Evidence map›Paper›PMID 40668175›Full record

ArticleJournal of experimental botany2025

From quantitative trait loci towards mechanisms: Linkage Integration Hypothesis Testing (LIgHT) sheds light on the mechanisms of genetically modulated stress tolerance.

Donghee Hoh, Isaac Osei-Bonsu, Atsuko Kanazawa, Nicholas Fisher, Jeffrey Cruz, Philip A Roberts, Bao-Lam Huynh, David M Kramer

Abstract read
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In one paragraph

Article in Journal of experimental botany, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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

What it found

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2 · The registry

The trial behind it

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

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5 · Who and what money

Authors and funding

8 authors.

Donghee HohMSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.ORCID 0000-0002-0221-6484
Isaac Osei-BonsuMSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
Atsuko KanazawaMSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
Nicholas FisherMSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
Jeffrey CruzMSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.
Philip A RobertsDepartment of Nematology, University of California, Riverside, CA 92521, USA.
Bao-Lam HuynhDepartment of Nematology, University of California, Riverside, CA 92521, USA.
David M KramerMSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA.

Funding

AgBioResearch programJan IngenHousz InstituteJohn A. Hannah EndowmentNational Science FoundationPlant Science Fellowship (Michigan State University)US Agency for International DevelopmentU.S. Department of Energy, Office of Science, Basic Energy Sciences DE-FG02-91ER20021U.S. Department of Energy, Office of Science, Basic Energy Sciences DE-SC0007101
6 · The paper itself

Abstract

The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTLs) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea (Vigna unguiculata L. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of PSI and PSII, photoprotective non-photochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLMs). The patterns of QTL linkages indicated that chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLMs. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation appears to be modulated by thylakoid fatty acid composition, previously associated with the same genetic loci and now supported by broader mechanistic evidence. We propose that the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations.

Indexed as

Genetic LinkageQuantitative Trait LociStress, PhysiologicalVignaCold TemperatureLightPhotosynthesisPhotosystem II Protein ComplexPlant LeavesPhotosystem II Protein ComplexChilling stress (low-temperature stress)chlorophyll fluorescencecowpeadynamic environmental photosynthetic imagingMultispeQnatural genetic variationphotoinhibitionphotosynthesisproton motive forcequantitative trait loci

Identifiers

PMID40668175
PMCPMC12621098

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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.