PDF(Pubmed)
Abstract：
BACKGROUND: There 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.
RESULTS: We 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.
CONCLUSIONS: Our 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.
RESULTS: We 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.
CONCLUSIONS: Our 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.
摘要：
背景：研究家养山羊有角/调查表型的遗传基础具有长期的兴趣。这里,我们报道了一项全基因组关联研究(GWAS),用于检测影响山羊投票表型的遗传基因座.
结果：我们总共获得了13,980,209个双等位基因SNP，使用来自45只金堂黑（JT）山羊的基因分型测序数据，其中包括32只雌性山羊和9只雄性山羊，和四名接受调查的双性恋综合征(PIS)患者。使用基于混合模型的GWAS，我们确定了两个关联信号，它们位于1号染色体上的150,334,857-150,817,260bp（P=5.15×10-119）和128,286,704-131,306,537bp（P=2.74×10-15）。14个最显著相关的SNP的基因型分布与山羊的角状态完全相关,基于来自JT和另外两个中国有角品种的全基因组测序（WGS）数据。然而,变异注释表明,在相关区域内检测到的SNP均不是似是而非的因果突变.通过对WGS数据进行额外的读取深度分析和目视检查，我们发现了一个10.1kb的删除(CHI1:g.129424781_129434939del）和480kb的重复（CHI1：150,334,286-150,818,098bp），在受检和受PIS影响的山羊的相关区域中包含两个基因KCNJ15和ERG。值得注意的是,10.1kb的缺失也作为480kb重复的插入位点，通过PCR和Sanger测序验证。我们的WGS基因分型显示，所有有角山羊对于参考等位基因都是纯合的，没有任何结构变体（SV），而受PIS影响的山羊对于两个SV都是纯合的。我们还证明了有角，投票,来自JT和其他三个中国有角品种的333只山羊中，受PIS影响的个体可以通过PCR扩增和两个SV中两个片段的琼脂糖凝胶电泳进行准确分类。
结论：我们的研究结果表明，1号染色体上的两个基因组区域是影响山羊群体表型的主要基因座。我们提供了一种诊断PCR来准确分类有角，投票,和受PIS影响的山羊,这将使可靠的基因测试能够预测山羊的早期角状态。
结果：我们总共获得了13,980,209个双等位基因SNP，使用来自45只金堂黑（JT）山羊的基因分型测序数据，其中包括32只雌性山羊和9只雄性山羊，和四名接受调查的双性恋综合征(PIS)患者。使用基于混合模型的GWAS，我们确定了两个关联信号，它们位于1号染色体上的150,334,857-150,817,260bp（P=5.15×10-119）和128,286,704-131,306,537bp（P=2.74×10-15）。14个最显著相关的SNP的基因型分布与山羊的角状态完全相关,基于来自JT和另外两个中国有角品种的全基因组测序（WGS）数据。然而,变异注释表明,在相关区域内检测到的SNP均不是似是而非的因果突变.通过对WGS数据进行额外的读取深度分析和目视检查，我们发现了一个10.1kb的删除(CHI1:g.129424781_129434939del）和480kb的重复（CHI1：150,334,286-150,818,098bp），在受检和受PIS影响的山羊的相关区域中包含两个基因KCNJ15和ERG。值得注意的是,10.1kb的缺失也作为480kb重复的插入位点，通过PCR和Sanger测序验证。我们的WGS基因分型显示，所有有角山羊对于参考等位基因都是纯合的，没有任何结构变体（SV），而受PIS影响的山羊对于两个SV都是纯合的。我们还证明了有角，投票,来自JT和其他三个中国有角品种的333只山羊中，受PIS影响的个体可以通过PCR扩增和两个SV中两个片段的琼脂糖凝胶电泳进行准确分类。
结论：我们的研究结果表明，1号染色体上的两个基因组区域是影响山羊群体表型的主要基因座。我们提供了一种诊断PCR来准确分类有角，投票,和受PIS影响的山羊,这将使可靠的基因测试能够预测山羊的早期角状态。
