The Structure and Function of the Expressed Portion of the Wheat Genomes

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The Structure and Function of the Expressed
Portion of the Wheat Genomes
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The Structure and Function of the Expressed
Portion of the Wheat Genomes
The long term goal of this project is to decipher
the chromosomal location and biological function
of all genes in the wheat genomes.
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Value and uses of wheat
The Structure and Function of the Expressed
Portion of the Wheat Genomes
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Cal Qualset, U Calif DANR, Davis James Anderson,
U Minnesota Olin Anderson, U Calif DANR,
Albany Timothy Close, U Calif Riverside Jorge
Dubcovsky, U Calif Davis Jan Dvorak, U Calif
Davis Bikram Gill, Kansas State U Kulvinder Gill,
U Nebraska J Perry Gustafson, U Missouri Shahryar
Kianian, N Dakota State U Nora Lapitan, Colorado
State U Henry Nguyen, Texas Tech U Mark Sorrells,
Cornell U M Kay Walker-Simmons, Washington State
U
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Objectives and Experimental Approach
1. Produce cDNA libraries from as many tissue and
condition combinations as possible.
Produce multiple cDNA libraries with a target of
30 total after quality testing, normalizing and
subtraction to reduce redundancy.
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Objectives and Experimental Approach
1. Produce cDNA libraries from as many tissue and
condition combinations as possible.
Produce multiple cDNA libraries with a target of
30 total after quality testing, normalizing and
subtraction to reduce redundancy.
2. Determine the base-pair sequence of these
cDNAs, yielding ESTs.
Carry out 5end sequencing of cDNA libraries,
with 3 sequencing of putative singletons.
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Objectives and Experimental Approach
1. Produce cDNA libraries from as many tissue and
condition combinations as possible.
Produce multiple cDNA libraries with a target of
30 total after quality testing, normalizing and
subtraction to reduce redundancy.
2. Determine the base-pair sequence of these
cDNAs, yielding ESTs.
Carry out 5end sequencing of cDNA libraries,
with 3 sequencing of putative singletons.
3. Map into wheat deletion stocks a set of 10,000
unique ESTs.
Map ESTs into bins defined by wheat deletion
stocks target is 10,000 mapped ESTs.
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Objectives and Experimental Approach
1. Produce cDNA libraries from as many tissue and
condition combinations as possible.
Produce multiple cDNA libraries with a target of
30 total after quality testing, normalizing and
subtraction to reduce redundancy.
2. Determine the base-pair sequence of these
cDNAs, yielding ESTs.
Carry out 5end sequencing of cDNA libraries,
with 3 sequencing of putative singletons.
3. Map into wheat deletion stocks a set of 10,000
unique ESTs.
Map ESTs into bins defined by wheat deletion
stocks target is 10,000 mapped ESTs.
4. Determine the expression of the mapped ESTs
relative to reproductive biology of wheat.
Using arrays, analyze the expression of the
mapped ESTs, focusing on five aspects of wheat
reproduction.
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Objectives and Experimental Approach
1. Produce cDNA libraries from as many tissue and
condition combinations as possible.
Produce multiple cDNA libraries with a target of
30 total after quality testing, normalizing and
subtraction to reduce redundancy.
2. Determine the base-pair sequence of these
cDNAs, yielding ESTs.
Carry out 5end sequencing of cDNA libraries,
with 3 sequencing of putative singletons.
3. Map into wheat deletion stocks a set of 10,000
unique ESTs.
Map ESTs into bins defined by wheat deletion
stocks target is 10,000 mapped ESTs.
4. Determine the expression of the mapped ESTs
relative to reproductive biology of wheat.
Using arrays, analyze the expression of the
mapped ESTs, focusing on five aspects of wheat
reproduction.
5. Process, analyze, and display data accumulated
in this project (bioinformatics).
Develop and enhance means to analyze, interpret,
and visualize project data (data processing,
database modifications, and web page maintenance).
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Objectives and Experimental Approach
1. Produce cDNA libraries from as many tissue and
condition combinations as possible.
Produce multiple cDNA libraries with a target of
30 total after quality testing, normalizing and
subtraction to reduce redundancy.
2. Determine the base-pair sequence of these
cDNAs, yielding ESTs.
Carry out 5end sequencing of cDNA libraries,
with 3 sequencing of putative singletons.
3. Map into wheat deletion stocks a set of 10,000
unique ESTs.
