Forthcoming SP2-related events:

• Tropical Legume Genomics Workshop (part of the IV International Conference on Legume Genomics and Genetics), Sunday 7th December 2008, Puerto Vallarta, Mexico. More information  

This subprogramme focuses on developing genomic tools, technologies and approaches to achieve an understanding of genetic principles across many significant crop species in developing countries. SP2's primary role is to discover and validate the function of key genes that are involved in stress tolerance, notably drought. To do this, we examine gene expression using phenotpyically-informative crops - or genotypes within a crop - and validate the causal relationship between expression and phenotype using appropriate genetic stocks (targeted mutations, over- and under-expression systems).

In collaboration with the other subprogrammes, SP2 brings together an array of genetic resources and applies analytical tools to uncover the expression-phenotype relationship to genomic variation (with SP1) and relates expression and genotypic polymorphisms to phenotypic performance (with SP3).

The consortium nature of GCP unites the CGIAR and NARS programmes, research organisations which have the unique ability to produce and record extensive phenotypic data across crop species and investigate the subsequent variation on a molecular level by utilising genetic mapping or association analysis techniques. For most of the 22 CGIAR mandate crops¹, quite extensive genetic maps within each species are already available. Comparative maps are most advanced for the cereals: rice, sorghum, maize, barley, millet and wheat. Beyond mapping, an expanding amount of sequence information, paired with improved informatic tools, has enabled us to identify orthologous genes that may allow for the prediction of gene functions across large families of plant species.

Since the successful mapping of the complete rice genome, and with extensive sets of expressed sequences for many other crops available, cDNA microarrays and oligo gene chips are now much more applicable than a few years ago. By examining the expression of many genes simultaneously under a specific condition - under drought stress, for example - the complex interactions of different biochemical pathways can be understood and, consequently, genes can be identified that are responsible for improving a complex trait. The same approach applies to other means of genome-wide expression analyses, including protein and metabolite profiling. The resulting information facilitates the dissection of genetic and metabolic systems.

Structural and functional conservation in gene regulatory circuits is particularly relevant for identifying genes with large effects on phenotypes. Manipulation of regulatory elements can bring about dramatic changes in phenotypes that are often viewed as being controlled by many genes with minor effects. Part of SP2's work involves conducting parallel studies on stress tolerance using well-developed biological systems to yield near-term results. This will include drought as well as other stress tolerance traits as a basis to investigate drought tolerance. Additionally, we investigate possible interactive effects (synergistic or antagonistic) of stress responses, recognising that multiple stress tolerance is needed in delivering pre-breeding products to end-users (farmers, consumers).

Subprogramme 2 is positioned to apply innovations in medical and laboratory practices and future conceptual advances to crop genomics. Some of our efforts will be devoted to assembling genetic knowledge on stress tolerance (drought and others) through a combination of informatics analysis and empirical studies using advanced genetic stocks available to the GCP. We are also committed to mobilising high-quality phenotyping of selected genetic materials for functional validation. This will include systematic phenotyping of mutants and evaluation of NIL (near isogenic lines) with unique chromosomal segments for functional validation. Finally, as active participants in the research consortium, we continue to contribute to the development of genomic tools and "designer" genetic stocks in selected crops to enable applications of successful approaches to better crops in a diverse range of environments.

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1} Andean roots and tubers, barley, cassava, chickpea, coconut, cowpea, finger millet, forages, groundnut, lentil, maize, Musa, pearl millet, Phaseoulus, pigeon pea, potato, rice, sorghum, soybean, sweet potato, wheat, and yam.