Genomic Structural Variations Provide Insights Into Litter Size and Teat Number Traits in Hu Sheep

ABSTRACT Litter size and the teat number are important economic indicators in sheep production. However, the correlation between litter size and teat number traits, as well as molecular mechanisms underlying the high fecundity of Hu sheep, remains unclear. Here, we conducted whole genome sequencing on 300 Hu sheep with an average depth of 16.51X, and identified 64,759 structural variations (SVs). After quality control, GC ranged from 41.5% to 44.5%, and Q30 ranged from 86.8% to 95.5%. SVs are a major source of genetic diversity and play crucial roles in phenotypic traits, environmental adaptation, and productivity in livestock species. Key loci and candidate genes were identified through genome‐wide association study (GWAS) and machine learning approaches. The GWAS used a mixed linear model. Subsequently, the expression levels of these candidate genes within the sheep reproductive system were investigated. Our study suggests that the genetic correlation between litter size and teat number traits was 0.15, and machine learning results also proved the reliability of our findings. The Hu sheep population was divided into two subgroups using SVs data. Subsequently, GWAS based on SVs revealed that both MAST2 and AFDN were significantly associated with litter size and teat number traits, and these two genes showed high expression levels in the sheep reproductive system. Notably, DEL in MAST2 significantly affected litter size and the teat number in Hu sheep. This study reveals the genetic variations in reproductive traits in Hu sheep, which will be valuable for understanding the underlying genetic mechanisms and guiding Hu sheep breeding.