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

1. 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

2. 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

3. 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

CollectData

AnalyzeData

PublishResults

•QTL locations published•Sometime gets into DB

•Segregation data often lost

Flow of QTL Data

CollectData

Gramene

AnalyzeData

PublishResults

Database(privateaccess)

GDPC

•Gramene•Store grain data•Define datatypes

•Reanalysis becomes possible•Comparison of results

Flow of QTL Data

CollectData

Gramene

AnalyzeData

PublishResults

Database(privateaccess)

GDPC

•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

Days To PollenDays To SilkPlant HeightEar Height

Days To PollenDays To SilkPlant HeightEar Height

Trait

12345

12345

Chromosome

SingleIMCIMMIM

SingleIMCIMMIM

MethodB73 x Ki3

0

1

2

3

4

5

6

0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80

B73 x Mo17

0

2

4

6

8

10

0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80

B73 x CML333

0

2

4

6

8

10

12

0 10 20 30 40 50 60 70 80 90 100 0 10 20 30 40 50 60 70 80

AssociationJoint

AssociationJoint

Candidate Gene P P-valueP>0.05P<0.05P<0.01P<0.001

P-valueP>0.05P<0.05P<0.01P<0.001

PCO074668

CL12681_1

D8 PCO075618

CL15481

Gramene: QTL Dissector

Pop.

Pop.

Pop.

Interface 5:Comparative Maps

• 27 maps with consistent marker set will be generated

• Linked with other maize and grass maps

http://www.maizegenetics.net