Sorghum (Sorghum bicolor L. Moench) is one of the most important cereal crops cultivated in arid and semiarid regions for food, feed and biofuel production. Cold and drought stresses reduce photosynthesis in sorghum, limiting biomass production and yield. It is necessary to understand the genetic mechanisms controlling stress response to develop cultivars with increased cold and drought tolerance. We performed genome wide association studies (GWAS) for gas exchange and chlorophyll fluorescence traits in sorghum. The main objective was to discover genes/genomic regions that control the photosynthetic capacity under optimal, low temperature and drought stress conditions. Two experiments were conducted in growth chambers. For cold, 304 sorghum genotypes were measured during three periods: control (six days, 28ïÿýC/24ïÿýC day/night); cold (seven days, 15ïÿýC day/night); and recovery (five days, 28ïÿýC/24ïÿýC day/night). For drought, we developed a low-cost automated irrigation system that allowed a controlled dry-down treatment of plants. Using this system, photosynthetic parameters were measured in 324 sorghum genotypes during three periods of contrasting soil volumetric water content: control (three days, \u3e30%); drought (seven days of dry-down; three days at 15%); and recovery (five days, \u3e30%). A large variation was found in seven photosynthetic traits under optimal and stress conditions and in three derived variables: cumulative response, ratio drought-control, and ratio drought- recovery. For cold, a total of 143 unique genomic regions were discovered associated with at least one trait in a particular treatment or with derived variables. Ten regions on chromosomes 3, 4, 6, 7, and 8 that harbor multiple significant markers in linkage disequilibrium (LD) were consistently identified as being associated with gas exchange and chlorophyll fluorescence traits. Several candidate genes within those intervals have predicted functions based on homologous genes related to carotenoids, phytohormones, thioredoxin, components of PSI and antioxidants. For drought, a total of 60 genomic regions were associated with one or more traits in a particular treatment or with derived variables. The most relevant candidate genes have annotated functions for stress signaling, carotenoid biosynthesis, oxidative stress protection, and dehydration protection. Our discoveries provide useful information for the selection of sorghum genotypes with improved photosynthetic performance under optimal and stress conditions
