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Water deficit is the most severe stress factor in crop production threatening global food security. In this study, we evaluated the genetic variation in photosynthetic traits among 200 wheat cultivars evaluated under drought and rainfed conditions. Significant genotypic, treatments, and their interaction effects were detected for chlorophyll content and chlorophyll fluorescence parameters. Drought stress reduced the effective quantum yield of photosystem II (YII) from the anthesis growth stage on. Leaf chlorophyll content measured at anthesis growth stages was significantly correlated with YII and non-photochemical quenching under drought conditions, suggesting that high throughput chlorophyll content screening can serve as a good indicator of plant drought tolerance status in wheat. Breeding significantly increased the photosynthetic efficiency as newer released genotypes had higher YII and chlorophyll content than the older ones. GWAS identified a stable drought-responsive QTL on chromosome 3A for YII, while under rainfed conditions, it detected another QTL on chromosome 7A for chlorophyll content across both growing seasons. Molecular analysis revealed that the associated alleles of AX-158576783 (515.889 Mbp) on 3A co-segregates with the NADH-ubiquinone oxidoreductase (

Additional file 7: Fig. S2. Clusters of expression profiles of Syn86 and Zentos.

Additional file 11: Fig. S3. Melting curves of some PCR products derived from the amplification of reference and target genes.

Additional file 3: Fig. S1. Density plots with the log10 normalized expression values of the libraries from the four genotypes studied.

Additional file 8: Table S6. Gene ontology terms over-represented in the gene clusters from Syn86 and Zentos.