Convergent domestication of bitter apples and pears by selecting mutations of MYB transcription factors to reduce proanthocyanidin levels

Fruit domestication has long aimed to reduce bitterness, yet the molecular mechanisms behind this trait remain only partially understood. Wild apples and pears naturally accumulate high levels of bitter proanthocyanidins (PAs), also known as condensed tannins. In this study, a convergent domestication process was identified in both fruits, involving the selection of weak alleles of MYB transcription factors that regulate PA biosynthesis. In apples, domestication targeted the MYB-Tannin-Tamer (MdMYBTT) gene. A 411-base pair transposable element inserted into the third exon of this gene in cultivated varieties produced a truncated, non-functional protein unable to activate the PA biosynthetic gene Anthocyanidin Reductase 1 (ANR1). The resulting mdmybtt allele led to reduced PA levels and was fixed in domesticated apples through positive selection. Likewise, in pears, a 57-base pair insertion in the promoter of the MYBPA1 gene suppressed its expression in cultivated varieties, limiting PA production. This insertion created the mybpa1 allele, which was similarly fixed during pear domestication. These findings highlight a shared evolutionary strategy to reduce fruit bitterness by selecting mutations that suppress PA synthesis. These findings offer valuable insights into the molecular basis of domestication and inform breeding efforts to optimize both flavor and nutritional quality.