基于70 K SNP芯片分析济宁青山羊保种群体的遗传结构

doi:10.11843/j.issn.0366-6964.2023.07.016

Abstract

Abstract: This study aimed to analyze the genetic diversity, kindship, and population structure of Jining gray goat conservation population. The Illumina 70 K goat SNP chip was used to screen the whole genome SNPs in 40 Jining gray goats, the genetic structure, kinship, and inbreeding coefficient of the breeding Jining gray goats were analyzed by Plink software, GCTA tool and R language to reveal the genetic relationship between the individuals. The results showed that a total of 67 088 SNPs were detected, and the call rate was higher than 98%. There were 57 991 SNPs met the demand of quality control, and 85.5% of which were polymorphic sites. The average effective allele number was 1.697, the average polymorphism information content was 0.283, and the minor allele frequency was 0.293, which implied that the genetic diversity was abundant in Jining gray goats conservation population. The average observed heterozygosity was 0.409, greater than that of expected heterozygosity (0.418). The average IBS genetic distance was 0.333 4, and the IBS genetic distance of 23 breeding bucks was 0.330 3. A total of 347 runs of homozygous (ROH) were detected in 40 individuals. The inbreeding coefficient of whole population was 0.047 9 based on the ROH value, which indicated a low level of inbreeding and rich in population genetic diversity. Combined the results of IBS matrix, G matrix, and phylogenetic tree, 23 bucks were clustered into 14 families according to the coefficient of relationship was 0.1. In conclusion, the Jining gray goats have rich genetic diversity, low level of inbreeding, and with remarkable conservation effect. It is suggested that, the number and structure of families in Jining gray goat conservation population should be focused in the future work.

Key words: Jining gray goat, SNP chip, genetic diversity, relationship, population genetic structure

CLC Number:

S827.2

ZHANG Renbao, ZHOU Donghui, ZHOU Lisheng, GAO Xiaoxiao, LIU Nan, HE Jianning. Analysis of Genetic Structure of Conservation Population in Jining Gray Goats Based on 70 K SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2836-2847.

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Analysis of Genetic Structure of Conservation Population in Jining Gray Goats Based on 70 K SNP Chip

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