利用高密度SNP芯片分析杭猪的群体遗传结构

doi:10.11843/j.issn.0366-6964.2022.08.009

Abstract

Abstract: The purpose of this study was to better understand the genetic diversity, relationship and family structure of Hang pigs conserved population, protect and utilize the genetic resources of Hang pigs efficiently. The 50K SNP chip was used to detect the single nucleotide polymorphism (SNP) in 30 Hang pigs (4 male and 26 female). And the quality control of SNP genotyping results was conducted by Plink software to calculated the minor allele frequency, observed heterozygosity, expected heterozygosity and polymorphism information content so as to analyze the genetic diversity of Hang pigs conserved population. The runs of homozygosity (ROH) was calculated and identity by state (IBS) distance matrix was constructed by Plink software, the inbreeding coefficient was then calculated based on ROH. The genetic relationship was analyzed according to the G matrix result constructed by Gmatrix software. The boar phylogenetic tree which constructed by Mega X software was used to analyze the family structure of Hang pigs conserved population. The results showed that, 57 466 SNPs were detected in 30 Hang pigs, the average genotyping rate was 0.988 3±0.000 4, there were 34 156 SNPs passing quality control. The average minor allele frequency, polymorphism information content, average observed heterozygosity and average expected heterozygosity were 0.228±0.137, 0.255±0.098, 0.359±0.181 and 0.314±0.140, respectively. The average IBS genetic distance of Hang pigs conserved population and boar were 0.241 7±0.033 6 and 0.178 3±0.025 5, respectively, and the result of G matrix was consistent with IBS genetic distance, the IBS genetic distance and G matrix results showed that some individuals in Hang pigs conserved population were closer to each other. A total of 828 ROHs were detected in 30 Hang pigs, and the length of 83.33% of these ROHs was less than 10 Mb, and the average length was (6.96±9.62) Mb, and the average total length of individual ROH was (191.95±201.56) Mb. The average inbreeding coefficient based on ROH of Hang pigs conserved population and boar were 0.078±0.082 and 0.219±0.082, respectively, indicated that the inbreeding degree of Hang pigs conserved population was not serious, but there was inbreeding in boar. The phylogenetic tree result showed that, there were only two families in Hang pigs conserved population, and one family contained all 4 boars and the other family only contained sows. In summary, the blood number of the boar of conserved population in the Hang pigs conserved farm was few, the inbreeding degree of sow was low, but there was inbreeding in boar, it was necessary to introduce new blood or create new blood to maintain the balance of family structure, so as to facilitate the long-term preservation of Hang pigs genetic resources and prevent the loss of genetic diversity.

Key words: Hang pigs, SNP chip, genetic diversity, relationship, family structure

CLC Number:

S828.2

LIU Chenlong, LU Dan, ZHOU Quanyong, WAN Mingchun, HAO Xiaodong, ZHANG Xianhe, ZHENG Ruiqiang, JI Huayuan. Analysis of Population Genetic Structure of Hang Pigs by High Density SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(8): 2502-2513.

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Analysis of Population Genetic Structure of Hang Pigs by High Density SNP Chip

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