID:26333666.
Nei, M., and Li, W.-H. 1979. Mathematical model for studying
genetic variation in terms of restriction endonucleases. Proc.
Natl. Acad. Sci. U.S.A. 76(10): 5269–5273. doi:10.1073/pnas.76.
10.5269. PMID:291943.
Nolte, W., Thaller, G., and Kuehn, C. 2019. Selection signatures
in four German warmblood horse breeds: tracing breeding
history in the modern sport horse. PLoS ONE, 14(4): e0215913.
doi:10.1371/journal.pone.0215913. PMID:31022261.
N=Diaye, A., Chen, G.K., Palmer, C.D., Ge, B., Tayo, B.,
For personal use only.
Mathias, R.A., et al. 2011. Identification, replication, and fine-
mapping of loci associated with adult height in individuals of
African ancestry. PLoS Genet. 7(10): e1002298. doi:10.1371/
journal.pgen.1002298. PMID:21998595.
Olivieri, B.F., Mercadante, M.E.Z., Cyrillo, J.N., Branco, R.H.,
Bonilha, S.F.M., de Albuquerque, L.G., et al. 2016. Genomic
regions associated with feed efficiency indicator traits in an
experimental Nellore cattle population. PLoS ONE, 11(10):
e0164390. doi:10.1371/journal.pone.0164390. PMID:27760167.
Petersen, J.L., Mickelson, J.R., Rendahl, A.K., Valberg, S.J.,
Andersson, L.S., Axelsson, J., et al. 2013. Genome-wide analy-
sis reveals selection for important traits in domestic horse
breeds. PLoS Genet. 9(1): e1003211. doi:10.1371/journal.pgen.
1003211. PMID:23349635.
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M.A.,
Bender, D., et al. 2007. PLINK: a tool set for whole-genome
association and population-based linkage analyses. Am. J.
Hum. Genet. 81(3): 559–575. doi:10.1086/519795. PMID:
17701901.
Rubin, C.-J., Megens, H.-J., Barrio, A.M., Maqbool, K., Sayyab, S.,
Schwochow, D., et al. 2012. Strong signatures of selection in
the domestic pig genome. Proc. Natl. Acad. Sci. U.S.A. 109(48):
19529–19536. doi:10.1073/pnas.1217149109. PMID:23151514.
Salek Ardestani, S., Aminafshar, M., Zandi Baghche Maryam, M.B.,
Banabazi, M.H., Sargolzaei, M., and Miar, Y. 2020. Whole-genome
signatures of selection in sport horses revealed selection
footprints related to musculoskeletal system development
processes. Animals, 10(1): E53. doi:10.3390/ani10010053.
PMID:31888018.
Sevane, N., Dunner, S., Boado, A., and Cañon, J. 2017. Polymor-
phisms in ten candidate genes are associated with conforma-
tional and locomotive traits in Spanish purebred horses.
J. Appl. Genet. 58(3): 355–361. doi:10.1007/s13353-016-0385-y.
PMID:27917442.
Signer-Hasler, H., Flury, C., Haase, B., Burger, D., Simianer, H.,
Genome Vol. 63, 2020
Leeb, T., and Rieder, S. 2012. A genome-wide association
study reveals loci influencing height and other conformation
traits in horses. PLoS ONE, 7(5): e37282. doi:10.1371/journal.
pone.0037282. PMID:22615965.
Staiger, E.A., Al Abri, M., Pflug, K.M., Kalla, S., Ainsworth, D.,
Miller, D., et al. 2016. Skeletal variation in Tennessee Walk-
ing Horses maps to the LCORL/NCAPG gene region. Physiol.
Genomics, 48(5): 325–335. doi:10.1152/physiolgenomics.
00100.2015. PMID:26931356.
Teumer, A., Qi, Q., Nethander, M., Aschard, H., Bandinelli, S.,
Beekman, M., et al. 2016. Genomewide meta-analysis identi-
fies loci associated with IGF-I and IGFBP-3 levels with impact
on age-related traits. Aging Cell, 15(5): 811–824. doi:10.1111/
acel.12490. PMID:27329260.
Van Oosterhout, C. 2009. A new theory of MHC evolution: be-
yond selection on the immune genes. Proc. R. Soc. B Biol.
Sci. 276(1657): 657–665. doi:10.1098/rspb.2008.1299. PMID:
18986972.
Wang, X., Liu, J., Zhou, G., Guo, J., Yan, H., Niu, Y., et al. 2016.
Whole-genome sequencing of eight goat populations for the
detection of selection signatures underlying production and
adaptive traits. Sci. Rep. 6: 38932. doi:10.1038/srep38932.
PMID:27941843.
Weir, B.S., and Cockerham, C.C. 1984. Estimating F-statistics for
the analysis of population structure. Evolution, 38(6): 1358–
1370. doi:10.1111/j.1558-5646.1984.tb05657.x. PMID:28563791.
Wood, A.R., Esko, T., Yang, J., Vedantam, S., Pers, T.H.,
Gustafsson, S., et al. 2014. Defining the role of common vari-
ation in the genomic and biological architecture of adult
human height. Nat. Genet. 46(11): 1173–1186. doi:10.1038/ng.
3097. PMID:25282103.
Xia, J., Fan, H., Chang, T., Xu, L., Zhang, W., Song, Y., et al. 2017.
Searching for new loci and candidate genes for economically
important traits through gene-based association analysis of
Simmental cattle. Sci. Rep. 7: 42048. doi:10.1038/srep42048.
PMID:28169328.
Yang, J., Li, W.-R., Lv, F.-H., He, S.-G., Tian, S.-L., Peng, W.-F., et al.
2016. Whole-genome sequencing of native sheep provides
insights into rapid adaptations to extreme environments.
Mol. Biol. Evol. 33(10): 2576–2592. doi:10.1093/molbev/
msw129. PMID:27401233.
Yang, X.-L., Zhang, S.Y., Zhang, H., Wei, X.-T., Feng, G.J., Pie, Y.F.,
and Zhang, L. 2019. Three novel loci for infant head circum-
ference identified by a joint association analysis. Front.
Genet. 10: 947. doi:10.3389/fgene.2019.00947. PMID:31681408.
Zhang, C., Ni, P., Ahmad, H.I., Gemingguli, M., Baizilaitibei, A.,
Gulibaheti, D., et al. 2018. Detecting the population structure
and scanning for signatures of selection in horses (Equus
caballus) from whole-genome sequencing data. Evol. Bioinform.
Online, 14: 1176934318775106. doi:10.1177/1176934318775106.
PMID:29899660.
Zhang, F., Dai, L., Lin, W., Wang, W., Liu, X., Zhang, J., et al. 2016.
Exome sequencing identified FGF12 as a novel candidate
gene for Kashin-Beck disease. Funct. Integr. Genomics, 16(1):
13–17. doi:10.1007/s10142-015-0462-z. PMID:26290467.
Zhang, W., Li, J., Guo, Y., Zhang, L., Xu, L., Gao, X., et al. 2016.
Multi-strategy genome-wide association studies identify the
DCAF16-NCAPG region as a susceptibility locus for average
daily gain in cattle. Sci. Rep. 6: 38073. doi:10.1038/srep38073.
PMID:27892541.
Zhang, Z., Jia, Y., Almeida, P., Mank, J.E., van Tuinen, M.,
Wang, Q., et al. 2018. Whole-genome resequencing reveals
signatures of selection and timing of duck domestication.
GigaScience, 7(4): giy027. doi:10.1093/gigascience/giy027.
PMID:29635409.
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