New Discoveries from Old Data: Exploiting the World's Largest Collection of Sequenced Germplasm through GWAS

Innovations in technology and new sources of genetic diversity are required to meet the challenge of feeding the 10 billion people expected by 2050. The recent re-sequencing effort of 3,000 rice accessions by IRRI, in collaboration with BGI and CAAS provides new opportunities for rice breeding and the foundation for large-scale discovery of novel alleles to improve agriculture production, and thereby help feed the growing population.

In this case study, we use genome wide association (GWA) mapping to examine these alleles across the 3KRG to identify regions in the genome responsible for certain traits. Here, we test the robustness of historical phenotype data measured from a diverse panel from the 3K accessions to identify marker-trait associations. The historical data was collected over time in unreplicated trials as genebank characterization data for the source accession of the sequenced genetic stock. Results show significant associations for markers associated with several agronomic and yield traits, including culm number, grain length, grain width, 100-grain weight, and days to flowering, supporting findings from previous studies of rediscovered genes. We also show the usefulness of GWAS in exploiting genetic variations from a diverse germplasm collection that takes advantage of ancestral recombinations from different populations. Current efforts are on the way that investigates 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 that can be useful for breeding.