Genome-Wide Analysis of Genetic Diversity and Selection Signatures in Zaobei Beef Cattle.

Simple Summary: Positive natural selection increases the frequency of beneficial genetic variations, promoting an organism's adaptability and survival in specific environments. In this study, we conducted whole-genome resequencing and population genetic structure analysis to investigate the genetic diversity of Zaobei cattle, local yellow cattle from China. By comparing Zaobei cattle with Simmental cattle, we identified several genomic regions exhibiting positive selection. Gene annotation of these regions revealed key traits of Zaobei cattle, such as heat tolerance, fertility, and superior meat quality. These findings not only help understand the characteristics of Zaobei cattle but also provide valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value. This investigation provides a comprehensive analysis of genomic diversity and selection signatures in Zaobei beef cattle, an indigenous breed known for its adaptation to hot and humid climates and superior meat quality. Whole-genome resequencing was conducted on 23 Zaobei cattle, compared with 46 Simmental cattle to highlight genetic distinctions. Population structure analysis confirmed the genetic uniqueness of Zaobei cattle. Using methods such as DASDC v1.01, XPEHH, and θπ ratio, we identified 230, 232, and 221 genes through DASDC, including hard sweeps, soft sweeps, and linkage sweeps, respectively. Coincidentally, 109 genes were identified when using XPEHH and θπ ratio methods. Together, these analyses revealed eight positive selection genes (ARHGAP15, ZNF618, USH2A, PDZRN4, SPATA6, ROR2, KCNIP3, and VWA3B), which are linked to critical traits such as heat stress adaptation, fertility, and meat quality. Moreover, functional enrichment analyses showed pathways related to autophagy, immune response, energy metabolism, and muscle development. The comprehensive genomic insights gained from this study provide valuable knowledge for breeding programs aimed at enhancing the beneficial traits in Zaobei cattle. [ABSTRACT FROM AUTHOR]