With a rich breeding history, Nanyang cattle (NY cattle) have undergone extensive natural and artificial selection, resulting in distinctive traits such as high fertility, excellent meat quality, and disease resistance. This makes them an ideal model for studying the mechanisms of environmental adaptability. To assess the population structure and genetic diversity of NY cattle, we performed whole-genome resequencing on 30 individuals. These data were then compared with published whole-genome resequencing data from 432 cattle globally. The results indicate that the genetic structure of NY cattle is significantly different from European commercial breeds and is more similar to North–Central Chinese breeds. Furthermore, among all breeds, NY cattle exhibit the highest genetic diversity and the lowest population inbreeding levels. A genome-wide selection signal analysis of NY cattle and European commercial breeds using Fst, θπ-ratio, and θπ methods revealed significant selection signals in genes associated with reproductive performance and immunity. Our functional annotation analysis suggests that these genes may be responsible for reproduction (MAP2K2, PGR, and GSE1), immune response (NCOA2, HSF1, and PAX5), and olfaction (TAS1R3). We provide a comprehensive overview of sequence variations in the NY cattle genome, revealing insights into the population structure and genetic diversity of NY cattle. Additionally, we identify candidate genes associated with important economic traits, offering valuable references for future conservation and breeding efforts of NY cattle.

Background: Xianan cattle, the first cross-bred beef cattle developed in China, are recognized for their rapid growth, tolerance to rough feed, and high meat yield. These characteristics make them a valuable model for studies aimed at improving beef production traits. Methods: In this study, two complementary gene mapping strategies, selection signature analysis and association analysis, were employed to identify candidate genes associated with body weight. The analyses utilized resequencing data comprising 16,250,950 high-quality single nucleotide polymorphisms (SNPs). Twenty independent variables showed significant correlations with body weight, with effect sizes ranging from 239 kg to 629.37 kg, while controlling for a false discovery rate (FDR) of less than 0.5. Results: The most prominent signal was identified in the 54.24–54.39 MB region on chromosome 9, which contains the MANEA gene. Furthermore, we investigated the functional role of the MANEA gene at the cellular level. siRNA-mediated knockdown of MANEA resulted in significant alterations in the expression of downstream genes, notably MGAT1, MGAT3, FUT8, and HK1. Among these, the expression of MGAT1 was markedly increased, showing an increase of up to 600-fold compared to the control. Conclusions: These results offer critical insights into the molecular mechanisms underlying body weight regulation and provide a foundation for developing strategies to enhance economically important production traits in beef cattle.

The conservation of agricultural animal resources holds significant importance for addressing future breeding demands and promoting sustainable utilization of regional livestock genetic resources. As one of China’s five major fine cattle breeds, Nanyang cattle exhibit notable characteristics, including strong adaptability and a docile temperament. Through whole-genome comparative analysis of the Nanyang cattle core conservation population and free-ranging populations in mountainous areas, this study systematically investigated the genetic diversity, population structure, and adaptive evolutionary mechanisms of this indigenous Chinese cattle breed. Population structure analysis revealed that both groups belong to a single genetic lineage of Nanyang cattle without significant genetic differentiation; however, the free-ranging population demonstrated a slower linkage disequilibrium decay rate. Combined F_ST and θπ ratio analyses identified 170 positively selected genes, with KEGG enrichment highlighting glutamatergic synapse and African trypanosomiasis immune pathways. PLCB4, as a shared gene across both pathways, may exert pleiotropic functions in environmental adaptation. The core conservation population likely exhibits reduced diversity in neuroplasticity-related genes under artificial selection, whereas the free-ranging population retained more genes associated with environmental adaptation and immune response. These findings provide genomic evidence for formulating differentiated conservation strategies for Nanyang cattle, necessitating balanced co-optimization of production trait breeding and natural adaptability preservation.