Whole-genome Sequencing Reveals the Genetic Relationships and Selection Signatures of the Min Pig | [Pakistan Journal of Zoology • 2022]

Author(s):

1. Zhang Dong-jie: Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, P.R. China

2. He Xin-miao: Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, P.R. China; Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Harbin 150086, P.R. China

3. Wang Wen-tao: Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, P.R. China; Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Harbin 150086, P.R. China

4. Liu Di: Institute of Animal Husbandry, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, P.R. China; Key Laboratory of Combining Farming and Animal Husbandry, Ministry of Agriculture, Harbin 150086, P.R. China

Abstract:

The Min pig is indigenous to China. The genetic background of this breed was previously unclear, limiting the utility of the Min pig. In this study, the whole genomes of ten Min pigs and four Northeast wild boars were sequenced and the analysis yielded 8,988,338 non-redundant SNPs plus 1,231,680 InDels. A phylogenetic tree was constructed and a principal component analysis (PCA) was performed based on previously published SNP data from 66 individual pigs. Both analyses indicated the Min pig fell between the European and Asian pigs, while the Northeast wild boar was closely related to the Asian domestic and wild pig breeds. Selective sweep analysis indicated that 181 genes in the Min pig genome had been subjected to selection, including several genes encoding zinc finger proteins. Additional genes associated with myokinesis and lipid metabolism were also identified as under selection. Only SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptors) interactions in the vesicular transport pathway were identified as under selection (P=0.0029). This study describes the genomic framework of the Min pig and identifies signatures of selection. These results provide a useful genomic background for further studies of the genetic mechanisms associated with important economic traits in the Min pig.

Page(s): 1187-1198

DOI: 10.17582/journal.pjz/20200709040722

Published: Journal: Pakistan Journal of Zoology, Volume: 54, Issue: 3, Year: 2022

Keywords:

whole genome sequencing , Genetic relationship , Selection signatures , Min pig , Northeast wild boar

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