Project Proposal for Creation of ICARDA Bioinformatics capacity:

A SP4 Commissioned Research

1. Title: Creation of Bio-informatics Capacity for Central and West Asia and North Africa

2. Budget total requested:  US$ 49,500

3. Project description:

3.1 Background:

The current pace of development in Biotechnology (fast marker systems, sequencers, micro-arrays/chip technologies generating several hundreds of thousands of genes) and Information and Communication Technology (fast access to large databases, powerful tools to manipulate them) is speeding the volume of genomic data exponentially with time worldwide. The existing (large) amount of data on ICARDA mandate organisms and tools to exploit their interpretation and sharing with CG Centers, ARIs and its NARSs has potential to set clear direction to collect more information to enable the centers to develop genomic and knowledge products.  DNA arrays contain the secrets of the gene expressions, which describe the genotype and determine the phenotype in a given environment. DNA arrays and other high-throughput technologies will continue to generate huge amount of data and even more powerful software tools will be required to process, analysis, visualize, interpret and present the genomic data. The existing data (more than 100,000 data points annually) and tools at ICARDA facilitate gene mapping and QTL estimation, molecular data for biodiversity and phylogenetic analysis, SNP detection etc. We continue to target the identification of genes for various stress factors (drought, cold and biotic stresses), genes sequences, the proteins they produce and their biochemical pathways, and their functions. There is a need to store, manage, analyze and interpret molecular data of ICARDA’s mandate crops and their relatives and facilitate their exploitation and use for efficient development of desired germplasm. ICARDA is an active partner in the Generation Challenge Program and to meet its various commitments in the project, it is enhancing its biotech capabilities in terms of hardware (recently procured ABI 3100 sequencer in addition to ABI 777, a PCR equipment, Affymetrix microarray equipments etc), software and human-ware.   Furthermore, to fully exploit the opportunities offered by participation in the Generation Challenge Program capacity in the field of comparative and functional genomics is required, both having an important bioinformatics component.

3.2 The Problem:

ICARDA currently has limited manpower resources in this area, distributed in various programs/units which undertake specific components of bioinformatics. Unlike many single-discipline oriented projects, genomic projects due to their complex and integrated nature, need experts from a spectrum of disciplines to complete the projects. In coming years, we plan to explore ways develop its manpower resources using training, conference participation, exposure to the new science tools, and recruiting a Bioinformatician to its teams of biotechnologists, breeders and other plant scientists, biometrician and software developers and information system specialists.

3.3 Purpose:

ICARDA has been aiming to develop Bioinformatics capacity at ICARDA and to promote the development and use of state-of-the-art bioinformatic tools for all crop improvement and biodiversity conservation programs to support its Integrated Gene Management megaproject research activities as well as developing capacity building in the NARSs of CWANA  

3.4 Objectives:

1. Exploitation of public genome databases

2. Development of ICARDA databases integrating molecular and phenotypic data

3. Analysis of genomic data and interpretation, including data mining for SSRs in ESTs, their clustering, primer development and SNP detection, expression profiling etc

4. Development of bioinformatics support for microarrays analysis

5. Enhance bioinformatics-suited languages such as BioPerl/perl 

6. Strengthen the capacity of NARS and other partners to implement efficient data management systems. 

3.5 Outputs:

Enhanced capability to exploit

Genomic data information databases for plant material and (molecular assisted) selected material

Bioinformatics software and their exploitation

Identified stress tolerant genes

SSR-EST and SNP identification

BioPerl/Perl for databases searches and SSR tabulation

Identified candidate genes by microarray analysis

Six ICARDA scientists trained

Five NARS scientists trained

4. Project development and implementation procedure: 

 During the two year period 2005 – 2006, the project will :

• Develop a process to identify and prioritize bioinformatics areas for developing capacity ; identify the staff member for training in various areas- Biometrician,Database specialists, Analyst programmer, identify the ARIs for training, and prepare a schedule of implementation of the capacity building

• Procure and develop software for statistical analysis of genomic data

• Train ICARDA staff in bioinformatics at ARIs: The training areas would be including:

1. Information systems, Perl/BioPerl, statistics and informatics

2. Genomic databases, search tools, sequence alignment

3. Molecular evolution, phylogeny

4. Genotyping, SSR-EST and SNP detection

5. Proteomics: High-throughput in proteomics, protein expressions, structure visualization, homology modeling, structural proteomics and protein interaction prediction

6. Pre requisite topics in the areas of biology, biotechnology, computational biology and statistics

•  Assist and train NARS in establishing their own Bioinformatics facilities

5. Stakeholders:

The primary stakeholders are crop scientists in ICARDA, NARSs and ARIs.  Farmers will ultimately benefit from improved germplasm.  The partners from ICARDA, ARI and selected NARS will be involved in planning, execution, testing and evaluation with varied level and degree of involvement as seen most effective.

6. Collaborating institutions and staff: ICARDA:  ICARDA- scientists

Training will be received at ARIs including, Scottish Crops Research Institute, Chinese Academy of Agricultural Sciences, University of Adelaide, IPK- Gatersleben, Stanford University, Cornell University, Canadian Bioinformatics Workshops

NARS:  Agricultural Genetic Engineering Research Institute (AGERI), Egypt; University of Tishrin, Syria; Agricultural Biotechnology Research Institute of Iran (ABRII); National Institute of Agricultural Research (INRA), Morocco

7. Expected uses and users of research results:

The results of the project are intended to be used by national and international crop scientists and biotechnologists in their germplasm improvement programs. The beneficiaries of the immediate results will be those crop scientists; the ultimate beneficiaries will be farmers and consumers who will benefit from the improved germplasm generated by crop improvement programs.

8.  Budget plan for 2005-2006: