Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat

Background Litter size is the most important reproductive trait which plays a crucial role in goat production. Therefore, improvement of litter size trait has been of increasing interest in goat industry as small improvement in litter size may lead to large profit. The recent Cashmere goat breeding program produced a high-reproductive genetic line of Arbas Cashmere goat. But the genetic mechanism of high reproduction rate remains largely unknown in this Chinese native goat breed. To address this question, we performed a genome-wide association studies (GWAS) using two groups of goats varying in fecundity. Objectives Our study was aimed to investigate the significant SNPs and genes associated with high reproduction trait in Inner Mongolia Arbas Cashmere Goat. Methods We used logistic model association to perform GWAS using 47 goats from high fecundity group (similar to 190%) and 314 goats from low fecundity group (similar to 130%) of the Arbas Cashmere goat breed. Results We identified 66 genomic regions associated with genome wide significant level wherein six loci were found to be associated with reproduction traits. Further analysis showed that five key candidate genes including KISS1, KHDRBS2, WNT10B, SETDB2 and PPP3CA genes are involved in goat fecundity trait. Gene ontology enrichment analysis revealed that several biological pathways could be involved in the variation of fecundity in female goats. Conclusions The identified significant SNPs or genes provide useful information about the underlying genetic control of fecundity trait which will be helpful to use them in goat breeding programs for improving the reproductive efficiency of goats.