Review: Progress on genome-wide association studies and selection signature analysis for agronomic traits in Chinese sheep and goats.

As some of the earliest domesticated animals, sheep and goats hold significant historical importance in Chinese animal husbandry. With the rapid advancement of modern biotechnology, genome wide association studies (GWAS) and selection signature analyses have become indispensable tools in livestock genetic research. This review summarizes recent progress in applying these methods to sheep and goat breeding in China, analyzes the current problems in the research and proposes research strategies. GWAS and selection signature analyses have identified key genomic regions associated with agronomically important traits. For instance, genes such as LHX2, FGF12 and Notch3 are implicated in hair follicle growth and development, while RBM11, SMARCA5 and GAB1 are linked to body size in sheep. Additionally, BMPRIB has been proposed as a determinant of reproductive performance and growth rate in both sheep and goats. Despite progress, challenges remain, including incomplete reference genomes, limited phenotypic data, suboptimal algorithms, and a lack of functional validation and practical application of findings. Future work must prioritize genomic refinement, multi-omics integration, and algorithm development. Enhanced international collaboration will be crucial to deciphering the genetic basis of key traits, driving global industry advancements. These efforts will enable highly precise breeding strategies. By accurately identifying and selecting individuals with desirable genetic characteristics, breeders can significantly enhance the efficiency of genetic improvement. Taking Hua sheep 50k chip as an example, it can screen out sheep individuals with high reproductive genes (such as BMPRIB) in the very early stage, increase the lambing rate by 27.7%, accelerate the propagation of excellent breeding groups, provide a large number of breeding sheep resources with excellent genetic performance for the global sheep industry, and improve the overall quality of germplasm. Ultimately, this will contribute to the sustainable development of sheep and goat production worldwide.