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Updated: May 16, 2026

Tomato Analyzer: A Useful Software Application to Collect Accurate and Detailed Morphological and Colorimetric Data from Two-dimensional Objects
Published on: March 16, 2010
eQTL Meta-Analysis Reveals Conserved and Population-Specific Regulatory Variation Underlying Nutritional Trait
Jiantao Zhao1,2, Xin Wang2,3, Jing Zhang4
1Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Fruits and Vegetables, Xinjiang Academy of Agricultural Sciences, Urumqi, Xinjiang, China.
Abstract:
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.
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