Genome-Wide Analysis Reveals Genetic Structure and Selective Sweeps in Chinese Indigenous Pig Breeds

Abstract

Background Chinese indigenous pigs exhibit considerable phenotypic diversity, but their population structure and the genetic basis of agriculturally important traits have not been explored. Results Here, we sequenced the whole genomes of 24 individual pigs representing 22 breeds distributed throughout China. For comparison with European and commercial breeds (one pig per breed), we integrated seven published pig genomes with our new genomes. Our results showed that pig domestication occurred at three places in Southeastern Asia, namely the Mekong region, the middle to downstream regions of the Yangtze River, and Tibetan highlands. Moreover, we demonstrated that classic morphological characteristics such as coat color are not consistent with genetic data. We found that genetic material from European pigs likely introgressed into five Chinese breeds. Two new subpopulations of domestic pigs have been identified in South and North China that encompass morphology-based criteria. The Southern Chinese subpopulation comprises the classical Southern China Type and part of the Central China Type, whereas the Northern Chinese subpopulation comprises the North China Type, the Lower Yangtze River Basin Type, the Southwest Type, the Plateau Type, and the remainder of the Central China Type. Eight haplotypes and two recombination sites were identified within a conserved 40.09 Mb linkage-disequilibrium block on the X chromosome. Potential selection and domestication signatures were identified, mainly influencing body size, along with adaptations to cold and hot temperature environments. Conclusions Our findings provide insights into the phylogeny of Chinese indigenous pig breeds, and will be of enormous benefit in identifying beneficial genes to develop superior pig breeds.