Whole-genome SNP markers reveal conservation status, signatures of selection and introgression in Chinese Laiwu pigs

Laiwu pigs
are a Chinese indigenous breed that is renowned for its exceptionally high
intramuscular fat content (average greater than 6%), providing an excellent
genetic resource for the genetic improvement of meat quality of modern
commercial pigs. To uncover genetic diversity, population structure, signature
of selection and potential exotic introgression in this breed, we sampled 238
Laiwu pigs from a state-supported conservation
population and genotyped these individuals using GeneSeek 80K SNP BeadChip.
We then conducted in-depth population genetics analyses for the Laiwu pig in a
context of 1116 pigs from 42 Eurasian diverse breeds. First, we show that the
current Laiwu population has more abundant genetic diversity than the
population of 18 years ago likely due to gene flow from European commercial
breeds. Both neighbor-joining (NJ) and principal component analyses indicate the
introgression of European haplotypes into Laiwu pigs. The admixture analysis reveals
that an average 26.66% of Laiwu genetic components are of European origin.
Then, we assigned the tested individuals to different families according to
their clustering patterns in the NJ tree, and proposed a family-based
conservation strategy to reduce the risk of inbreeding depression in Laiwu pigs.
Next, we explored three statistics (ROH and iHS and EigenGWAS) to identify a
list of candidate genes for fat deposition, reproduction and growth in Laiwu
pigs. Last, we detected a strong signature of introgression from European pigs
into Laiwu pigs at the GPC6 locus that regulates the growth of
developing long bones. Further association analyses indicate that the
introgressed GPC6 haplotype contributed to the improvement
of growth performance in Laiwu pigs. Altogether, this study not only
benefits the better conservation of the Laiwu pig, but also advances our knowledge
of the poorly understood effect of human-mediated introgression on phenotypic
traits in Chinese indigenous pigs.