eQTL Meta‐Analysis Reveals Conserved and Population‐Specific Regulatory Variation Underlying Nutritional Trait Evolution and Domestication in Tomato

Deciphering how genetic variation shapes transcriptional regulation is key to understanding the regulatory architecture of complex crop traits. Here, we present a comprehensive meta-analysis of expression quantitative trait loci (eQTLs) across five diverse tomato populations. We construct a genome-wide atlas of 40 928 eQTLs, comprising 9463 cis- and 31 465 trans-eQTLs, and reveal thousands of loci detectable only through meta-analysis. A substantial fraction of these eQTLs is associated with transcription factors (TFs), including a co-regulated cluster of two TFs and one transcriptional regulator targeted by a shared trans-eQTL hotspot harboring a key enzyme gene in gibberellin biosynthesis. Genes underlying nutritional quality traits, including sugars, organic acids, carotenoids, and folates, are predominantly controlled by strong cis-eQTLs. We further delineate a MYB12-centered regulatory network coordinating flavonoid metabolism that also extends to folate biosynthesis. Remarkably, MYB12 functions as a trans-regulator linking flavonoid and folate pathways, contributing to the reduced folate content characteristic of pink-fruited tomatoes. Together, this eQTL meta-analysis provides a high-resolution regulatory map of transcriptional variation in tomato and highlights key regulators of fruit nutritional quality, providing biological insights and practical targets for crop improvement.