Plant & Animal Genomes XVIII Conference

January 9-13, 2010
Town & Country Convention Center
San Diego, CA

The Gramene Genetic Diversity Module: A Resource For Genotype-Phenotype Association Analysis In Grass Species

Genevieve DeClerck¹ , Terry Casstevens⁴ , Charles Chen¹ , Ken Youens-Clark² , Immanuel Yap¹ , Chih-Wei Tung¹ , Paul Derwent⁶ , Will Spooner² , Keyan Zhao⁷ , Peter Bradbury³ , Doreen Ware^2,3 , Edward Buckler^3,4 , Susan McCouch¹

¹  Dept. of Plant Breeding and Genetics, Cornell University, 240 Emerson Hall, Ithaca, NY, 14853, USA

²  Cold Spring Harbor Laboratory, 1 Bungtown Rd, Cold Spring Harbor, NY, 11724, USA

³  USDA-ARS Robert W. Holley Center, Cornell University, Ithaca, NY, 14853, USA

⁴  Institute of Genomic Diversity, Cornell University, Ithaca, NY, 14853, USA

⁵  Dept. of Botany and Plant Pathology, Oregon State University, 3082 Cordley Hall, Corvallis, OR, 97331, USA

⁶  European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

⁷  Dept. of Biological Statistics and Computational Biology, Cornell University, 1198 Comstock Hall, Ithaca, NY, 14853, USA

The Gramene Genetic Diversity module (gramene.org/diversity) focuses on the integration of diversity data from several plant species, concentrating on rice, maize and Arabidopsis. The goal is to enable users to elucidate genetic mechanisms underlying complex trait variation within and between these data sets by associating genotype with phenotype measurements. Recent additions to the diversity module include 160K rice SNP allele data points for 20 rice lines (McNally et. al., PNAS 2009) and allele data from the 'Arabidopsis 2010' project 250K SNP-chip for 931 Arabidopsis ecotypes (Nordborg Lab website). A new tool called SNP Query (gramene.org/db/diversity/snp_query) has been developed for performing coordinate-based searches of these new large volume SNP data sets. Additional high-throughput SNP work from the Maize HapMap project as well as phenotype data for all three central Diversity species will be added as the experimental results are made public. For performing analyses, a Java Web Start enabled version of TASSEL can be launched with live Diversity database connectivity to streamline data loading. Filtered data sets can likewise be extracted for external use with the GDPC Browser. The Diversity module handles storage of genotype, phenotype and corresponding germplasm data through use of version 4.0 of the Genomic Diversity and Phenotype Data Model (GDPDM) database schema.