Data from: Genome-wide association study for tobiano spotting coat color in Korean Jeju × Thoroughbred horse population

Korean Jeju horse features a small to medium frame size and stature having
varieties of coat colors including grey, milky, spotted and bay1.
Crossbreeding with Thoroughbred has been a long tradition in Korea to have
intermediate frame size horse suitable for racing, leisure activities and
meat production2. Tobiano white-spotting pattern is preferred by many
horse breeders and owners which is inherited as an autosomal dominant
trait1,3. Polymorphisms in proto-oncogene receptor tyrosine kinase (KIT)
gene were strongly associated with tobiano and sabino coat color pattern
in American and European horse breeds3,5. In addition, ECA3 inversion
locus near KIT gene also significantly associated with tobiano spotting
pattern in horses4,5. Here, we report SNPs and harbored genes associated
with tobiano coat color in a crossbred horse population through
genome-wide SNP association analysis. In this study, coat color patterns
of 142 crossbred horses (Jeju indigenous horse × Thoroughbred) were
verified according to previously described methods3,5 and coded as “0” or
“1” (Figure S1). Genomic DNA was extracted from blood samples using DNeasy
96 blood DNA extraction Kit (QIAGEN, USA). Genotyping was performed using
Equine SNP 50K BeadChip (Illumina, San Diego, USA) at AGBD, NIAS, Korea. A
total of 45,204 SNPs passed the set quality control criteria as minor
allele frequency (MAF<0.01), missing genotype (GENO>0.10)
and Hardy-Weinberg equilibrium (HWE<0.0001) in 142 individuals.
Finally, a set of 16,223 independent SNPs were generated through –indep
–pairwise 25 5 0.25 pruning6. Genome wide association study revealed 18
Bonferroni adjusted SNPs located on chromosome 3 (ECA3) significantly
associated with tobiano coat color in the studied population (Figure 1,
Table S1). These SNPs broadly plotted on 40 Mbp region (from 39 to 79 Mbp)
of ECA3 which might be due to high LD among the significant SNPs. The most
significant association was found between ECA3 inversion locus (77657979
bp) and tobiano pattern (P< 5.56×10-17) while the second highest
association was detected with SNP rs68555258 (48853535 bp; P<
4.04×10-12, Table S1). Apart from this, genotypes of ECA3 inversion locus
by pyrosequencing matched perfectly in our study (Table S2). All tobiano
horses (n = 37) were heterozygous for inversion locus (+/To) while
solid-colored horses (n = 103) were homozygous (+/+). ECA3 inversion is
located 70 kbp downstream from KIT gene which possessed causal variants
for tobiano pattern in horse5,6. The Biomart and Variant Effect Predictor
tools in Ensembl Genome Browser (http://www.ensembl.org/index.html)
identified several significant SNPs harboring genes of which GPRIN3,
ARHGAP24, SCFD2, RASSL11B and WDFY3 are noticeable (Table S3). Based on
our genome wide association and inversion locus genotyping results, it is
suggested that ECA3 inversion locus variant is either causative or
completely linked with causative variants for tobiano coat color in this
crossbred horse population. Moreover, a set of putative mutations in other
genes might be in high LD with causative variants that could be explored
for functional annotations associated with tobiano coat color pattern in
horse population.