Data from: Genetic diversity, linkage disequilibrium and selection signatures in Chinese and Western pigs revealed by genome-wide SNP markers

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
r20.3 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.