Identification of Signatures of Selection for Litter Size and Pubertal Initiation in Two Sheep Populations

SIMPLE SUMMARY: Fecundity is an important economic trait of sheep that directly affects their economic and productive efficiency. Our study aimed to identify single nucleotide polymorphism (SNP) loci associated with sheep puberty or litter size which could be used in future breeding programs to improve fertility. We obtained one SNP on GNAQ gene (NC_040253.1: g.62677376G > A), which was associated with litter size in Cele Black sheep. Perhaps this SNP could be a criterion to screen polytocous sheep. ABSTRACT: Fecundity is an important economic trait in sheep that directly affects their economic and productive efficiency. Our study aimed to identify SNP loci associated with sheep puberty or litter size which could be used in future breeding programs to improve fertility. Genomic DNA was obtained from Hetian and Cele Black sheep breeds and used for reduced-representation genome sequencing to identify SNP loci associated with pubertal initiation and litter size. Selective signatures analysis was performed based on the fixation index and nucleotide diversity, followed by pathway analysis of the genes contained in the selected regions. The selected SNP loci in the genes associated with pubertal initiation and litter size were validated using both sheep breeds. In total, 384,718 high quality SNPs were obtained and 376 genes were selected. Functional annotation of genes and enrichment analysis identified 12 genes associated with pubertal initiation and 11 genes associated with litter size. SNP locus validation showed that two SNP on PAK1 and four on ADCY1 may be associated with pubertal initiation, and one SNP on GNAQ gene (NC_040253.1: g.62677376G > A) was associated with litter size in Cele Black sheep. Our results provide new theoretical support for sheep breeding.