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

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

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

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  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

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