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

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

doi:10.1093/jxb/eraf323

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

Journal Article · Wed Jul 16 00:00:00 EDT 2025 · Journal of Experimental Botany

DOI:https://doi.org/10.1093/jxb/eraf323· OSTI ID:2998735

^[1]; Osei-Bonsu, Isaac ^[2]; Kanazawa, Atsuko ^[3]; Fisher, Nicholas ^[4]; Cruz, Jeffrey ^[1]; Roberts, Philip A. ^[5]; Huynh, Bao-Lam ^[5]; Kramer, David M. ^[1]

Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory
Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory; Crops Research Institute, Kumasi (Ghana); Kwame Nkrumah Univ. of Science and Technology (Ghana)
Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory; Jan IngenHousz Institute, Wageningen (Netherlands)
Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory; Univ. of Greenwich (United Kingdom)
Univ. of California, Riverside, CA (United States)

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.

View Accepted Manuscript (DOE)

Research Organization:: Michigan State Univ., East Lansing, MI (United States). MSU-DOE Plant Research Laboratory

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

Grant/Contract Number:: FG02-91ER20021; SC0007101

OSTI ID:: 2998735

Alternate ID(s):: OSTI ID: 2998780

Journal Information:: Journal of Experimental Botany, Journal Name: Journal of Experimental Botany; ISSN 1460-2431; ISSN 0022-0957

Publisher:: Oxford University Press (OUP)Copyright Statement

Country of Publication:: United States

Language:: English

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Genetically-determined variations in photosynthesis indicate roles for specific fatty acid species in chilling responses

Journal Article · Wed Mar 16 00:00:00 EDT 2022 · Plant, Cell and Environment · OSTI ID:1980643

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

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