Whole-Genome Resequencing Reveals Genetic Diversity and Wool Trait-Related Genes in Liangshan Semi-Fine-Wool Sheep.

Simple Summary: The Liangshan semi-fine-wool sheep is a composite breed, developed in Southwest China by crossing local coarse-wool sheep (Liangshan native sheep), fine-wool sheep (e.g., Xinjiang Merino sheep), and semi-fine-wool sheep (e.g., Border Leicester and Romney sheep). This breed not only has soft wool with a spinning count from 48 to 50s but also exhibits excellent adaptability to the local cold and humid environment. Nevertheless, recent declines in wool market demand and the lack of continuous genetic improvement initiatives have resulted in a reduction in its population size. In this study, we systematically investigated the genetic composition of this breed through comparative genomic analyses. Compared to Chinese sheep populations (e.g., Yunnan sheep), our findings unveiled a shorter genetic distance between Liangshan semi-fine-wool sheep and non-Chinese breeds like Border Leicester and Romney sheep. Additionally, we identified many plausible candidate genes and signaling pathways associated with wool traits specific to Liangshan semi-fine-wool sheep. These results provide important references and genomic resources that can be harnessed for future genetic breeding improvements for Liangshan semi-fine-wool sheep. Understanding the genetic makeup of local sheep breeds is essential for their scientific conservation and sustainable utilization. The Liangshan semi-fine-wool sheep (LSS), a Chinese semi-fine-wool breed renowned for its soft wool, was analyzed using whole-genome sequencing data including 35 LSS, 84 sheep from other domestic breeds, and 20 Asiatic mouflons. We investigated the genetic composition of LSS by conducting analyses of the population structure, runs of homozygosity, genomic inbreeding coefficients, and selection signature. Our findings indicated that LSS shares greater genetic similarity with Border Leicester and Romney sheep than with Tibetan (TIB), Yunnan (YNS), and Chinese Merino sheep. Genomic analysis indicated low to moderate inbreeding coefficients, ranging from 0.014 to 0.154. In identifying selection signals across the LSS genome, we pinpointed 195 candidate regions housing 74 annotated genes (e.g., IRF2BP2, BVES, and ALOX5). We also found the overlaps between the candidate regions and several known quantitative trait loci related to wool traits, such as the wool staple length and wool fiber diameter. A selective sweep region, marked by the highest value of cross-population extended haplotype homozygosity, encompassed IRF2BP2—an influential candidate gene affecting fleece fiber traits. Furthermore, notable differences in genotype frequency at a mutation site (c.1051 + 46T > C, Chr25: 6,784,190 bp) within IRF2BP2 were observed between LSS and TIB and YNS sheep (Fisher's exact test, p < 2.2 × 10−16). Taken together, these findings offer insights crucial for the conservation and breeding enhancement of LSS. [ABSTRACT FROM AUTHOR]