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
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
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. 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

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