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Deciphering the Population Characteristics of Leiqiong Cattle Using Whole-Genome Sequencing Data
by
, ,
Yingwei Guo
1,†,
Zhihui Zhao
2,†,
Fei Ge
1,
Haibin Yu
2,
Chenxiao Lyu
1,3,
Yuxin Liu
1,
Junya Li
1,* and
Yan Chen
1,* 1
State Key Laboratory of Animal Biotech Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China
2
College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
3
Institute of Animal Husbandry and Veterinary Science, Tianjin Academy of Agricultural Sciences, Tianjin 300381, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Animals 2025, 15(3), 342; https://doi.org/10.3390/ani15030342
Submission received: 23 December 2024
/
Revised: 18 January 2025
/
Accepted: 22 January 2025
/
Published: 24 January 2025
(This article belongs to the Collection Advances in Cattle Breeding, Genetics and Genomics)
Simple Summary
Leiqiong cattle, native to China’s southernmost region, are prized for resisting disease and enduring heat. However, two distinct subgroups of these cattle—one in Hainan and the other in Guangdong—have evolved differently due to their separate environments. Our research utilized whole-genome sequencing data to investigate how these cattle have genetically diverged from each other and other commercial cattle breeds. We found that the Hainan subgroup has preserved a purer ancestry and exhibits less genetic variation, likely due to its isolated location. In contrast, the Guangdong subgroup shows greater genetic diversity and evidence of mixing with commercial breeds, likely resulting from historical crossbreeding. Our study identified genes that may account for the cattle’s disease resistance and other adaptive traits. Understanding these genetic differences enhances our appreciation of the impact of breeding practices and geographic isolation on livestock. This knowledge not only aids in conserving unique genetic traits but also informs breeding strategies to ensure the sustainability and resilience of cattle breeds in changing environments.
Abstract
Long-term geographic isolation and breeding programs both influence population characteristics. Leiqiong cattle, a native breed from the southernmost region of China, are renowned for disease and heat resistance, with two subgroups on Hainan Island and the Leizhou Peninsula. However, the genomic differences between them remain unexplored. In this study, we conducted genomic comparisons using whole-genome sequencing data from the two subgroups of Leiqiong cattle and three commercial breeds to assess their population structures. Leiqiong cattle in Hainan exhibited lower genetic diversity and a pure ancestral content due to their isolation from the mainland. In contrast, the subgroup in Guangdong displayed higher genetic diversity and mixed ancestry, influenced by the intrusion of commercial breeds. The genetic divergence between them was evaluated by estimating a genetic distance of 0.08 and a split time of 3400 to 4250 years ago, highlighting the role of geographical barriers in speciation. Notably, two candidate genes were identified through selection sweeps, including PIP4K2A, potentially related to immunity, and TNFSF4, possibly involved in hair follicle development. Our findings reveal the different genetic structures and genomic characteristics in the two subgroups of Leiqiong cattle, providing valuable insights into their evolutionary history and establishing a foundation for future breeding strategies.
