Data Sets

Genotypic data is composed of information on DNA sequence variation at many thousands of loci in the genome, which enables us to estimate the genetic relationships between diverse rice varieties and ancestral populations. It helps us to characterize genetic diversity at the sequence level. And it gives us the ability to look for genetic variation associated with phenotypic traits.

To collect large amounts of genetic information for hundreds or thousands of individual rice plants, we are developing efficient genotyping platforms as part of the Rice SNP Consortium (see RiceSNP.org for more information.) We have been able to utilize previous work from the OryzaSNP, the OMAP and our rice re-sequencing projects to identify single base differences in the DNA sequence of diverse rice varieties and related wild accessions. The differences we are tracking are called SNPs or single nucleotide polymorphisms. SNPs and other molecular markers can vary between plants, populations, and species, and thus may be used to characterize different individuals and groups. Thousands of SNPs can be assembled on an array platform similar to a computer chips and used to efficiently assess the genetic diversity of an individual rice plant.

We show the results of a genome-wise association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa from 82 countries that were systematically phenotyped from 34 traits:

• Keyan Zhao, Chih-Wei Tung, Georgia C. Eizenga, Mark H. Wright, M. Liakat Ali, Adam H. Price, Gareth J. Norton, M. Rafiqul Islam, Andy Reynolds, Jason Mezey, Anna M. McClung, Carlos D. Bustamante & Susan R. McCouch (2011). Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Comm 2:467 | DOI: 10.1038/ncomms1467, Published Online 13 Sep 2011.

We describe the construction and usage of a 1536 SNP chip to study the genetic diversity in O. sativa in this recent publication:

• Zhao K, Wright M, Kimball J, Eizenga G, McClung A, Kovach M, Tyagi W, Ali ML, Tung CW, Reynolds A, Bustamante CD, McCouch SR (2010). Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome. PLoS One. 2010; 5(5): e10780. Published online 2010 May 24. doi: 10.1371/journal.pone.0010780

We describe the development of seven different 384-SNP assays designed for application in different subpopulations and species of rice, as described in this publication:

• Michael J. Thomson, Keyan Zhao, Mark Wright, Kenneth L. McNally, Jessica Rey, Chih-Wei Tung, Andy Reynolds, Brian Scheffler, Georgia Eizenga Anna McClung, Hyunjung Kim, Abdelbagi M. Ismail, Marjorie de Ocampo, Chromewell Mojica, Ma. Ymber Reveche, Christine J. Dilla-Ermita, Ramil Mauleon, Hei Leung, Carlos Bustamante, Susan R. McCouch (2011) High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform. Mol Breeding (on-line ahead of print) DOI 10.1007/s11032-011-9663-x.