Gramene: Interactions with NSF Project on Molecular and Functional Diversity in the Maize Genome Maize PIs (Doebley, Buckler, Fulton, Gaut, Goodman, Holland, Kresovich, McMullen, Stein, Ware)

Maize Project Goals Molecular Variation Sequencing survey of 1000 candidate loci Analysis of 4000 loci SNP discovery Sequence variation statistics Identify loci under selection SNP genotyping and analysis 1000 candidate loci Across diverse lines and landraces

Maize Project Goals Functional Variation Develop mapping populations in maize and teosinte (27 populations total) QTL map dozens of traits in multiple environments Linkage and association analysis of traits Develop a platform for the dissection of complex traits in maize

Maize Project Goals Informatics SNP Discovery (traces, contigs, alignments) Selection and diversity statistics of candidates Phenotypes, genotypes, and maps from pops. QTL analysis and result presentation

Informatics of many Diversity and QTL studies Collect Data Analyze Data Publish Results QTL locations published Sometime gets into DB Segregation data often lost

Flow of QTL Data Collect Data Database (private access) GDPC Analyze Publish Results Gramene Gramene Store grain data Define datatypes Reanalysis becomes possible Comparison of results

Flow of QTL Data Collect Data Database (private access) GDPC Analyze Publish Results Gramene GDPC (ARS-supported) Middleware advantages Simplify DB design Simplify analysis tool design Pull from multiple DB

Interface 1:Candidate Gene Annotation Sequence Position –genetic and physical Diversity statistics Plant anatomy terms Associated protein annotation

Interface 2: SNP Display Alignment display Relationship to gene structure Diversity statistics Eventually connected to QTL analysis

Interface 3:Germplasm displays Organize germplasm in tree displays Connect to germplasm resources (eg. GRIN) Link to data based on taxa groups

Interface 4: QTL display Integrate linkage and association analysis Organize information from multiple mapping projects by: Trait Population Environment Connection to raw data Buckler ARS group will develop and implement DB algorithms

Gramene: QTL Dissector B73 x Ki3 1 2 3 4 5 6 10 20 30 40 50 60 70 80 90 100 B73 x Mo17 8 B73 x CML333 12 Trait Days To Pollen Days To Silk Plant Height Ear Height Chromosome 1 2 3 4 5 Method Single IM CIM MIM P-value P>0.05 P<0.05 P<0.01 P<0.001 Candidate Gene P PCO074668 D8 PCO075618 Association Joint CL12681_1 CL15481

Interface 5:Comparative Maps 27 maps with consistent marker set will be generated Linked with other maize and grass maps

http://www.maizegenetics.net