Lijiang Resequencing analysis Raw sequence reads

Gene flow provides an important genetic source for improving the performance of economically important traits in livestock. For decades, many breeders in China have used hybridization strategies to improve animal performance. Here, we generated whole-genome sequencing data of a Chinese native LJ (Lijiang) breed. Combined with previously published data, we explored and compared the genetic population structure and introgression components from European commercial breeds (EP) between LJ and other Chinese indigenous pig populations. The results showed that LJ pigs along with some other Chinese domestic pigs were significantly introgressed from EP. A haplotype-based method was used to quantify the introgression, and we purposed different ways of introgression from EP into Tibetan pigs, including direct and indirect way, for the latter, we suggested LJ could be a promising potential mediator for transmitting EP haplotypes. Finally, we analyzed the correlation of EP introgression and the number of thoracic vertebrae in LJ pigs, and identified candidate genes that might affect this trait, such as VRTN and STUM. Our study demonstrates the presence of introgressed European haplotypes in LJ pigs and provides an example of EP introgression resulting in phenotypic changes in Chinese indigenous pigs.