Phenotypic screening for tolerance of flooding during germination using an indica and a tropical japonica panels

Genome-wide association studies provide promising platform for linking genomics and phenomics using diverse germplasm accessions for the identification of donors for tolerance to abiotic or biotic stress, in a facile and manageable approach, hence expediting crop improvement and facilitating the development of varieties suitable for unfavorable conditions. This study is conducted as part of the Phenomics of Rice Adaptation and Yield (PRAY) project and aims to screen a panel of Oryza sativa indica and tropical japonica subpopulations for tolerance of anaerobic conditions during germination (Ag). A total of 562 germplasm accessions (296 indicas and 266 tropical japonicas) were screened for Ag under greenhouse conditions. Seeds were directly sown in trays half filled with soil and covered with approximately 1 cm of fine soil, then submerged under 10 cm of water. Survival rate was determined as the number of seedlings that were able to emerge from the water surface after 21 days. Four varieties (Khao Hlan On, Mazhan Red, Khaiyan, and Kharsu) served as tolerant checks while IR42 and FR 13A served as sensitive checks. The screening revealed that most of the indicas had lower germination rate under anoxia as compared to tropical japonica (76% and 51% of the accessions were below 30% emergence, respectively). Likewise, most of the tropical japonicas (46%) displayed considerably higher germination of 40-70% under anaerobic conditions as opposed to the indicas (23%) though both subpopulations had representatives with high survival of approximately 70-80% under anaerobic conditions. This suggests possible existence of different tolerance mechanisms that had evolved in indicas and tropical japonicas; however the latter purported, considerable tolerance to anoxia during germination. Further studies will confirm these genetic variations between and within these two groups and QTLs associated with tolerance within each group will be mapped using GWAS.