Whole genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple

Soluble sugar and organic acids are key determinants of fruit organoleptic quality and directly affect the commodity value and economic returns of fruit crops. We conducted whole genome sequencing (WGS) of the apple varieties ‘Gala’ and ‘Xiahongrou’, along with their F1 hybrid, to construct a high-density bin map. Our quantitative genetic analysis pinpointed 53 quantitative trait loci (QTL)s related to 11 sugar and acid traits. We identified a candidate gene, MdNADP-ME, responsible for malate degradation, on a stable QTL of linkage group (LG) 15. Sequence analysis revealed an A/C SNP in the promoter region (MEp-799) that influences the binding of the transcription factor MdMYB2, impacting MdNADP-ME expression. In our study of various apple genotypes, this SNP was linked to malate and fructose levels. We also developed a dCAPS marker associated with fruit fructose content. These results substantiate the role of MdNADP-ME in maintaining the equilibrium of sugar and acid content in apple fruits.