Whole-Genome Scanning for Selection Signatures Reveals Candidate Genes Associated with Growth and Tail Length in Sheep

Simple Summary Sheep are bred to provide livestock products for humans. At present, sheep production systems tend to be specialized and refined, and mutton sheep production is an important part of these systems. Compared to Chinese indigenous sheep breeds, Western sheep breeds have rapid growth rate, larger physique, and higher meat yield. Growth rate and body size are critical to mutton sheep production. The population structure and genome-wide selection signatures can be used to identify genetic differences in sheep growth rate and body size. Therefore, in this study, a genome-wide investigation of the growth rate and body size between Chinese indigenous sheep breeds and introduced sheep breeds was performed. Furthermore, we also investigated the tail length trait between long- and short-tailed sheep breeds. The results showed that we identified candidate genes associated with growth rate, body size, and tail type, and elucidated the potential function of these genes.Abstract Compared to Chinese indigenous sheep, Western sheep have rapid growth rate, larger physique, and higher meat yield. These excellent Western sheep were introduced into China for crossbreeding to expedite the enhancement of production performance and mutton quality in local breeds. Here, we investigated population genetic structure and genome-wide selection signatures among the Chinese indigenous sheep and the introduced sheep based on whole-genome resequencing data. The PCA, N-J tree and ADMIXTURE results showed significant genetic difference between Chinese indigenous sheep and introduced sheep. The nucleotide diversity (pi) and linkage disequilibrium (LD) decay results indicated that the genomic diversity of introduced breeds were lower. Then, Fst & pi ratio, XP-EHH, and de-correlated composite of multiple signals (DCMS) methods were used to detect the selection signals. The results showed that we identified important candidate genes related to growth rate and body size in the introduced breeds. Selected genes with stronger selection signatures are associated with growth rate (CRADD), embryonic development (BVES, LIN28B, and WNT11), body size (HMGA2, MSRB3, and PTCH1), muscle development and fat metabolism (MSTN, PDE3A, LGALS12, GGPS1, and SAR1B), wool color (ASIP), and hair development (KRT71, KRT74, and IRF2BP2). Thus, these genes have the potential to serve as candidate genes for enhancing the growth traits of Chinese indigenous sheep. We also identified tail-length trait-related candidate genes (HOXB13, LIN28A, PAX3, and VEGFA) in Chinese long-tailed breeds. Among these genes, HOXB13 is the main candidate gene for sheep tail length phenotype. LIN28A, PAX3, and VEGFA are related to embryonic development and angiogenesis, so these genes may be candidate genes for sheep tail type traits. This study will serve as a foundation for further genetic improvement of Chinese indigenous sheep and as a reference for studies related to growth and development of sheep.