Revealing Genetic Diversity and Population Structure of Endangered Altay White-Headed Cattle Population Using 100 k SNP Markers

• Published in: Animals (Basel) Vol. 12; no. 22; p. 3214
• Main Authors: Liu, Bo, Tao, Weikun, Feng, Donghe, Wang, Yue, Heizatuola, Nazigul, Ahemetbai, Tenes, Wu, Weiwei
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 20-11-2022; MDPI
• Subjects: Adaptability; Alleles; Altay white-headed cattle; Animal husbandry; Animal populations; Blood; Breeding; Cattle; Changing environments; Cluster analysis; Conservation; Environmental changes; Gene frequency; Gene polymorphism; Genetic analysis; Genetic distance; Genetic diversity; Genetic resources; Genetic structure; Genomes; Genotyping; Heterozygosity; Hybridization; Inbreeding; Milk; Polymorphism; Population genetics; Population structure; Quality control; Single-nucleotide polymorphism; SNP chip; Software; Species extinction; species in imminent danger; Study Protocol; Beijing China; China; species in imminent danger; genetic diversity; SNP chip; population structure; Altay white-headed cattle
• ISSN: 2076-2615; 2076-2615
• DOI: 10.3390/ani12223214

Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.