Two gene clusters and their positive regulator SlMYB13 that have undergone domestication-associated negative selection control phenolamide accumulation and drought tolerance in tomato

Tomato is an ideal model for studying how plants effectively coordinate specialized metabolites to adapt to environmental change. Among plant metabolites, phenolamides, which are conjugates of hydroxycinnamic acid derivatives and polyamines, play important roles in plant adaptation to abiotic and biotic stresses. However, the molecular mechanisms underlying phenolamides metabolism and regulation in tomato, as well as the effects of domestication in breeding on phenolamide diversity, have not been fully elucidated. Here, we performed a metabolite-based genome-wide association study (mGWAS) to identify two biosynthetic gene clusters containing twelve genes involved in phenolamide metabolism, including four biosynthesis genes (two 4CL genes, one C3H gene, and one CPA gene), seven decoration genes (five AT genes and two UGT genes), and one transport protein (DTX29). We also discovered that SlMYB13 positively regulates two gene clusters, thereby promoting phenolamide accumulation. Moreover, phenolamides accumulation induced the scavenging of reactive oxygen species (ROS) and the increase of abscisic acid (ABA) content to enhance drought tolerance in tomato, which was further validated through the exogenous application of Fer-Put. Finally, the combined “HapB” (i.e., SlAT1.1-CHapB, SlAT1.2-AHapB, SlAT1.3-CHapB, SlCV86-THapB, SlDH29-THapB, and SlMYB13-GHapB) were negatively selected during tomato domestication and improvement, leading to a reduction in phenolamide content, and consequently, a diminished drought tolerance. In this study, we systematically dissected the mechanism of phenolamide biosynthesis through a multi-omics approach, and revealed the effects of human domestication on plant metabolic diversity and environmental adaptation during tomato breeding.