Evidence map›Paper›PMID 42132963›Full record

SynthesisAdvanced science (Weinheim, Baden-Wurttemberg, Germany)2026

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

Jiantao Zhao, Xin Wang, Jing Zhang, Ryan McQuinn, Je Min Lee, Itay Gonda, Ari Feder, Yimin Xu, Baike Wang, Qinghui Yu and 5 more

Abstract readMeta-Analysis
PubMed Full text at PMC Publisher
In one paragraph

Synthesis in Advanced science (Weinheim, Baden-Wurttemberg, Germany), 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

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Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Jiantao ZhaoKey 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.
Xin WangBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Jing ZhangCollege of Horticulture, Northwest A&F University, Yangling, Shaanxi, China.
Ryan McQuinnBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Je Min LeeBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Itay GondaBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Ari FederBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Yimin XuBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Baike WangKey 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.
Qinghui YuKey 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.
Denise M TiemanHorticultural Sciences, University of Florida, Gainesville, Florida, USA.
Sanwen HuangNational Key Laboratory of Tropical Crop Breeding, Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China.
Harry KleeHorticultural Sciences, University of Florida, Gainesville, Florida, USA.
James J GiovannoniBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.
Zhangjun FeiBoyce Thompson Institute, Cornell University, Ithaca, New York, USA.ORCID https://orcid.org/0000-0001-9684-1450

Funding

National Key Research and Development Program of China 2023YFF1000100scientific research start-up funding from Hubei Hongshan Laboratory 11020102Special project of scientific and technological innovation of Xinjiang Research Institute of Arid Area Agriculture XJHQNY-2025-2US National Science Foundation IOS-1855585Young Scientist Fostering Funds for the National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Xinjiang Uygur Autonomous Region Tianshan Talents Training Program-Young top-notch scientific and technological talents 2024TSYCCX0096
6 · The paper itself

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.

Indexed as

DomesticationGene Expression Regulation, PlantGenetic VariationQuantitative Trait LociSolanum lycopersicumTranscription FactorsTranscription FactorseQTLfruit nutritionmeta‐analysistomato

Identifiers

PMID42132963
PMCPMC13335988

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.