ARS | Publication request: A diverse collection of purified rice accessions for genomic studies

Submitted to: Plant and Animal Genome
Publication Type: Proceedings
Publication Acceptance Date: January 1, 2009
Publication Date: January 10, 2009
Citation: Ali Md. Liakat, Eizenga, G.C., Jia, M.H., Kimball, J.A., Iorga, R., McCouch, S.R., McClung, A.M. 2009. A diverse collection of purified rice accessions for genomic studies. In: Proceedings of Plant and Animal Genome Conference XVII, January 10-14, 2009, San Diego, CA. P. 226.

Technical Abstract: A diverse set of Oryza sativa accessions was identified as part of a study to explore transgressive variation in rice. Genetically homogeneous rice accessions are required for association studies, thus 389 O. sativa accessions selected from 77 countries were purified by identifying a representative plant from each. A single panicle and seed image from each accession was scanned and archived as a reference. These accessions were fingerprinted with 36 SSR markers distributed throughout the genome. Analysis of the genetic diversity revealed 328 total alleles with a mean of 9.11 alleles per locus, a mean polymorphism information content (PIC) value of 0.63 and a mean gene diversity of 0.68. The accessions clustered into five ancestral groups (sub-populations), indica (83 accessions), aus (59), aromatic (15), tropical japonica (96) and temperate japonica (106) based on analyses with PowerMarker and Structure software. Thirty accessions with <60% ancestry from any single group were identified as ‘admixtures’, with the predominate mixture between temperate and tropical japonica. The gene diversity of the indica and aus groups (0.45 and 0.43, respectively) was significantly higher than that of the aromatic, temperate japonica or tropical japonica groups (0.30, 0.32 and 0.32, respectively). AMOVA will be performed to estimate within- and between-group variation. This collection is currently being genotyped with higher-resolution SNP arrays that will allow us to explore these sub-groups in more detail. Upon completion of this project, purified seed stocks will be available through the USDA-ARS Genetic Stocks Oryza (GSOR) center.