Creating An Allele Index For NPGS: Bioinformatic Issues

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Creating An Allele Index For NPGS Bioinformatic
Issues

• Edward Buckler
• USDA-ARS at Cornell University, Ithaca, NY

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• AIM Make more useful plants by conserving,
  finding and combining better alleles.

NEED The National Germplasm conserves 464,000
accessions and may contain 100,000,000 distinct
alleles, but there is no index.
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Genetic mapping is the basis of the index, and
QTL mapping approaches now exist for virtually
all types of populations.

• Near gene level resolution achieved in multiple
  species
• Identification of genes controlling flowering,
  starch, nutrients, wood quality
• Positive Results in
• Maize
• Rice
• Arabidopsis
• Conifers

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What needs to happen?
Genotyping (0.5Mdp per accession)
Phenotyping (500dp per accession)
Bioinformatics (GRIN)
Mapping Tools
Breeder Decision Tools
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What data is currently available outside NPGS?

• Several large NSF Plant Genome projects on
  diversity with NPGS germplasm at the heart of
  these projects
• Numerous smaller projects (however, most data
  gets lost over time from these)
• Millions of genotypic and phenotypic data points
  in just maize, wheat, and rice projects.
• Database aware analysis tools (eg. TASSEL)

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Alignment SNP Display
Panzea Web Data Access
Upload Tools
Display
GDPDM Gramene Panzea (Maize) Rice Evol.
GRIN?
GDPC Data Browser
GDPC
Other Analysis Tools
TASSEL
Germinate
GRIN
DBs
Middleware
Analysis
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• GDPDM
• Germplasm
• Genotype
• Phenotype
• Environment
• Used by maize, wheat, and rice diversity projects.

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Alignment SNP Display
Panzea Web Data Access
Upload Tools
Display
GDPDM Gramene Panzea (Maize) Rice Evol.
GDPC Data Browser
GDPC
Other Analysis Tools
TASSEL
Germinate
GRIN
DBs
Middleware
Analysis
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Purpose
The purpose of GDPC is to simplify access to the
large genomic and phenotypic datasets that are
becoming available in plant biology.
www.maizegenetics.net/gdpc
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GDPC Data Flow Diagram
www.maizegenetics.net/gdpc
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GDPC Data Flow Diagram
www.maizegenetics.net/gdpc
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Databases

• Where has GDPC been mapped?
• Panzea (GDPDM schema)
• Gramene (GDPDM)
• Germinate (generic schema)
• GRIN (passport data)

www.maizegenetics.net/gdpc
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GDPC Select Data Service
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GDPC Select Taxa
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GDPC Nucleotide Data
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GDPC Trait Data
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GDPC Browser Demo
GDPC Marker Data
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Current GDPC Limitations

• XML is not efficient for large datasets
• Several avenues are possible for improving
  efficiency
• More visualization and analysis tools need to be
  developed
• Linkage Mapping
• Breeder Decision Tools
• Geographic interfaces
• Pedigree Interfaces (in progress)

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What should GRIN consider?

• Becoming the lead repository for genotypic and
  phenotypic diversity data
• Lead efforts for the consolidation of community
  diversity data
• Implement several middleware or web services
  standards (eg. GDPC and perhaps others IRRI)
• Collaborate on the development of data
  visualization tools

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All of the software can be accessed through
www.maizegenetics.netwww.sourceforge.netwww.pan
zea.orgwww.gramene.org