Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers

Abstract

To investigate population structure, linkage disequilibrium (LD) pattern and selection signature at the genome level in Chinese and Western pigs, we genotyped 304 unrelated animals from 18 diverse populations using porcine 60 K SNP chips. We confirmed the divergent evolution between Chinese and Western pigs and showed distinct topological structures of the tested populations. We acquired the evidence for the introgression of Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity revealed that historical inbreeding reduced genetic variability in several Chinese breeds. We found that intrapopulation LD extents are roughly comparable between Chinese and Western pigs. However, interpopulation LD is much longer in Western pigs compared with Chinese pigs with average r(2) (0.3) values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs. The finding indicates that higher-density markers are required to capture LD with causal variants in genome-wide association studies and genomic selection on Chinese pigs. Further, we looked across the genome to identify candidate loci under selection using F(ST) outlier tests on two contrast samples: Tibetan pigs versus lowland pigs and belted pigs against non-belted pigs. Interestingly, we highlighted several genes including ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in Tibetan pigs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports indicates that the underlying genetic basis for high-altitude adaptation in Tibetan pigs, Tibetan peoples and yaks is likely distinct from one another. Moreover, we identified the strongest signal of directional selection at the EDNRB loci in Chinese belted pigs, supporting EDNRB as a promising candidate gene for the white belt coat color in Chinese pigs. Altogether, our findings advance the understanding of the genome biology of Chinese and Western pigs.

Figure 1. The geographic locations of Chinese pigs in the present study.

BMX, Bamaxiang; DS, Dongshan; EHL, Erhualian; GX, Ganxi; JH, Jinhua; KL, Kele; MIN, Min; RC, Rongchang; SUT, Sutai; SZL, Shaziling; TC, Tongcheng; TG, Tibetan (Gansu); TT, Tibetan (Tibet); WB, Chinese wild boars.

Figure 2. Genetic diversity within and between Chinese and Western pigs.

(A) The genetic distance (D) between pairs of animals. Blue bars represent D within Chinese pigs; green bars represent D within Western pigs; red bars denote D between Chinese and Western pigs. (B) The neighbor-joining tree of the tested populations based on genome-wide allele sharing.

Figure 3. Population structures of Chinese and Western pigs revealed by principal component analysis.

Figure 4. Extent of LD (predicted r²) as a function of inter-SNP distance between Chinese and Western pigs and within each population.

Figure 5. Autozygosity frequency distribution of runs of homozygosity (ROH) in Chinese and Western pig populations.

Figure 6. Genome-wide distribution of log₁₀ Bayes factor values in two contrasts.

(A) Tibetan pigs versus non-plateau pigs. (B) Belted pigs against non-belted pigs. The chromosomes are plotted along the x-axis, and log₁₀ Bayes factor values are plotted along the y-axis. Chromosomes are indicated by different colors, and the threshold indicating signature of selection is denoted with a dashed grey line. In the upper panel, three highlighted genes that are likely involved with Tibetan high-altitude adaptation are circled in red, and the gene names are labeled above. For the contrast analysis between belted pigs and non-belted pigs, the top signal was detected at the EDNRB locus that is indicated in the lower panel.