Genome-wide genotyping uncovers genetic diversity, phylogeny, signatures of selection, and population structure of Chinese Jiangquhai pigs in a global perspective1.

Jiangquhai pigs are one of the 42 representative local breeds listed in the national livestock genetic resources conservation project of China. This breed is known for its prolificacy, desirable meat quality, and excellent adaptability to crude feed and local environments. In this study, we genotyped 105 Jiangquhai pigs from the state conservation farm using GeneSeek GGP Porcine 80K SNP chip, and explored the SNP data to unravel genetic diversity, evolutionary phylogeny, signatures of selection, and population structure of Jiangquhai pigs in a context of 33 global breeds. Five indices of observed heterozygosity, expected heterozygosity, effective population size, runs of homozygosity, and linkage disequilibrium extent indicate that the Jiangquhai breed are still rich in genetic diversity in comparison with other breeds also from East China despite the recent decline of its population size. Phylogenetic, principal component, TreeMix, and admixture analyses show that Jiangquhai pigs represent an authentic genetic resource and have close genetic relationships with East Chinese breeds, their geographical neighbors. A genome scan unravels a list of reproduction-related genes potentially under selection in Jiangquhai pigs. Using the neighbor-joining clustering approach, we reconstructed the family structure of the conservation population of Jiangquhai pigs. This finding allowed us to suggest a rotational mating scheme across the reconstructed families to reduce the risk of inbreeding depression in the population.