|Oryza SNP Project|
A consortium of NRI funded researchers at Colorado State University, The Institute for Genomic Research, the International Rice Research Institute, Perlegen Sciences, and the Max Planck Institute collaborated on the OryzaSNP Projectthat involved genome-wide single nucleotide polymorphism (SNP) discovery across a unique fraction of the rice genome. This partnership has identified SNPs from across the whole genome of 20 rice cultivars. SNPs are a marker of genetic variation between individuals of species that allow scientists to identify regions of genetic variation that may be linked. Examples of traits that might be linked include plant development, yield, disease resistance, drought tolerance, and nutritional value.
Rice is the world's top food crop and principal source of nourishment for nearly half the world's population. By identifying and comparing differences in DNA sequences, the new knowledge will accelerate development of hardier, more productive types of rice, particularly for people in the poorest but fastest growing nations. The consortium released all the SNP data at a public workshop held during the 5th International Symposium of Rice Functional Genomics, October 15-17, 2007, in Tsukuba, Japan. The research team facilitated discussions with participants on how to use the many SNPs generated to forward rice genomics, genetics and breeding.
USDA Collaborators with this project are Anna McClung and Georgia Eizenga.
See the list of Oryza SNP cultivars here.
* Reference: McCouch, Susan R., M.H. Wright, C-W. Tung, L.G. Maron, K.L. McNally, M. Fitzgerald, N. Singh, G. DeClerck, F. A-Perez, P. Korniliev, A.J. Greenberg, M.E.B. Naredo, S.M.Q. Mercado, S.E. Harrington, Y. Shi, D.A. Branchini, P.R.K-Falcao, H. Leung, K. Ebana, M. Yano, G. Eizenga, A. McClung, and J. Mezey. 2016. Open access resources for genome-wide association mapping in rice. Nat Commun . doi:DOI: 10.1038/NCOMMS10532
* Reference: Georgia C. Eizenga, Md. Liakat Ali, Rolfe J. Bryant, Kathleen M. Yeater, Anna M. McClung, Susan R. McCouch. 2014. Registration of the Rice Diversity Panel 1 for Genome-Wide Association Studies. J Plant Reg 8(1):109.
- Reference: McNally, K.L., K.L. Childs, R. Bohnert, R.M. Davidson, K. Zhao, V.J. Ulat, G. Zeller, R.M. Clark, D.R. Hoen, T.E. Bureau, R. Stokowski, D.G. Ballinger, K.A. Frazer, D.R. Cox, B. Padhukasahasram, C.D. Bustamante, D. Weigel, D.J. Mackill, R.M. Bruskiewich, G. Ratsch, C. R. Buell, H. Leung, and J.E. Leach. 2009. Genomewide SNP variation reveals relationships among landraces and modern varieties of rice. Proc Natl Acad Sci DOI/10.1073/pnas.0900992106.
- Reference: McNally, K., R. Bruskiewich, D. Mackill, D. Weigel, K. Frazer, K. Childs, R. Buell, J. Leach, H. Leung. 2007. The OryzaSNP Project - SNP Discovery in Diverse Rice. Mol Pl Breed 5(2):246-247.
- Reference: McNally, Kenneth L., Richard Bruskiewich, David Mackill, C. Robin Buell, Jan E. Leach, and Hei Leung. 2006. Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes. Pl Physiol 141:26-31.
The Genetic Stocks - Oryza (GSOR) Collection will be a U.S.distributor of the OryzaSNP germplasm. Please contact GSOR to request accessions from this set at GSOR@ars-grin.gov