Genebanks, Genomes and GWAS

One way of addressing the impending global food crisis of sustainably feeding the 10B people in 2050 is by exploiting the genetic diversity in genebanks. To date, only a fraction of rice genetic diversity is being tapped. Recently, the release of the 3,000 rice genomes by IRRI, in collaboration with CAAS and BGI, unlocks new prospects for improving agriculture production and developing rice suitable for the changing climate to support the growing population.  To set the foundation for broader and more extensive investigations of discovering novel alleles, we utilized the power of GWAS (genome-wide association study) to detect marker-trait associations using the 3KRG and historical phenotype data, collected over time as genebank characterization data from unreplicated studies for the parental accessions of the diverse genetic stocks in the 3K panel. We detected significant markers associated with several agronomic and yield traits, including culm length, grain length, grain width, 100-grain weight, and days to flowering, concordant with previous studies. Further, we showed the utility of GWAS in unraveling the genetic history of ancestral recombinations from diverse populations. Collaborative research projects at IRRI are underway, examining the responses of rice to biotic and abiotic stresses from the 3K panel using GWAS. Future efforts are directed to validating markers from these studies and identifying donors for population development useful for breeding.