Genetic Relationships and Population Structure of Pear Accessions from Anhui, China, Based on Genotyping-by-Sequencing

Pear (Pyrus) is one of the most economically important fruits in temperate regions. Anhui Province is situated in the central region of China and is an area very suitable for the cultivation of pears. A variety of local pear accessions were cultivated in Anhui Province and were named “Anhui pear”, mainly contained “Dangshan pear” and “Huizhou snow pear”. However, little is known about the genetic relationships and population structure of Anhui pears. Here, we analysed the genetic diversity and population structure of 81 pear germplasm resources (48 from Anhui Province) using 242,447 genome-wide single nucleotide polymorphisms (SNPs) by genotyping-by-sequencing (GBS). In our phylogenetic tree, Anhui pears were mainly clustered together with P. pyrifolia and P. bretschneideri, indicating that Anhui pears are closely relationship-related to the sand pear (P. pyrifolia) and the white pear (P. bretschneideri). The combined result of principal component analysis and population structure analysis was sufficient to support the phylogenetic tree. In addition, Dangshan pears and P. bretschneideri were clustered together, and they had almost no genetic differentiation; however, there was rich genetic exchange between them, indicating that Dangshan pears may belong to the same evolutionary branch as white pears. However, Huizhou snow pears did not cluster together with Dangshan pears and clustered into a separate subclass, suggesting that gene flow between the southern and northern regions of Anhui Province was restricted by geographic isolation. These findings may provide important information for broadening the genetic selection of breeding sources, and further utilizing marker-assisted selection to choose new pear varieties that are suitable for Anhui Province.