Whole-genome resequencing uncovers population structure and candidate molecular markers for litter size in hetian sheep

This study leveraged whole-genome resequencing to investigate the genetic architecture, population structure, and kinship dynamics of the Hetian sheep population. By integrating genomic data with reproductive trait analysis, we aimed to identify key candidate genes associated with litter size. The findings provide new insights into the genetic mechanisms underlying litter size and establish a molecular foundation for the application of marker-assisted selection and genetic improvement in sheep breeding. WGRS was performed on 198 Hetian sheep. After stringent quality control, 5,483,923 high-quality SNPs were retained for downstream analysis and functionally annotated using ANNOVAR. Population genetic structure was assessed based on stratification patterns and kinship coefficients. The analysis revealed that the Hetian sheep population harbors substantial genetic diversity and exhibits a generally low level of inbreeding. Among the individuals analyzed, 157 were grouped into 16 families based on third-degree kinship (kinship coefficients between 0.12 and 0.25), while 41 individuals showed no detectable third-degree relationships, suggesting high genetic independence within the population. A genome-wide association study (GWAS) using a general linear model (GLM) identified 11 candidate genes potentially associated with litter size, including LOC101120681, LOC106990143, LOC101114058, GALNTL6, CNTNAP5, SAP130, EFNA5, ANTXR1, SPEF2, ZP2, and TRERF1. Among these, 23 SNPs located within five core candidate genes (LOC101120681, LOC106990143, LOC101114058, GALNTL6, and CNTNAP5) were selected for validation using the Sequenom MassARRAY® genotyping platform. Of the 23 SNPs tested, 22 were confirmed as true variants. However, the majority (17/22) showed no statistically significant association with litter size (P >0.05), highlighting the need for further validation in larger populations. Although the Hotan sheep population exhibits high genetic diversity and low levels of inbreeding, most SNPs are not significantly associated with litter size, indicating that there are currently some limitations to this study. These results should be considered preliminary and require further validation in larger and more diverse populations.