Genomic signatures of diversity, adaptation and selection in indigenous Central Plains cattle in China

Chinese cattle mainly originate from two lineages, Bos taurus and Bos indicus , which have undergone extensive admixture in the Central Plains (CP) of China. Owing to this hybridization, CP cattle exhibit desirable traits such as high meat quality, tolerance to rough forage, and strong disease resistance, making them representative breeds for beef production in China. In this study, five representative CP breeds (Luxi, Bohai Black, Qinchuan, Mengshan, and Jiaxian Red cattle) were included for analysis to investigate their evolutionary history and ancestry composition. In this study, we generated whole-genome sequencing data for 120 cattle from two CP breeds (including Luxi and Bohai Black cattle), and integrated these data with publicly available whole-genome sequences from 106 cattle representing three additional CP breeds (Mengshan, Jiaxian Red, and Qinchuan cattle), as well as 225 domestic cattle data from the public database. Population genetic diversity analysis revealed that the genetic diversity of CP cattle is closely associated with their taurine and indicine ancestry components. Among the five populations, Luxi cattle showed the highest level of genetic diversity, followed by Jiaxian Red, Bohai Black, Qinchuan, and Mengshan cattle. Notably, Luxi cattle exhibited prominent signals of positive selection, with a strongly selected region on BTA3 (8.90–9.40 Mb) containing four genes ( SLAMF1 , SLAMF6 , CD84 , and VANGL2 ) involved in immune-related functions, and another candidate region on BTA2 (125.68–125.81 Mb) containing three genes ( WASF2 , AHDC1 , and FGR ), which mainly related to the binding with actin. Furthermore, in the analysis of coat color in Bohai Black cattle, we identified a previously reported missense mutation of the melanocortin 1 receptor ( MC1R ) gene (BTA18:14,705,671; rs109688013), which is predicted to alter protein structure. Taurine–indicine hybrids provide a valuable resource for enhancing key traits in cattle. The genetic diversity, selection signatures, and functional information identified here deepen our understanding of CP cattle evolutionary dynamics and offer insights for improving breeding programs.