Identification of favorable SNP alleles related to fruit traits in diverse apple germplasm

Abstract

Background: The Apple ( Malus × domestica Borkh.) is a valuable fruit crop worldwide, and receives considerable attention as one of the model plants of the Rosaceae family. The primary purpose of apple breeding programs is to generate novel apple cultivars with fruit quality traits that have high commercial value. To advance fruit-tree breeding systems, it is necessary to investigate the association between genomes and targeted traits. Genome-wide association studies (GWAS) are promising to analyze the associations between the genome and traits in fruit tree crops. Results: In this study, we evaluated 10 major fruit quality traits including titratable acidity (TA), soluble solids content (SSC), and skin color from 301 apple germplasms for four years (2015-2018). GWAS analysis was performed using SNP data generated via genotyping by sequencing (GBS) and identified SNPs significantly related to the fruit quality traits. For TA, significant association loci were detected on chromosome 16 and genes in the candidate regions related to malate transporter. The GWAS loci of SSC was found on chromosome 15, where genes related to sucrose synthase and transporter are located. Significant SNPs associated with fruit skin color were identified on genetic region near the MYB1 gene on chromosome 9, which regulates anthocyanin biosynthesis. SNPs identified by the GWAS and Linkage disequilibrium (LD) analysis were further confirmed with high resolution melting (HRM) analysis to discover specific polymorphisms in the melting curve. Conclusion: Overall, these results could identify several candidate genes and SNP markers associated with the fruit quality traits, thus validation of these SNPs enabled marker-assisted selection (MAS). The candidate SNPs and genes observed in this study will contribute to a better understanding of genetic basis for the important fruit quality traits and provide tools for generation of novel cultivars with the quality traits for advancement of apple industry.