Genome-Wide Association Study of Chlorophyll Fluorescence and Hyperspectral Indices in Drought-Stressed Young Plants in Maize

Background/Objectives: Global maize production is considerably affected by drought aggravated by climate change. No genome-wide association study (GWAS) or candidate gene analysis has been performed using chlorophyll fluorescence (ChlF) and hyperspectral (HS) indices measured in young plants challenged by a water deficit. Our objective was to conduct a GWAS of nine ChlF and HS indices measured in a diversity panel of drought-stressed young plants grown in a controlled environment using a maize single nucleotide polymorphism (SNP) 50k chip. Methods: A total of 165 inbred lines were genotyped using the Infinium Maize50K SNP array and association mapping was carried out using a mixed linear model. Results: The GWAS detected 37 respective SNP markers significantly associated with the maximum quantum yield of the primary photochemistry of a dark-adapted leaf (Phi_Po), the probability that a trapped exciton moves an electron into the electron transport chain further than QA (Psi_o), the normalized difference vegetation index (NDVI), the Zarco–Tejada and Miller Index (ZMI), greenness, modified chlorophyll absorption in reflectance (MCARI), modified chlorophyll absorption in reflectance 1 (MCARI1), and Gitelson and Merzlyak indices 1 and 2 (GM1 and GM2). Conclusions: Our results contribute to a better understanding of the genetic dissection of the ChlF and HS indices, which is directly or indirectly related to physiological processes in maize, supporting the use of HS imaging in the context of maize breeding.