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 r2 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 FST 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.

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data

“…In addition, linkage disequilibrium values ( r 2 0.3 , predicted as described by Ai et al . 2013) ranged from 15 kb (Middle Meishan) to 34 kb (Fengjing), and the interpopulation linkage disequilibrium extent across the six Chinese pigs breeds was only 9 kb (Fig. S1), which is close to the estimation of Ai et al .…”

“…2003; Ai et al . 2013). Specifically, the Middle Meishan breed exhibited a higher level of polymorphisms than did the Small Meishan breed, implying that the Small Meishan breed might have a smaller effective population or might have experienced intensive selection that decreased the extent of its polymorphisms.…”

“…Recently, several studies have also extensively evaluated the genetic variations of some Chinese pigs using high‐density SNP markers (Ai et al . 2013, 2014) or whole‐genome sequencing data (Ai et al . 2015).…”

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

“…If the growth-related genes and immunity-related genes defined in the previous step are both in an LD region, the region can be considered to be a pleiotropic block with growth and immune function. LD with average r 2 0:3 values, which is known as useful LD (Aerts et al, 2006), is~100kb for Western pigs and 10kb for Chinese pigs (Ai et al, 2013 and, and thus the length of the LD was set conservatively as 10kb in this study.…”

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

“…Ai, Huang, and Ren (2013), working with Chinese pigs in Tibet, and Burgos‐Paz et al. (2012) with American pigs, found selection signatures correlated with the extremes of environmental conditions (high‐altitude adaptation), linked to altitude and circulatory system, respectively.…”