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

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.

Keywords: Altay white-headed cattle; SNP chip; genetic diversity; population structure; species in imminent danger.

Figure 1

DNA gel electrophoresis.

Figure 2

Distribution of SNPs on each chromosome before and after quality control. Note: the abscissa indicates the chromosome number, and the ordinate indicates the number of SNPs.

Figure 3

Genetic Diversity Analysis results. Note: (a). Minimum allele frequency distribution (the abscissa indicates the minimum allele frequency interval, and the ordinate indicates the SNP proportion). (b). Distribution of the Polymorphism Information Content (the abscissa represents the PIC interval value, and the ordinate represents the SNP proportion). (c). Heterozygosity analysis (Note: the abscissa indicates the classification of Ho and He, and the ordinate indicates the heterozygosity value).

Figure 4

ROH analysis results. Note: (a). Distribution of Roh length by population (the abscissa represents the length interval of ROH, and the ordinate represents the population proportion). (b). Distribution of the ROH number on each chromosome (the abscissa represents chromosome number, and the ordinate represents ROH quantity). (c). Sample number distribution of individual ROH length (the abscissa represents the length interval of Roh, and the ordinate represents the number of individuals).

Figure 5

Distribution of the inbreeding coefficient froh based on Roh. Note: This violin chart is mainly used to show the distribution of data. The white dot in the center represents the median of the population FROH, and the upper and lower edges of the black box in the middle represent the upper and lower quartiles of the population FROH, respectively. The width of the violin chart indicates the probability density distribution of the population FROH. The wider part of the violin chart indicates that there are a larger number of samples at this level, and vice versa.

Figure 6

Principal component analysis results.

Figure 7

Visualization results of the genome kinship analysis. Note: This figure shows the genomic kinship coefficient between two individuals. The closer the color, the closer the kinship. The abscissa and ordinate indicate the individual IDs.

Figure 8

Visualization results of the genetic distance analysis. Note: This figure shows the genetic distance between two individuals. The closer the color is, the closer the genetic relationship is. The abscissa and ordinate represent the individual IDs.

Figure 9

Cluster analysis results of bull samples. Note: one color represone family.

Figure 10

Clustering analysis results of all samples. Note: the color marked in the evolutionary tree is the bull sample, and one color represents a family.