Natural variation in MdMYB31 underlies volatile ester accumulation and fruit aroma evolution during apple domestication

The volatile organic compounds (VOCs) produced by fruits are the defining elements of their distinct aroma. Understanding the genetic basis underlying natural variation of fruit VOCs profiles can help breeders develop high-quality fruit varieties. Here, we uncover a natural variation responsible for the diversity of VOC profiles in apple species. Fruit VOCs in 110 Malus accessions from 19 species were quantified. It was demonstrated that fruit odour became more pronounced during domestication, and VOC esters (VOC-ESTs) impart characteristic fruity odour to ripe fruit of cultivated apple (Malus × domestica Borkh.) compared with wild apples. Quantitative trait locus (QTL) mapping using a segregating population derived from Honeycrisp (low VOC-ESTs) × Qinguan (high VOC-ESTs) revealed a stable QTL region (EST-LG06) on linkage group 06 related to VOC-ESTs. It contained a MYB transcription factor gene (MdMYB31) that is tightly associated with VOC-ESTs accumulation by up-regulating key alcohol acyl transferase genes, including MdAAT1 and MdAAT2. Further analyses show that natural variation in MdMYB31's coding region affects its transcriptional regulatory activity, leading to different VOC-EST profiles among different apple germplasms. Importantly, the MdMYB31 genotype with stronger transcriptional regulatory activity has been selected during apple domestication, alongside the enhancement of fruit odour. Collectively, our findings highlight a major breakthrough in determining the genetic basis underlying phenotypic variation in apple VOC-ESTs accumulation, and set the foundation for breeding aromatic apple cultivars through molecular breeding.