Identification of the Gene Co-Expression Networks Regulating Acidity in Developing Apple Fruit

Apple fruit acidity which significantly affects fruit taste and overall flavor is primarily determined by the concentration of malic acid. Previous studies demonstrated that apple acidity levels were predominantly controlled by the major QTL Ma (malic acid) on linkage group 16. In addition to Ma, several other QTLs were also reported of significant modifying effect on acidity. More recently, we have shown that a pre-mature stop codon leading SNP in one of the two aluminum-activated malate transporter (ALMT)-like genes (called Ma1) at the Ma locus is strongly associated with fruit acidity in apple, suggesting that Ma1 is the gene underpinning Ma. Although the Ma locus largely governs fruit acidity variations in diverse apples, it does not explain the developmental changes of fruit acidity in a given genotype. To understand this aspect of fruit acidity, we took a transcriptomics approach using RNA-seq data from fruit of ‘Golden Delicious’ taken at 14 growth and developmental stages from one week after full bloom (WAF1) through maturity (WAF20). The fruit malate concentrations were 12.2±1.6 mg/g in samples WAF3-WAF8 (high), 5.4±0.4 mg/g in WAF16-WAF20 (low) and 7.4±0.5 mg/g in WAF1-WAF2 and WAF10-WAF14 (medium). For RNA-seq analysis, we first developed an improved apple reference transcriptome that could cover reads of >75% on average. Preliminary analysis showed that >2000 genes (including Ma1) or transcripts were expressed differentially between the low acid group and the others. We are currently examining these genes in detail to construct the gene co-expression networks relevant to acidity variations in developing fruit.