Evidence map›Paper›PMID 42098144›Full record

ArticleNature communications2026

The incomplete dominance of gene expression controlled by Trans-eQTL hotspots contributes to heterosis in maize.

Gen Xu, Xuerong Yang, Mingyue Zhang, Congbin Kang, Ziang Tian, Yunhui Qi, Meijie Luo, Peng Liu, Jeffrey Ross-Ibarra, Jinliang Yang and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature communications, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

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

2 citing papers in PubMed.

  1. Article
  2. Article
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

11 authors.

Gen Xu *Department of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA.ORCID http://orcid.org/0000-0001-5701-4751
Xuerong Yang *State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.ORCID http://orcid.org/0000-0003-3414-3117
Mingyue Zhang *State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.
Congbin KangState Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.ORCID http://orcid.org/0000-0002-7729-7274
Ziang TianState Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China.ORCID http://orcid.org/0009-0002-0890-4648
Yunhui QiDepartment of Statistics, Iowa State University, Ames, IA, USA.
Meijie LuoBeijing Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Institute, Beijing Academy of Agriculture and Forestry Sciences, Beijing, China.
Peng LiuDepartment of Statistics, Iowa State University, Ames, IA, USA.
Jeffrey Ross-IbarraDepartment of Evolution and Ecology, Center for Population Biology, and Genome Center, University of California, Davis, CA, USA.ORCID http://orcid.org/0000-0003-1656-4954
Jinliang YangDepartment of Agronomy and Horticulture, Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA. jinliang.yang@unl.edu.ORCID http://orcid.org/0000-0002-0999-3518
Hongjun LiuState Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, China. hongjunl@sdau.edu.cn.ORCID http://orcid.org/0000-0001-5123-688X

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Heterosis, or hybrid vigor, is a key genetic and agricultural phenomenon driven by non-additive effects, though its mechanisms remain debated. To examine these effects at the transcriptomic level, we integrate population-scale transcriptomic and phenotypic data in maize. We find that ∼30% of expressed seedling genes in many hybrids deviate from mid-parent values, consistent with incomplete dominance. While overall expression is largely controlled by cis-eQTLs, non-additive expression is disproportionately regulated by trans-eQTLs. These trans-eQTLs cluster into hotspots that coordinately control hundreds of genes, often within co-expression networks and enriched for transcription factors. We validate one hotspot involving ZmR1, a bHLH transcription factor, showing its role in regulating widespread incomplete dominance and enhancing heterosis in seedling and agronomic traits. These findings support a model in which trans-acting factors shape expression dominance and contribute to heterosis, providing a framework for crop improvement.

Indexed as

Gene Expression Regulation, PlantHybrid VigorQuantitative Trait LociZea maysGene Expression ProfilingGenes, DominantGenes, PlantPhenotypePlant ProteinsSeedlingsTranscriptomePlant Proteins

Identifiers

PMID42098144
PMCPMC13381767

What OpenQuestion holds

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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.