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Abstract In nature, plants experience rapid changes in light intensity and quality throughout the day. To maximize growth, they have established molecular mechanisms to optimize photosynthetic output while protecting components of the light‐dependent reaction and CO₂fixation pathways. Plant phenotyping of mutant collections has become a powerful tool to unveil the genetic loci involved in environmental acclimation. Here, we describe the phenotyping of the transfer‐DNA (T‐DNA) insertion mutant line SALK_008491, previously known asnhd1‐1. Growth in a fluctuating light regime caused a loss in growth rate accompanied by a spike in photosystem (PS) II damage and increased non‐photochemical quenching (NPQ). Interestingly, an independentnhd1null allele did not recapitulate the NPQ phenotype. Through bulk sequencing of a backcrossed segregating F₂pool, we identified an ~14‐kb large deletion on chromosome 3 (Chr3) in SALK_008491 affecting five genes upstream ofNHD1. BesidesNHD1, which encodes for a putative plastid Na⁺/H⁺antiporter, the stromal NAD‐dependent D‐3‐phosphoglycerate dehydrogenase 3 (PGDH3) locus was eradicated. Although some changes in the SALK_008491 mutant's photosynthesis can be assigned to the loss of PGDH3, our follow‐up studies employing respective single mutants and complementation with overlapping transformation‐competent artificial chromosome (TAC) vectors reveal that the exacerbated fluctuating light sensitivity in SALK_008491 mutants result from the simultaneous loss of PGDH3 and NHD1. Altogether, the data obtained from this large deletion‐carrying mutant provide new and unintuitive insights into the molecular mechanisms that function to protect the photosynthetic machinery. Moreover, our study renews calls for caution when setting up reverse genetic studies using T‐DNA lines. Although second‐site insertions, indels, and SNPs have been reported before, large deletion surrounding the insertion site causes yet another problem. Nevertheless, as shown through this research, such unpredictable genetic events following T‐DNA mutagenesis can provide unintuitive insights that allow for understanding complex phenomena such as the plant acclimation to dynamic high light stress. 

The responses of plant photosynthesis to rapid fluctuations in environmental conditions are thought to be critical for efficient conversion of light energy. Such responses are not well represented under laboratory conditions, but have also been difficult to probe in complex field environments. We demonstrate an open science approach to this problem that combines multifaceted measurements of photosynthesis and environmental conditions, and an unsupervised statistical clustering approach. In a selected set of data on mint (Mentha sp.), we show that the “light potential” for increasing linear electron flow (LEF) and nonphotochemical quenching (NPQ) upon rapid light increases are strongly suppressed in leaves previously exposed to low ambient PAR or low leaf temperatures, factors that can act both independently and cooperatively. Further analyses allowed us to test specific mechanisms. With decreasing leaf temperature or PAR, limitations to photosynthesis during high light fluctuations shifted from rapidly-induced NPQ to photosynthetic control (PCON) of electron flow at the cytochrome b6f complex. At low temperatures, high light induced lumen acidification, but did not induce NPQ, leading to accumulation of reduced electron transfer intermediates, a situation likely to induce photodamage, and represents a potential target for improving the efficiency and robustness of photosynthesis. Finally, we discuss the implications of the approach for open science efforts to understand and improve crop productivity. 

The capacity of photoautotrophs to fix carbon depends on the efficiency of the conversion of light energy into chemical potential by photosynthesis. In nature, light input into photosynthesis can change very rapidly and dramatically. To analyze how genetic variation in Arabidopsis thaliana affects photosynthesis and growth under dynamic light conditions, 36 randomly chosen natural accessions were grown under uniform and fluctuating light intensities. After 14 days of growth under uniform or fluctuating light regimes, maximum photosystem II quantum efficiency (Fv/Fm) was determined, photosystem II operating efficiency (ΦPSII) and non-photochemical quenching (NPQ) were measured in low light, and projected leaf area (PLA) as well as the number of visible leaves were estimated. Our data show that ΦPSII and PLA were decreased and NPQ was increased, while Fv/Fm and number of visible leaves were unaffected, in most accessions grown under fluctuating compared to uniform light. There were large changes between accessions for most of these parameters, which, however, were not correlated with genomic variation. Fast growing accessions under uniform light showed the largest growth reductions under fluctuating light, which correlated strongly with a reduction in ΦPSII, suggesting that, under fluctuating light, photosynthesis controls growth and not vice versa.