The multiple-stress effects on plant physiology and gene expression are being intensively studied lately, primarily in model plants such as Arabidopsis, where the effects of six stressors have simultaneously been documented. In maize, double and triple stress responses are obtaining more attention, such as simultaneous drought and heat or heavy metal exposure, or drought in combination with insect and fungal infestation. To keep up with these challenges, maize natural variation and genetic engineering are exploited. On one hand, quantitative trait loci (QTL) associated with multiple-stress tolerance are being identified by molecular breeding and genome-wide association studies (GWAS), which then could be utilized for future breeding programs of more resilient maize varieties. On the other hand, transgenic approaches in maize have already resulted in the creation of many commercial double or triple stress resistant varieties, predominantly weed-tolerant/insect-resistant and, additionally, also drought-resistant varieties. It is expected that first generation gene-editing techniques, as well as recently developed base and prime editing applications, in combination with the routine haploid induction in maize, will pave the way to pyramiding more stress tolerant alleles in elite lines/varieties on time.

Progressing climate change necessitates the development of drought-tolerant crops, and understanding the temporal dynamics of genotype x environment interactions (GxE) is crucial. This study aimed to test established phenotyping methods (chlorophyll a fluorescence (ChlF) and hyperspectral (HS) imaging) to investigate the variability in 165 inbred maize lines’ responses to progressive drought stress. The inbred maize lines were grown under controlled conditions and were challenged with water withholding. Fifteen ChlF and HS indices were measured at three consecutive time points (M1, M2, and M3). Mixed models were employed to estimate the GxT interaction effects via Best Linear Unbiased Predictors (BLUPs) for each variable. A Principal Component Analysis (PCA) performed on the GxT BLUPs from each time point revealed a highly dynamic interaction structure. While the primary axis of GxT variation (PC1) was consistently associated with HI, which is related to plant vigor, across all measurement times, its importance intensified under severe stress (M3). The secondary axis (PC2) shifted markedly over time: after initial variations at M1, it was dominated by GxT effects in specific ChlF parameters related to photosynthetic regulation under moderate stress (M2), before shifting again under severe stress (M3) to reflect the GxT effects on indices potentially related to pigment degradation and other stress indicators.

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.