Nonphotochemical quenching kinetics GWAS in sorghum identifies genes that may play conserved roles in maize and Arabidopsis thaliana photoprotection

SUMMARY Photosynthetic organisms must cope with rapid fluctuations in light intensity. Nonphotochemical quenching (NPQ) enables the dissipation of excess light energy as heat under high light conditions, whereas its relaxation under low light maximizes photosynthetic productivity. We quantified variation in NPQ kinetics across a large sorghum (Sorghum bicolor) association panel in four environments, uncovering significant genetic control for NPQ. A genome‐wide association study (GWAS) confidently identified three unique regions in the sorghum genome associated with NPQ and suggestive associations in an additional 61 regions. We detected strong signals from the sorghum ortholog of Arabidopsis thaliana Suppressor Of Variegation 3 (SVR3) involved in plastid–nucleus signaling. By integrating GWAS results for NPQ across maize (Zea mays) and sorghum‐association panels, we identified a second gene, Non‐yellowing 1 (NYE1), originally studied by Gregor Mendel in pea (Pisum sativum) and involved in the degradation of photosynthetic pigments in light‐harvesting complexes. Analysis of nye1 insertion alleles in A. thaliana confirmed the effect of this gene on NPQ kinetics in eudicots. We extended our comparative genomics GWAS framework across the entire maize and sorghum genomes, identifying four additional loci involved in NPQ kinetics. These results provide a baseline for increasing the accuracy and speed of candidate gene identification for GWAS in species with high linkage disequilibrium. Significance Statement This study identifies naturally occurring genetic variants in sorghum, which alter NPQ kinetics, of particular significance given recent evidence linking variation in NPQ kinetics to increased photosynthetic productivity and crop yield. The multi‐species GWAS approach used here—and its validation via loss of function mutant phenotype—also provides a baseline for increasing the accuracy and speed of candidate gene identification for GWAS in species with high linkage disequilibrium.