Gramene: Interactions with NSF Project on Molecular and Functional Diversity in the Maize Genome

1. 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)

2. 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

3. 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

4. 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

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

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

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

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

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

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

11. 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

12. 12 B73 x CML333 10 8 6 4 2 0 0 0 10 20 30 40 50 60 70 80 90 10 20 30 40 50 60 70 80 100 10 B73 x Mo17 8 6 4 2 0 0 0 10 20 30 40 50 60 70 80 90 10 20 30 40 50 60 70 80 100 6 B73 x Ki3 5 4 3 2 1 0 0 0 10 20 30 40 50 60 70 80 90 10 20 30 40 50 60 70 80 100 Gramene: QTL Dissector 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 D8 PCO075618 PCO074668 Association Joint CL12681_1 CL15481

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

14. http://www.maizegenetics.net