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

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

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 s...

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Bibliographic Details
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
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Summary: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.
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ISSN:2076-2615
2076-2615
DOI:10.3390/ani12223214