# Presentation: 070464

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

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

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

**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.

##  Value and uses of wheat

** ****Value and uses of wheat**

## Slide 4

## 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

## Objectives and Experimental Approach

**Objectives and Experimental Approach**

- Produce multiple cDNA libraries with a target of 30 total after quality testing, normalizing and subtraction to reduce redundancy.

## Objectives and Experimental Approach

**Objectives and Experimental Approach**

- 2.	Determine the base-pair sequence of these cDNAs, yielding ESTs.

- Carry out  5’end sequencing of cDNA libraries, with 3’ sequencing of putative singletons.

- Produce multiple cDNA libraries with a target of 30 total after quality testing, normalizing and subtraction to reduce redundancy.

## Objectives and Experimental Approach

**Objectives and Experimental Approach**

- 2.	Determine the base-pair sequence of these cDNAs, yielding ESTs.

- 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.

- Carry out  5’end sequencing of cDNA libraries, with 3’ sequencing of putative singletons.

- Produce multiple cDNA libraries with a target of 30 total after quality testing, normalizing and subtraction to reduce redundancy.

## Objectives and Experimental Approach

**Objectives and Experimental Approach**

- 2.	Determine the base-pair sequence of these cDNAs, yielding ESTs.

- 3.	Map into wheat deletion stocks a set of 10,000 unique 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.

- Map ESTs into bins defined by wheat deletion stocks; target is 10,000 mapped ESTs.

- Carry out  5’end sequencing of cDNA libraries, with 3’ sequencing of putative singletons.

- Produce multiple cDNA libraries with a target of 30 total after quality testing, normalizing and subtraction to reduce redundancy.

## Objectives and Experimental Approach

**Objectives and Experimental Approach**

- 2.	Determine the base-pair sequence of these cDNAs, yielding ESTs.

- 3.	Map into wheat deletion stocks a set of 10,000 unique ESTs.

- 4.	Determine the expression of the mapped ESTs relative to reproductive biology of wheat.

- 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).

- Using arrays, analyze the expression of the mapped ESTs, focusing on five aspects of wheat reproduction.

- Map ESTs into bins defined by wheat deletion stocks; target is 10,000 mapped ESTs.

- Carry out  5’end sequencing of cDNA libraries, with 3’ sequencing of putative singletons.

- Produce multiple cDNA libraries with a target of 30 total after quality testing, normalizing and subtraction to reduce redundancy.

## Objectives and Experimental Approach

**Objectives and Experimental Approach**

- 2.	Determine the base-pair sequence of these cDNAs, yielding ESTs.

- 3.	Map into wheat deletion stocks a set of 10,000 unique ESTs.

- 4.	Determine the expression of the mapped ESTs relative to reproductive biology of wheat.

- 5.	Process, analyze, and display data accumulated in this project (bioinformatics).

- 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.

- Develop and enhance means to analyze, interpret, and visualize project data (data processing, database modifications, and web page maintenance).

- Using arrays, analyze the expression of the mapped ESTs, focusing on five aspects of wheat reproduction.

- Map ESTs into bins defined by wheat deletion stocks; target is 10,000 mapped ESTs.

- Carry out  5’end sequencing of cDNA libraries, with 3’ sequencing of putative singletons.

- Produce multiple cDNA libraries with a target of 30 total after quality testing, normalizing and subtraction to reduce redundancy.

## Obj. 5. Bioinformatics

**Objs. 1 & 2.****EST Production**

**cDNA libraries****Screening/normalizations****Sequencing****Data analysis****DNA storage/distribution**

**Obj. 6.****Genome****Structure &****Evolution**

**Obj. 3.****Mapping**

**Obj. 4.****Functional****Genomics**

**Obj. 5. Bioinformatics**

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

## Obj. 5. Bioinformatics

- Project Coordinator:** Calvin Qualset**Project Manager:** Patrick McGuire**

- Objectives 1 and 2.**EST Production**Coordinator:**Olin Anderson**

- Objective 5.**Bioinformatics**Coordinator:**Olin Anderson**

- Objective 3.**Mapping**Coordinator:**Bikram Gill**

- Objective 4.**Functional Genomics**Coordinator:**Mark Sorrells**

- Objective 6.**Genome Structure & Evolution**Coordinator:**Jan Dvorák**

**Objs. 1 & 2.****EST Production**

**cDNA libraries****Screening/normalizations****Sequencing****Data analysis****DNA storage/distribution**

**Obj. 6.****Genome****Structure &****Evolution**

**Obj. 3.****Mapping**

**Obj. 4.****Functional****Genomics**

**Obj. 5. Bioinformatics**

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

##  Use of chromosome deletion stocksExample: 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.

##  Use of chromosome deletion stocksExample: 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.

- If probe X produces a signal in this stock, ...

##  Use of chromosome deletion stocksExample: 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.

- ... and in this stock, ...

- If probe X produces a signal in this stock, ...

##  Use of chromosome deletion stocksExample: 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.

- ... and in this stock, ...

- ... but not in this stock, then ...

- If probe X produces a signal in this stock, ...

##  Use of chromosome deletion stocksExample: chromosome 6B

** ****Use of chromosome deletion stocks****Example: 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.

- ... and in this stock, ...

- ... but not in this stock, then ...

- ... 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, ...

##  Use of chromosome deletion stocksExample: chromosome 6B

** ****Use of chromosome deletion stocks****Example: 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.

- 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.

- ... and in this stock, ...

- ... but not in this stock, then ...

- ... 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, ...

## Functional Genomics: five aspects of wheat reproduction

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

##  Deliverables

##  Biology of bread wheat

** ****Biology of bread wheat**