3K Rice Genomes for Detailed, Multi-Level Phenotyping

The 3000 rice genomes project between CAAS, BGI and IRRI has given an unprecedented opportunity to better understand the population structure and genetic variation of the staple food for much of humanity. Using 3M filtered SNPs from an updated SNP calling pipeline for Nipponbare IRGSP1.0, all variety groups apart from the aromatic show highly significant association to subpopulations for their origin. This data can inform selection of target lines for phenotyping.  Depending on the trait and its complexity, large numbers of lines can be handled with augmented designs. Traits that are being phenotyped include morpho-agronomic and architecture traits, yield components, leaf anatomy, drought tolerance, seed physiology and leaf anatomy. 1900 of the 3K rice genotypes will be screened this 2015 WS by manual measurement, HTP tractor and drone platforms.  Historical phenotype data is already being used for GWAS. Bridging the 3K genomes and their phenotypes will translate the genomes to products for gobal breeding efforts and discovery.