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

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, Ape KI, Ape KI/ Tfi I, and Ape KI/ Mse I were selected to construct GBS libraries and the number of SNPs obtained from Ape KI/ Tfi I library were about six times more than that from the Ape KI library. In addition, the SNPs of Ape KI/ Tfi I library showed high accuracy in classification of Asian pear accessions. Thus, Ape KI/ Tfi I 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.