Targeted Genome Sequencing Analysis of the Ma Locus Controlling Fruit Acidity in Apple

Apple fruit acidity, which affects the overall taste and flavor of fruit, is mainly determined by malic acid content. Studies have shown that variations in fruit acidity levels are largely controlled by the major quantitative trait locus (QTL) Ma. Previously, we revealed that a mutation, called SNP1455, that leads to a premature stop codon in the coding sequence of Ma may have compromised the function of MA for fruit acidity in apple. To identify if there are any other mutations that might be significantly associated with acidity variations in addition to SNP1455, we conducted a targeted genome sequencing analysis of the Ma locus in 384 Malus accessions using Fludigm Access Array. Computer programs CLC Genomics Workbench and TASSEL were used for mapping of NGS reads, calling of SNPs or association studies. In total, we identified 20 SNPs that are significantly associated with treatable acidity based on their estimated genotype effect. Of these, seven SNPs were located in the exons while 13 in the introns. Among the seven exon SNPs, three were nonsynonymous variants, including SNP1455, while four were synonymous variants. Association analyses with fruit weight and harvest date were also conducted although significant variants were not identified.