Map ESTs into bins defined by wheat deletion
stocks target is 10,000 mapped ESTs.
4. Determine the expression of the mapped ESTs
relative to reproductive biology of wheat.
Using arrays, analyze the expression of the
mapped ESTs, focusing on five aspects of wheat
reproduction.
5. Process, analyze, and display data accumulated
in this project (bioinformatics).
Develop and enhance means to analyze, interpret,
and visualize project data (data processing,
database modifications, and web page maintenance).
6. Analyze gene density and distribution of
mapped ESTs and thus genes in the wheat genomes
(genome structure and evolution).
Analyze densities and distribution of related
genes determined from deletion map locations
combined with functionality.
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Obj. 5. Bioinformatics
Obj. 4.FunctionalGenomics
Obj. 3.Mapping
Objs. 1 2.EST Production
cDNA librariesScreening/normalizationsSequencing
Data analysisDNA storage/distribution
Obj. 6.GenomeStructure Evolution
The Structure and Function of the Expressed
Portion of the Wheat Genomes
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Project Coordinator Calvin QualsetProject
Manager Patrick McGuire
Objectives 1 and 2.EST ProductionCoordinatorOl
in Anderson
Objective 5.BioinformaticsCoordinatorOlin
Anderson
Obj. 5. Bioinformatics
Obj. 4.FunctionalGenomics
Obj. 3.Mapping
Objs. 1 2.EST Production
cDNA librariesScreening/normalizationsSequencing
Data analysisDNA storage/distribution
Objective 3.MappingCoordinatorBikram Gill
Objective 4.Functional GenomicsCoordinatorMark
Sorrells
Obj. 6.GenomeStructure Evolution
Objective 6.Genome Structure
EvolutionCoordinatorJan Dvorák
The Structure and Function of the Expressed
Portion of the Wheat Genomes
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Use of chromosome deletion stocksExample
chromosome 6B
In this physical model of the chromosome, the
dark areas are the heterochromatic bands which
serve as landmark patterns identifying this
chromosome uniquely. The arrows indicate
breakpoints of the deletion stocks available.
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Use of chromosome deletion stocksExample
chromosome 6B
If probe X produces a signal in this stock, ...
In this physical model of the chromosome, the
dark areas are the heterochromatic bands which
serve as landmark patterns identifying this
chromosome uniquely. The arrows indicate
breakpoints of the deletion stocks available.
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Use of chromosome deletion stocksExample
chromosome 6B
If probe X produces a signal in this stock, ...
and in this stock, ...
In this physical model of the chromosome, the
dark areas are the heterochromatic bands which
serve as landmark patterns identifying this
chromosome uniquely. The arrows indicate
breakpoints of the deletion stocks available.
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Use of chromosome deletion stocksExample
chromosome 6B
If probe X produces a signal in this stock, ...
and in this stock, ...
but not in this stock, then ...
In this physical model of the chromosome, the
dark areas are the heterochromatic bands which
serve as landmark patterns identifying this
chromosome uniquely. The arrows indicate
breakpoints of the deletion stocks available.
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Use of chromosome deletion stocksExample
chromosome 6B
one concludes that the DNA sequence in this
chromosome corresponding to the EST represented
by probe X is physically located in this region
or bin.
If probe X produces a signal in this stock, ...
and in this stock, ...
but not in this stock, then ...
In this physical model of the chromosome, the
dark areas are the heterochromatic bands which
serve as landmark patterns identifying this
chromosome uniquely. The arrows indicate
breakpoints of the deletion stocks available.
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Use of chromosome deletion stocksExample
chromosome 6B
one concludes that the DNA sequence in this
chromosome corresponding to the EST represented
by probe X is physically located in this region
or bin.
If probe X produces a signal in this stock, ...
and in this stock, ...
but not in this stock, then ...
In this physical model of the chromosome, the
dark areas are the heterochromatic bands which
serve as landmark patterns identifying this
chromosome uniquely. The arrows indicate
breakpoints of the deletion stocks available.
Cumulatively, these deletion stocks define bins
of various sizes in the physical chromosomes. The
full 10,000 ESTs developed in this project will
be mapped into these bins.
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Functional Genomics five aspects of wheat
reproduction
The Structure and Function of the Expressed
Portion of the Wheat Genomes
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Deliverables
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The Structure and Function of the Expressed
Portion of the Wheat Genomes
Biology of bread wheat