2017 ASHS Annual Conference

This study was performed to develop the SNP markers for the assessment of genetic diversity and genetic structure in 95 apple germplasm including bud sport cultivars using genotyping-by-sequencing (GBS). Using ApeKI for GBS library preparation and sequencing on an Illumina Hiseq 2000 paired-end read, 744 Mb of raw reads were yielded with an average length of 101 bp. After aligning each of 95 accessions’ trimmed reads to reference genome (Malus × domestica cv. Golden Delicious 1.0), an average of 5,952,222 reads (78.86%), which covered reference genome with an average of 2.18%, were successfully aligned to reference genome. An average number of mapped region were 78,406 with an average depth of 22.28. The mapped reads from 95 accessions were filtered with a minimal set of initial quality filters, resulting in union matrix of 786,247 SNPs. For the set of union SNP matrix, by applying subsequent filters, 12,014 SNPs were obtained and utilized for construction of phylogenetic tree using MEGA6 with neighbor-joining method. After analyzing genetic relationship between 95 accessions, they were classified into a total of 3 groups. Group I contained 31 cultivars including ‘Hongro’, ‘Gala’, ‘Golden Delicious’, and their bud sport cultivars, cross cultivars between them, and others. Group II was characterized as ‘Fuji’. These group consisted of 32 cultivars, including ‘Fuji’, its bud sport cultivars, progenies of ‘Fuji’, and other cultivars. Group III contained 32 cultivars including ‘McIntosh’. The results of research may be utilized for the establishment and management of apple germplasm collections.