ARS | Publication request: Fingerprinting a purified collection of 400 rice accessions from a diverse background

Submitted to: American Society of Agronomy Abstracts
Publication Type: Abstract
Publication Acceptance Date: July 7, 2008
Publication Date: October 5, 2008
Citation: Eizenga, G.C., Ali, M., Kimball, J., Mccouch, S.R., McClung, A.M. 2008. Fingerprinting a purified collection of 400 rice accessions from a diverse background. [abstract] American Society of Agronomy Abstracts. Houston, TX, Oct. 5-9, 2008. CDROM

Technical Abstract: Purified rice (O. sativa L.) accessions are necessary for many genomics studies. For this study, a diverse collection of approximately 400 rice accessions from 77 countries was purified by selecting a representative plant of each accession and advancing it to the next generation from a single panicle. Scanned images of the individual panicle and seed were obtained as a reference. The purified accessions were genotyped with 36 SSRs dispersed throughout the genome and overlapping with those used to genotype previous collections of rice germplasm. Use of a common set of SSRs and a standard set of control varieties provides the foundation for merging data so that the accessions included in this study can be compared genetically with other rice collections from around the world. Preliminary analysis of the genotypic data for these 400 accessions revealed the mean number of alleles was 9.14, mean PIC value was 0.63, and mean gene diversity was 0.67. In a previous study, 172 of the 400 accessions were grouped into one of five rice sub-populations (indica, aus, tropical japonica, temperate japonica, or aromatic) or were identified as having a mixed background. Using the software PowerMarker, the accessions in this study were clustered again into five groups as follows: 88 indica, 59 aus, 109 tropical japonica, 113 temperate japonica, 15 aromatic and six accessions that did not group with any cluster. To provide a genetically pure, reference seed sample for future genetic and genomic studies, a single panicle was harvested from the individual plant that was used for genotyping, and seeds from this panicle were grown to maturity, providing seed stocks as a resource for other researchers. We are characterizing these purified accessions for agronomic and seed traits over two seasons (years) and the sub-population structure will be explored in more detail using SNP genotypes being obtained for each of the 400 O. sativa accessions. When this project is complete, purified seed stocks will be available through the Genetic Stocks Oryza (GSOR) center in Stuttgart, AR and the USDA ARS GRIN (Germplasm Resources Information Network) system, and the genotypic and phenotypic information will be publicly available on our project web site (www.ricediversity.org) and through the Gramene database (www.gramene.org).