Physiological elucidation, genetic architecture, and metabolic landscape of tolerance to flooding during germination in rice

Arable lands and other natural resources for food production are declining due to urbanization and misuse; and weather is unfavorably fluctuating because of climate change. Together with the demands of the dramatically bloating population, food scarcity is imminent. Labor force for traditional agricultural practices such as transplanting, is declining and becoming expensive. These problems substantiate the urgent need for efficient, alternative crop production practices such as direct seeding (DSR). DSR has been slowly and progressively practiced in both irrigated and rainfed areas, but its wide adoption in floded or even waterlogged soils is hampered by the high sensitivity of rice to anaerobic conditions during germination, causing poor crop establishment, identifying donors of tolerance to anaerobic conditions during germination (AG) will facilitate varietal improvement for DSR and will help reduce production costs, besides other benefits. The Rice Diversity Panel 1 (343 accessions) consisting of 5 subpopulations was screened for AG tolerance. Genome wide association mapping was implemented and analyses revealed that most of the tolerant accessions are japonicas, with some indicas and admixes. Tolerance is associated with fast shoot growth and substantial root extension under flooding. Relating genotypic and phenotypic components indicates that the tolerance is controlled differently across subpopulations, suggesting the existence of multiple tolerance mechanisms. Most of the traits had association peaks on chromosomes 1, 4, 5, 6, 9, 11, and 12: some co-localized with known QTLs; others were novel. Candidate gene network analyses revealed that most genes are involved in metabolic processes and functions as catalysts and in binding. Metabolite profiling detected 1221 metabolites, 102 of which were differentially expressed: 68 up-regulated and 34 down-regulated. Bi parental populations were being developed using tolerant accessions to facilitate marker development for breeding, and metabolite profile will be studied during the course of germination to capture metabolic adjustments under flooded condition.