Flooding Tolerant Rice: Genetics, Breeding and Deployment.

Flooding affects over 15 million ha of rice lands worldwide, with various types including flooding during germination, referred to as anaerobic germination (AG), flash flooding during the vegetative stage, and stagnant flooding. Molecular approaches have begun to uncover the genetic bases of tolerance to flooding in rice.  For example, several major QTLs for AG tolerance have been mapped, and the gene underlying the major QTL AG1 has been identified and used for breeding. These QTLs can be pyramided to provide more robust tolerance of AG under field conditions. For flash flooding where plants are completely submerged for up to two weeks, the SUB1 gene has been identified and extensively deployed, with eight Sub1-lines in various genetic backgrounds developed at the International Rice Research Institute (IRRI) and released in several countries in Asia. Additional QTLs that can complement SUB1 have now been identified, and the SUB1 gene has been combined with other abiotic and biotic stresses to develop more resilient rice varieties.  For example, even though AG1 and SUB1 have seemingly opposite mechanisms, they have been successfully combined in a single genetic background.  Conventional breeding for tolerance to stagnant flooding, where water up to 50 cm can remain in the field up to harvest time, has been a key program at IRRI for several decades. More recently, QTLs for tolerance to stagnant flooding have been identified, providing novel approaches for varietal improvement and molecular studies of tolerance to stagnant flooding that have yet to be explored.  With recent genomics tools, such as CRISPR/Cas9 genome editing, allele mining using sequence data from 3,000 rice genomes, and high-throughput phenotyping, gene discovery efforts can now be accelerated.  Together, genetics studies and breeding for tolerance to flooding stresses will advance our knowledge on genetic mechanisms underlying tolerance and help enhance food security in stress-prone environments.