Genomic analysis reveals selection signatures of the Wannan Black pig during domestication and breeding

Abstract

Objective: The Wannan Black pig is a typical Chinese indigenous, disease-resistant pig breed with high fertility, and a crude-feed tolerance that has been bred by artificial selection in the south of Anhui province for a long time. However, genome variation, genetic relationships with other pig breeds, and domestication, remain poorly understood. Here, we focus on elucidating the genetic characteristics of the Wannan Black pig and identifying selection signatures during domestication and breeding.

Methods: We identified the whole-genome variation in the Wannan Black pig and performed population admixture analyses to determine genetic relationships with other domesticated pig breeds and wild boars. Then, we identified the selection signatures between the Wannan Black pig and Asian wild boars in 100-kb windows sliding in 10 kb steps by using two approaches: the fixation index (FST) and π ratios.

Results: Resequencing the Wannan Black pig genome yielded 501.52 G of raw data. After calling single-nucleotide variants (SNVs) and insertions/deletions (InDels), we identified 21,316,754 SNVs and 5,067,206 InDels (2,898,582 inserts and 2,168,624 deletions). Additionally, we found genes associated with growth, immunity, and digestive functions.

Conclusion: Our findings help in explaining the unique genetic and phenotypic characteristics of Wannan Black pigs, which in turn can be informative for future breeding programs of Wannan Black pigs.

Keywords: Genome Variation; Porcine Industry; Selection Signature; Wannan Black Pig.

Figure 1

Geographic origin of the 19 analyzed pig breeds, including Europe and America (n = 5; green circles), Africa and Sus (n = 4; blue circle), Asia (n = 10; red circles).

Figure 2

The Wannan Black pig.

Figure 3

Population genetic structure of pig populations. (A) Neighbor-joining tree constructed from single-nucleotide variants (SNVs) data among 19 subspecies. (B) Principle component analysis plot of pig populations. Different colors represent different subspecies. (C) Cross-validation errors for diverse k values. (D) Population structure of study population. The length of different colors represents proportions of ancestry from ancestral populations; breed names are indicated on the left.

Figure 4

Distribution of F_ST values and π ratios calculated in 100 kb windows with 10 kb steps. (A) Distribution of F_ST values among autosome chromosomes. The red line represents the 0.01 level, and the blue line represents the 0.05 level. (B) Distribution of π ratios among autosomal chromosomes. (C) Intersection of the two methods used to identify high-quality selection regions. Data points located to the right of vertical dashed line (corresponding to the 5% right tails of the empirical θπ ratio distribution), and above the horizontal dashed line (the 5% right tail of the empirical F_ST distribution) were identified as selected regions for Wannan black pig (red points).

Figure 5

Results of the gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) analyses for the genes harbored in the selection regions. (A) GO terms of the identified genes. (B) Top 20 enrichment pathways.