Genotyping-by-sequencing approaches using optimized two-enzyme combinations in Asian pears (Pyrus spp.)

Abstract

In genotyping-by-sequencing (GBS) library construction, restriction enzyme (RE) can influence the size and number of DNA fragments. The objective of the present study was to improve GBS efficiency in pears (Pyrus spp.) by selecting optimized RE combination. To prove GBS efficiency of selected RE combination, population structure and genetic diversity results of Asian pears were compared in two single nucleotide polymorphisms (SNP) sets derived from different GBS libraries. After in silico digestion, ApeKI, ApeKI/TfiI, and ApeKI/MseI were selected to construct GBS libraries and the number of SNPs obtained from ApeKI/TfiI library were about six times more than that from the ApeKI library. In addition, the SNPs of ApeKI/TfiI library showed high accuracy in classification of Asian pear accessions. Thus, ApeKI/TfiI combination is recommended for construction of GBS library in pears because such RE combination could provide genome-wide and numerous informative SNPs for pear genetic studies.