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.

Hubei indigenous cattle have adapted to diverse environmental conditions, exhibiting unique genetic traits associated with both economic and adaptive characteristics. Understanding their adaptive selection offers insight into their evolutionary history and genetic enhancements. In this study, we analyzed whole-genome sequencing (WGS) data from five Hubei indigenous cattle breeds to identify selection signals. Selective sweep analysis revealed the candidate genes (USH2A, TMTC2, ABCC12, and SUGT1) associated with sensory perception, backfat thickness, reproduction, and immune function. The further integration of cis-regulatory elements (CREs) and expression quantitative trait loci (eQTL) highlighted regulatory variants, influencing adaptive traits. Notably, positively selected genes such as RPS6KA2, CRLS1, MGST3, GPCPD1, and LDLRAP1 were associated with lipid metabolism, meat quality, and reproductive traits, influencing aldehyde volatile organic compounds (VOCs) and fat deposition. These findings highlight the understanding of the genetic basis of adaptation and production traits in Hubei indigenous cattle and provide valuable insights for their conservation and potential breeding strategies.

The availability of genome sequences and single-nucleotide polymorphism (SNP) chips allows us to investigate the various genomic characteristics of species by exploring genetic diversity to aid genetic selection. The SNP chip is a cost-effective genotyping platform essential for molecular breeding of livestock. In this study, we developed a liquid SNP capture chip suitable for five Hubei (China) indigenous beef cattle breeds based on whole-genome sequencing datasets. The panel consisted of 42,686 SNPs (~40 K). These SNPs were evenly distributed on each bovine chromosome, with the majority of SNPs having minor allele frequencies >0.05 and located within intergenic regions. The performance evaluation of this SNP chip panel was proceeded by genotyping 200 individuals, revealing that this panel has a high SNP call rate of 99.48%. The SNP chip panel was further used to examine the population structure of a beef cattle population with 205 individuals and demonstrated the ability to differentiate between foreign and indigenous cattle breeds. The SNP chip was also used to determine the runs of homozygosity (ROH) within a local Hubei beef cattle population of 195 individuals. We identified 2547 ROH and several genes associated with economically important traits in the study population. Our findings demonstrate that this chip not only contributes to the understanding of the genetic characteristics of local beef cattle breeds but also provides valuable genetic information for future breeding programs, thereby improving their production efficiency and economic value.

Leukocyte traits are crucial clinical indicators for various diseases, reflecting the immunity in dairy cows and indicating production performance and elimination rate. In Southern China, diseases caused by high temperature and humidity in summer significantly impact the production of dairy cows. Conducting a genome-wide association study (GWAS) on leukocyte counts and components in healthy individuals is essential for identifying genes involved in leukocyte production, differentiation or clearance, thereby aiding in the accurate identification of genetic sources of immune variation in dairy cows. This study measured leukocyte traits in 200 healthy dairy cows and conducted GWAS. The results revealed 70 single-nucleotide polymorphisms (SNPs). Of these, 15 SNPs were within genes and all in introns. Additionally, the BEN Domain-Containing Protein 5 (BEND5) gene, which regulates white blood cell count (WBC), percentage of basophils (%BASO) and percentage of lymphocytes (%LYMPH), and the Forkhead box J3 (FOXJ3) gene, which regulates WBC and %BASO, were identified as two crucial candidate genes. This study provides new evidence on the genetic basis of immunity differences in dairy cows in Southern China, suggesting that the SNPs and candidate genes identified could be valuable for dairy cow breeding.

Leukocyte traits are crucial clinical indicators for various diseases, reflecting the immunity in dairy cows and indicating production performance and elimination rate. In Southern China, diseases caused by high temperature and humidity in summer significantly impact the production of dairy cows. Conducting a genome‐wide association study (GWAS) on leukocyte counts and components in healthy individuals is essential for identifying genes involved in leukocyte production, differentiation or clearance, thereby aiding in the accurate identification of genetic sources of immune variation in dairy cows. This study measured leukocyte traits in 200 healthy dairy cows and conducted GWAS. The results revealed 70 single‐nucleotide polymorphisms (SNPs). Of these, 15 SNPs were within genes and all in introns. Additionally, the BEN Domain‐Containing Protein 5 ( BEND5 ) gene, which regulates white blood cell count (WBC), percentage of basophils (%BASO) and percentage of lymphocytes (%LYMPH), and the Forkhead box J3 ( FOXJ3 ) gene, which regulates WBC and %BASO, were identified as two crucial candidate genes. This study provides new evidence on the genetic basis of immunity differences in dairy cows in Southern China, suggesting that the SNPs and candidate genes identified could be valuable for dairy cow breeding.