基于SNP芯片的丫杈猪保种群体遗传结构研究

doi:10.11843/j.issn.0366-6964.2023.06.011

Abstract

Abstract: This experiment was conducted to study the genetic diversity, relationship and family structure of Yacha pigs conserved population. The single nucleotide polymorphism (SNP) in 166 Yacha pigs was detected by 50K SNP bead chip. The observed heterozygosity, expected heterozygosity, polymorphism information content and minor allele frequency were calculated by Plink software to analyze the genetic diversity of Yacha conserved population. The runs of homozygosity (ROH) were calculated and identity by state (IBS) distance matrix was constructed by Plink software. The genetic relationship was analyzed according to the G matrix result constructed by GCTA software. The phylogenetic tree constructed by Mega X software was used to analyze the family structure of Yacha conserved population. The results showed that, 45 211 SNPs were detected in 166 Yacha pigs, in which 36 243 SNPs passed quality control. The effective allele number, polymorphism information content, proportion of polymorphic markers, minor allele frequency were 1.529, 0.254, 0.875 and 0.233, respectively. The expected heterozygosity and observed heterozygosity were 0.329 and 0.344, respectively. The average IBS genetic distance of Yacha conserved population was 0.259 5, the result of IBS genetic distance and G matrix showed that most Yacha pigs had moderately genetic relationship. A total of 3 226 ROHs were detected, and the length of 40.96% of these ROHs was less than 100 Mb. The average inbreeding coefficient based on ROH was 0.069. The phylogenetic tree result showed that, there were 8 families in Yacha boars, which is the same as that by manual pedigrees, but with individual differences among families. In summary, the effective population size and the genetic diversity of Yacha conserved population is low, while the inbreeding degree is not serious. Therefore, it’s necessary to importing or creating new blood to expand the effective population content and improve the genetic diversity of the population.

Key words: Yacha pig, SNP chip, genetic diversity, genetic structure

CLC Number:

S828.2

TAO Xuan, YANG Xuemei, LIANG Yan, LIU Yihui, WANG Yong, KONG Fanjing, LEI Yunfeng, YANG Yuekui, WANG Yan, AN Rui, YANG Kun, Lü Xuebin, HE Zhiping, GU Yiren. Analysis of Genetic Structure of Conservation Population in Yacha Pig Based on SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2308-2319.

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Analysis of Genetic Structure of Conservation Population in Yacha Pig Based on SNP Chip

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