To alleviate global food insecurity in the face of global climate change, many strategies have been proposed including the possibility of planting improved crops developed through molecular breeding by using natural genetic variations. Although photosynthesis directly contributes to yield, exploring natural variations in photosynthesis is a highly under-investigated approach for improving crop yield. The photosynthetic performance under adverse environmental conditions has large natural variations, so exploring these variations would be the way to improving the tolerance of crops as well as to uncovering mechanistic bases by elucidating natural strategies for adaptation of certain variants. By exploring natural variations in genetic diversity with more detailed photosynthetic phenotyping, a novel approach, which is available to test (support or reject) hypothetical models that can be used to identify the genetic and mechanistic bases, is proposed in this work, and tested, leading to major findings.Firstly, I demonstrated this novel approach by exploring linkages between genetic polymorphisms and multiple, mechanistically-related phenotypes in a population of recombinant inbred lines (RILs) of cowpea (Vigna unguiculata. (L.) Walp.) generated from parent lines with significant differences in photosynthetic responses to chilling. The proposed co-association analysis showed mechanistic linkages among photosynthetic efficiency, photoprotection, photodamage and capture and feedback regulation by control of the thylakoid proton motive force, including with those for photosystem II (PSII) quantum efficiency (ΦII), nonphotochemical quenching (NPQ) in both the qE and qI forms, the redox state of QA (qL), the redox states of photosystem I (PSI), the activity of the thylakoid ATP synthase (gH+,) and the light-driven thylakoid proton motive force (pmf). The follow-up biochemical/biophysical assays show that genetic variations impact low temperature tolerance/sensitivity by modulating: 1) redox states of QA; 2) the thylakoid pmf, through effects on cyclic electron flow, leading to differences in the rates of photodamage to PSII. With the same approach, I observed variations in the relative compositions of the thylakoid-specific fatty acid and specifically, 16:1∆3‐transPG were strongly co-associated with the network of photosynthetic parameters, showing nearly linear dependence of PSII quantum efficiency (ΦII) across the RIL populations. These results suggest that the genetically determined variations in chilling responses of photosynthesis involve common, mechanistic or genetic linkages with 16:1∆3‐transPG composition. This correlation between lipid composition and photosynthetic responses at low temperature were qualitatively recapitulated in mutants or transgenic Arabidopsis lines with altered 16:1∆3‐transPG composition, suggesting that differential accumulation of 16:1∆3‐transPG leads to changes in photosynthetic responses at low temperature. The outcome of this dissertation by exploring natural variations is enlightening to underlying mechanisms and readily applicable to molecular breeding to improve photosynthesis for higher, more climate-resilient productivity.
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