Genome-wide genetic diversity and IBD analysis reveals historic dissemination routes of pear in China

Pear (Pyrus) is an important temperate fruit, which originates in the southwestern region of China and has more than 3000 year’s cultivation history. However, the historic routes of pear dissemination in China have not been fully elucidated. In this study, a total of 2,412,930 single nucleotide polymorphisms (SNPs) at a density of 4.74 SNP/kb were identified by resequencing. The SNP-based phylogenetic analysis revealed that 102 pear samples from 23 provinces in China were divided into two major clades and eight geographic groups, and these divisions were supported by results of a population structure analysis and principal component analysis (PCA). Combined with the results of population diversity and identity-by-descent (IBD) analysis, it was revealed that the dissemination direction of pear was from southwest to southeast and from south to north. In the southern region, the dispersal pattern of pear spreading from west to east was generally in line with the course of the Yangtze River and Pearl River. The southern pear spread by multiple routes to its north neighboring areas, and regions in the middle and lower reaches of the Yellow River played important roles in the further dissemination of pear in the northern region of China. Moreover, we identified comparative higher genetic diversity of Ussurian pear than other populations, which might be due to low degree of domestication and closely resembled the high diversity of its wild counterpart. Our study provides new information to further our understanding of pear evolution in China, while laying a foundation of data for population genetic research, germplasm protection, and utilization for pear breeding in the future.