A genome-wide association study for the detection of genes related to apple Marssonina Blotch disease resistance in apples

Abstract

Apple Marssonina Blotch (AMB), commonly referred to as apple blotch disease, is caused by Diplocarpon mali and represents one of the major diseases in Korean apple orchards. AMB can occur on the leaves and fruit, which lowers fruit quality and leads to early defoliation, reducing tree vigor and growth. In this study, a genome-wide association study (GWAS) was conducted to detect genes that may affect AMB disease infection. A multi-locus random SNP effect mixed linear model (mrMLM) method GWAS analysis was conducted with 192 apple germplasms (Malus spp.) in the Apple Research Institute at the National Institute of Horticultural & Herbal Science, Gunwi, Korea. Highly significant five SNP loci were selected from the results of the GWAS analysis and based on the Haploview 4.2 LD analysis data, candidate genes linked five SNP loci and their predicted functions were identified association to AMB resistance by Basic Local Alignment Search Tool of the National Center for Biotechnology Information. One of these candidate genes was identified include leucine rich repeat structure by BLAST. Highly susceptible and resistant cultivars to AMB were separately distinguished in the high resolution melting analysis using primers from two significant loci. Thus, the candidate genes linked to these two SNP loci are potentially strongly associated with AMB resistance.