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 (QTL) 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 photosystems I (PSI) and II (PSII), photoprotective nonphotochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLM). The patterns of QTL linkages indicated chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLM. 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 is modulated by thylakoid fatty acid composition, as suggested in Hoh et al., 2022. We propose the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations.
Highlight This work Introduces the Linkage Integration Hypothesis Testing (LIgHT) approach for mechanistic studies of natural variations, identifying photosynthetic regulatory mechanisms underlying natural variations to abiotic stresses by applying this approach.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Email: Donghee Hoh: hohdongh{at}msu.edu, Isaac Osei-Bonsu: ob.isaac{at}gmail.com, Atsuko Kanazawa: kanazawa{at}msu.edu, atsuko.kanazawa{at}jan-ingenhousz-institute.org, Nicholas Fisher: n.e.fisher{at}gmail.com, Jeffrey Cruz: cruzjeffa{at}gmail.com, Philip A. Roberts: philip.roberts{at}ucr.edu, Bao-Lam Huynh: baolam.huynh{at}ucr.edu, David M. Kramer: kramerd8{at}msu.edu, david.kramer{at}jan-ingenhousz-institute.org
Abbreviations
- LEF
- linear electron flow
- CEF
- cyclic electron flow
- PSI
- photosystem I
- PSII
- photosystem II
- ΦII
- quantum efficiency of photosystem II
- QTL
- quantitative trait loci
- NPQ
- nonphotochemical quenching
- LIgHT
- Linkage Integration Hypothesis Testing
- RILs
- recombinant inbred lines
- pmf
- proton motive force
- Chr
- chromosome
- NLM
- nyctinastic leaf movements
- QA
- primary quinone acceptor of PSII redox state of the PSII (QA)
- qL
- a fraction of PSII centers in open states
- ESTs
- expressed sequence tags
- MQM
- Multiple QTL Mapping
- KOG
- EuKaryotic Orthologous Groups
- KO
- Kyoto Encyclopedia of Genes and Genomes
- GO
- Gene Ontology
- DI
- deionized water
- HL
- high light
- CT
- control temperature
- LT
- low-temperature
- PCON
- photosynthetic control
- P700
- primary electron donor of PSI
- kb6f
- rate constant for P700+ re-reduction kb6f
- H+
- proton
- e-
- electron
- CB27
- California Blackeye 27
- IRAD
- Institute de Recherche Agricole pour le Développement
- DEPI
- Dynamic Environmental Phenotype Imager
- Fv/Fm
- maximal PSII quantum efficiency
- NPQt
- non-photochemical quenching calculated using a theoretical (t) Fv/Fm value
- qIt
- photoinhibition-related quenching calculated using a theoretical (t) Fv/Fm value
- qEt
- energy-dependent quenching calculated using a theoretical (t) Fv/Fm value
- trx
- thioredoxin
- AGPase
- ADP-glucose pyrophosphorylase
