Abstract
BackgroundThere is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats.ResultsWe obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs.ConclusionOur results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats.
Highlights
As a major form of sexual weaponry in intra-male competition, horns in natural populations of ruminants serve the purpose of self-defense against predators [1]
Based on the sequence characteristics of the associated genomic region, we further demonstrated the usefulness of a diagnostic PCR with two primer pairs for the classification of horned, polled, and polled intersex syndrome (PIS)-affected phenotypes in several Chinese goat breeds, which provide a robust molecular genetic test for the early-in-life prediction of horn status in goats
The total fraction of genetic variance explained by the first two principal components was low (12.01 and 1.68%) (Additional file 2). Two genomic regions both on chromosome 1 were associated with the horned and polled phenotypes After the Hardy-Weinberg test (Fisher’s exact test) in PLINK, 13,980,209 biallelic Single nucleotide polymorphism (SNP) (P-value > 10− 6) on all 29 autosomes remained for the genome-wide association study (GWAS)
Summary
As a major form of sexual weaponry in intra-male competition, horns in natural populations of ruminants serve the purpose of self-defense against predators [1]. The genetic basis of the horned and polled phenotypes has been extensively investigated in ruminants. Their genomic positions are closely located on the proximal end of bovine chromosome 1, a total of four different genetic variants are associated with the polled phenotypes in cattle with diverse origins [9]. An 11.7-kb deletion located at ~ 129 Mb on chromosome 1 is thought to be responsible for the polled intersex syndrome (PIS) in Saanen goats [17], which adds to the complexity of the identification of the causal variants affecting the polled phenotype in goats. There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. We report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats
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