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. 2022 Mar 24:13:860669.
doi: 10.3389/fgene.2022.860669. eCollection 2022.

Population Genetic Structure and Selection Signature Analysis of Beijing Black Pig

Wenjing Yang  1 , Zhen Liu  1 , Qiqi Zhao  1 , Heng Du  1 , Jian Yu  1 , Hongwei Wang  2 , Xiance Liu  2 , Hai Liu  2 , Xitao Jing  2 , Hongping Yang  2 , Guohua Shi  2 , Lei Zhou  1 , Jianfeng Liu  1
Affiliations

Population Genetic Structure and Selection Signature Analysis of Beijing Black Pig

Wenjing Yang et al. Front Genet. .

Abstract

Beijing Black pig is an excellent cultivated black pig breed in China, with desirable body shape, tender meat quality and robust disease resistance. To explore the level of admixture and selection signatures of Beijing Black pigs, a total number of 90 individuals covering nine pig breeds were used in our study, including Beijing Black pig, Large White, Landrace, Duroc, Lantang pig, Luchuan pig, Mashen pig, Huainan pig and Min pig. These animals were resequenced with 18.19 folds mapped read depth on average. Generally, we found that Beijing Black pig was genetically closer to commercial pig breeds by population genetic structure and genetic diversity analysis, and was also affected by Chinese domestic breeds Huainan pig and Min pig. These results are consistent with the cross-breeding history of Beijing Black pig. Selection signal detections were performed on three pig breeds, Beijing Black pig, Duroc and Large White, using three complementary methods (FST, θπ, and XP-EHH). In total, 1,167 significant selected regions and 392 candidate genes were identified. Functional annotations were enriched to pathways related to immune processes and meat and lipid metabolism. Finally, potential candidate genes, influencing meat quality (GPHA2, EHD1, HNF1A, C12orf43, GLTP, TRPV4, MVK, and MMAB), reproduction (PPP2R5B and MAP9), and disease resistance (OASL, ANKRD13A, and GIT2), were further detected by gene annotation analysis. Our results advanced the understanding of the genetic mechanism behind artificial selection of Beijing Black pigs, and provided theoretical basis for the subsequent breeding and genetic research of this breed.

Keywords: beijing black pig; candidate genes; genetic diversity; selection regions; whole-genome sequencing.

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Conflict of interest statement

HW, XL, HL, XJ, HY, and GS were employed by Beijing Heiliu Stockbreeding Technology Co.,Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
SNV characteristics of Beijing Black population. (A) Genome-wide distribution of detected SNVs on 19 chromosomes for the Beijing Black pigs. X-axis represents the number of SNVs. Y-axis represents 18 autosomes and X chromosome. (B) The percentage of Beijing Black SNVs within the dbSNP database. (C) Genome-wide annotation of Beijing Black genetic variations. X-axis represents the number of genetic variations (log10) within various functional regions. Y-axis represents various functional regions.
FIGURE 2
FIGURE 2
Phylogenetic relationship and population structure of Beijing Black and other eight breeds tested in this study. BJB, Beijing Black pig; HN, Huainan pig; MS, Mashen pig; LT, Lantang pig; LC, Luchuan pig; MIN, Min pig; DU, Duroc; LD, Landrace; LW, Large White. (A) Neighbor-joining phylogenetic tree constructed from SNV data among nine populations. (B) Principle component analysis for the first two PCs of 90 pigs. (C) ADMIXTURE analysis with four presumed ancestral groups (K = 4).
FIGURE 3
FIGURE 3
Genetic diversity of Beijing Black pigs. (A) Heatmap of FST distance between breeds. (B) The average number of ROH fragments of each breed. The number of ROH was classified into seven categories.
FIGURE 4
FIGURE 4
Genome-wide distribution of selection signatures detected by FST, θπ, and XP-EHH on 18 chromosomes from top to bottom. X-axis represents 18 autosomes, and Y-axis represents statistic values of each method. The θπ values are log2 normalized, and the XP-EHH values are standardized. Red line displays the threshold level of 5%. (A) Global distribution of statistic values of three methods between Beijing Black pigs and Duroc. (B) Global distribution of statistic values of three methods between Beijing Black pigs and Large White.
FIGURE 5
FIGURE 5
(A) Venn diagram shows the overlap in the number of candidate regions detected by different populations. The left circle represents the numbers of candidate regions detected by more than two methods between Beijing Black pig and Large White. The right circle represents the numbers of candidate regions detected by more than two methods between Beijing Black pig and Duroc. (B) The number of SNPs with high ΔAF in each region between Beijing Black pig and other two breeds.
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