Genetic relationships and population structure of pears (Pyrus spp.) assessed with genome-wide SNPs detected by genotyping-by-sequencing

Abstract

Pears (Pyrus spp.) are temperate trees and their fruits are consumed throughout the world, but their genetic relationships are difficult to identify due to low morphological diversity. We estimated the genetic relationships and population structure of 231 pear accessions using 10,186 genome-wide single nucleotide polymorphisms (SNPs) driven by genotyping-by-sequencing (GBS). In our phylogenetic tree and population structure analysis, the accessions were classified into two major groups (group I and II), which were characterized by European and Asian pears, and two subgroups in group II. Of the subgroups in group II, group II-1 contained P. pyrifolia and group II-2 consisted of P. bretschneideri, P. ussuriensis, and P. betulifolia. Principal component analysis classified the pears more precisely than the phylogenetic tree, and P. betulifolia, which belonged to group II-2, was divided into two additional groups. These results suggest that genome-wide GBS–SNPs are suitable to estimate the genetic diversity of pear germplasms, including Asian and European pears, and are also valuable for understanding the genetic structure and evolution of pears, predicting breeding materials, and genome-wide association studies. Furthermore, the information resulting from this study could be useful for the management of Korean pear germplasms and development of breeding materials.