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

SIMPLE SUMMARY: Under a low-input production system, local cattle have extraordinary adaptability to a variety of environments. However, due to various reasons, Native Altay white-headed cattle selection and breeding have not received enough attention. In addition, a large number of excellent foreign cattle varieties have been introduced, and unplanned hybridization has been carried out. The number of pure Altay white-headed cattle has been decreasing, with the breed even facing the danger of extinction. The genetic diversity index is of great significance for evaluating population structure and formulating conservation strategies. The genetic variation and population structure of Altay genetic resources were studied using 100 k SNP genotyping data from Altay white-headed cattle. Our results show that the genetic structure of the Altay white-headed cattle population is different, but the level of genetic differentiation is low, and the genetic diversity is low. In conclusion, our findings provide genetic information about the Altay white-headed cattle population, which can be used for future conservation and breeding research. ABSTRACT: 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.