Genetic Dissection of the Photosynthetic Parameters of Maize (Zea mays L.) in Drought-Stressed and Well-Watered Environments

Photosynthesis is a critical function that allows adaptation to drought stress in maize (Zea mays L.). Therefore, elucidation of the genetic control of photosynthetic performance under drought stress and the associated molecular markers is of great importance for marker-assisted selection (MAS). Here, we detected 54 quantitative trait loci (QTLs) affecting the net photosynthetic rate (Pn), stomatal conductance (Gs), intercellular CO2 concentration (Ci), transpiration rate (Tr), ribulose 1,5-biphosphate carboxylase activity (RuBP), and water use efficiency (WUE) of the ear leaf across two F4 populations in drought-stressed and well-watered environments by single-environment mapping with composite interval mapping (CIM), and 43 QTLs identified under drought stress, indicating that the tolerance to photoinhibition is a key factor affecting drought stress tolerance in maize. We further dissected 54 QTLs via joint analysis of all environments with mixed-linear-model-based CIM (MCIM), including 24 involved in QTL-by-environment interactions (QEIs), 87.5% QEIs identified under drought stress, 14 pairs showing epistatic interactions with dominance-by-additive/dominance effects under contrasting environments. We further identified eight constitutive QTLs (cQTLs) across two populations by CIM/MCIM, which could be used for genetic improvement of maize via QTL pyramiding. The co-localization of five cQTLs in bin 1.07_1.10/6.05/7.02_7.04/8.03/10.03 under contrasting environments in both populations strongly supported pleiotropy. Additionally, 17 candidate genes located at the above-mentioned cQTLs were involved in photomorphogenesis, photosynthesis, and stress response. These results provide insights into the genetic mechanisms responsible for photosynthesis under different water availability conditions, and reveal alleles that could potentially be used for MAS-based development of drought tolerant maize cultivars.