Whole-Genome Sequencing of Dorper × Hu Hybrid Sheep for Screening Selection Signatures Associated with Litter Size

Sheep are an economically important livestock species, and reproductive performance is a key trait affecting productivity. The Dorper × Hu hybrid sheep (DHS), widely bred in China, provides a valuable model for studying the genetic basis of prolificacy. This study aimed to investigate the genomic architecture and identify candidate genes associated with high litter size in DHS using whole-genome selective sweep analysis and genome-wide association study (GWAS). A total of 31 DHS individuals with complete reproductive records were sequenced and compared with publicly available genomic data from 20 Hu sheep (HUS) and 10 Dorper sheep (DPS). Population genetic structure and diversity were assessed using phylogenetic trees, principal component analysis (PCA), and ADMIXTURE analysis. To identify key genomic regions associated with litter size, we performed selective sweep analysis between the polytocous and monotocous subpopulations of DHS using multiple methods within a 50 kb sliding window framework, including FST, θπ ratio, XP-CLR, and XP-EHH; we also conducted GWAS. DHS exhibited a distinct genetic structure with admixed ancestry and elevated genetic diversity. Genetic diversity analysis showed that DHS retained moderate levels of heterozygosity and polymorphism, comparable to or exceeding those of its parental breeds. Comparative analysis between polytocous and monotocous DHS identified reproduction-associated genes, including <i>MUC1</i>, <i>PLCB4</i>, <i>SIN3A</i>, and <i>ELAVL2</i>, enriched in pathways such as ovarian steroidogenesis, insulin secretion, and circadian entrainment. Furthermore, genome-wide association study (GWAS) identified 140 significant loci (<i>p</i> < 10^-5) associated with reproductive traits. From these, 10 candidate SNPs were selected for validation through single-marker association analysis in 200 DHS individuals, among which two loci-g.88680390 C>A (<i>SLC24A2</i>/<i>MLLT3</i>) and g.18197516 T>C (<i>ABCA1</i>)-showed significant correlations with litter size. These findings enhance our understanding of the genetic basis of prolificacy in DHS and provide valuable molecular markers for genomic selection in sheep-breeding programs.