Affiliation:
1. Academy of Animal Science and Veterinary Medicine Qinghai University Xining China
2. Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau Ministry of Agriculture and Rural Affairs Xining China
3. Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province Xining China
4. College of Animal Science and Technology Northwest A&F University Yangling China
5. Golmud Animal Husbandry and Veterinary Station of Qinghai Province Golmud China
6. Agro‐Technical Extension and Service Center in Haixi Prefecture of Qinghai Province Delingha China
7. Department of Livestock and Poultry Production, Faculty of Veterinary and Animal Sciences University of Poonch Rawalakot Rawalakot Pakistan
Abstract
AbstractQaidam cattle are a typical Chinese native breed inhabiting northwest China. They bear the characteristics of high cold and roughage tolerance, low‐oxygen adaptability and good meat quality. To analyze the genetic diversity of Qaidam cattle, 60 samples were sequenced using whole‐genome resequencing technology, along with 192 published sets of whole‐genome sequencing data of Indian indicine cattle, Chinese indicine cattle, North Chinese cattle breeds, East Asian taurine cattle, Eurasian taurine cattle and European taurine cattle as controls. It was found that Qaidam cattle have rich genetic diversity in Bos taurus, but the degree of inbreeding is also high, which needs further protection. The phylogenetic analysis, principal component analysis and ancestral component analysis showed that Qaidam cattle mainly originated from East Asian taurine cattle. Qaidam cattle had a closer genetic relationship with the North Chinese cattle breeds and the least differentiation from Mongolian cattle. Annotating the selection signals obtained by composite likelihood ratio, nucleotide diversity analysis, integrated haplotype score, genetic differentiation index, genetic diversity ratio and cross‐population extended haplotype homozygosity methods, several genes associated with immunity, reproduction, meat, milk, growth and adaptation showed strong selection signals. In general, this study provides genetic evidence for understanding the germplasm characteristics of Qaidam cattle. At the same time, it lays a foundation for the scientific and reasonable protection and utilization of genetic resources of Chinese local cattle breeds, which has great theoretical and practical significance.