Integrating selective signature analysis and genome-wide association study to identify candidate genes associated with litter size in Leizhou goat （A revised version）.
Abstract
Objective Litter size is a key trait for evaluating reproductive performance of goats, which can directly influence the breeding efficiency and profitability of production cycles. However, a comprehensive understanding of its genetic architecture, including the causative mutations and their functional impacts, remains scarce, thus hindering its application in precision breed-ing. Methods A total of 92 female Leizhou goats were genotyped through whole-genome se-quencing (WGS), and their litter size were measured for three consecutive births. Subsequently, based on the genotype and phenotype data, population genetic structure analysis, selection signature analysis, and genome-wide association study (GWAS) were performed. Results We identified a total of 20,802,514 SNPs in the 92 Leizhou goats. Analysis of genetic structure revealed that the high-litter-size group exhibited greater genetic diversity than the low-litter-size group, although no significant genetic differentiation was detected between them. We identified 340 putative selective regions and 346 candidate genes across the genome. A total of 37 candidate genes were identified as being closely associated with reproductive traits, including BMP6, MAPK8, RPTOR, etc. In GWAS results, we identified 63 quantitative trait loci (QTLs) for litter size at suggestive significance (P＜1×10-5). After, 207 candidate genes were annotated, and 4 of them were highlighted that have been previously reported to be associated with reproductive processes (e.g., TMEM100, PDGFD, NLRP9, and ARHGAP22). By integrating the results from both approaches, we identified MAPK8 as a potential candidate gene associated with litter size. Furthermore, our findings from motif recognition, transcrip-tion factor prediction, and previous studies lead us to propose that the BMP6-GATA4-MAPK8 signaling pathway may play a key role in regulating litter size in goats. Conclusion Our findings identify several candidate genes and putative associated variants for litter size, providing valuable insights into the genetic basis of reproductive traits in goats.