Population Structure and Selection Signal Analysis of Nanyang Cattle Based on Whole-Genome Sequencing Data

Abstract

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.

Keywords: Nanyang cattle; genetic diversity; population structure; whole-genome resequencing.

Figure 1

Genetic structure analysis of the Nanyang population. (a) Principal component analysis based on whole-genome sequencing data. (b) Phylogenetic analysis constructed based on genetic distance. (c) Model-based clustering of breeds was performed using ADMIXTURE, with K values ranging from 2 to 4.

Figure 2

Analysis of ROH distribution patterns and genetic diversity. (a) Proportion of ROH segments across the entire genome in different breeds. (b) Linkage disequilibrium analysis based on whole-genome resequencing. (c) Nucleotide diversity across different breeds. The black line in the boxplot is the median line, and the outside points are outliers. (d) Average inbreeding coefficients for each breed. The black line in the boxplot is the median line, and the outside points are outliers.

Figure 3

Analysis of selection signals and function enrichment in NY cattle. (a) Manhattan plots based on the Fst and θπ-ratio. (b) Selective sweep results for Fst and θπ-ratio. Fst and θπ-ratio are plotted on the X and Y axes, respectively, with horizontal and vertical gray dashed lines denoting the top 1% values of Fst (0.41) and θπ-ratio (1.209). Red dots represent significantly similar candidate selection windows identified by both methods.