Unlocking the Variation Hidden in Rice Germplasm Collections with Genomics.

Cultivated Asian rice (Oryza sativa) was domesticated from O. rufipogon (O. nivara).  The O. sativa subspecies indica and japonica diverged in ancient times, and based on DNA markers, further subdivided into the five major subpopulations, aus, indica, aromatic, tropical japonica and temperate japonica.  Recently, five O. sativa diversity panels were genotyped with SNP markers using either a high density rice array (HDRA) composed of 700,000 SNPs, whole genome resequencing resulting in 1.8 to 2.6 million SNPs, or genotyping-by-sequencing.  This resulted in a wealth of public genomic data that could be put to work to explore population structure, introgressed regions, and identify putative genes underlying traits of agronomic importance.  We will demonstrate the power of genome-wide association (GWA) mapping for seedling germination under cold temperature utilizing the “Rice Diversity Panel 1” (RDP1) composed of over 400 O. sativa accessions.  We have created an in-house database and genome browser from these publically available data resources to explore the QTL regions identified by GWA mapping and identify candidate genes, determine haplotypes unique to each subpopulation associated with QTL, and compare results to previous GWA mapping studies using other diversity panels and bi-parental QTL mapping studies.  To increase the power of GWA mapping and better utilize the genotypes available, the diversity panel identified as “RDP2” consisting of 1,400 O. sativa accessions and genotyped with HDRA was imported from IRRI and will be available through the Genetic Stocks-Oryza (GSOR) in about a year.  Similarly, GWA mapping is being conducted with a collection of approximately 100 O. rufipogon (O. nivara) accessions, genotyped with HDRA and evaluated for agronomic, morphological, seed, and disease traits to identify potential novel genes lost during domestication.