Tools for Potato Structural and Functional Genomics

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Potato is a crop of worldwide importance and one of the most important dicotyledonous sources of food for humans. In light of threats to worldwide potato production by late blight, research on the plant's response to infection by microbial pathogens will be critical to environmentally sound agricultural production. A century of breeding efforts in potato have resulted in the introduction of resistance traits from abundant wild Solanum germplasm collections to pathogen susceptible cultivated species. However, breeding of cultivated potato for a single disease resistance trait can take years and pathogens rapidly evolve to overcome single resistance traits. Potato breeders are in need of additional information and genetic resources to compete with the challenges of ever changing pathogen populations. Genetic studies have identified untapped pathogen resistance traits in wild Solanum species. Accumulating evidence suggests that regions of wild potato genomes may contain large clustered arrays of resistance loci to several different pathogens. Recent developments in biotechnology have greatly facilitated genetic research in potato, including recent advances in genomic sequencing which allow for the rapid collection and analysis of vast amounts of DNA sequence data. The genomes of two wild potato species containing many resistance traits are available as deep bacterial artificial chromosome (BAC) libraries. The genomic sequences of these important regions will be determined, allowing interspecific comparisons as well as the development of allele-specific molecular markers that can be used by researchers for introgression of desirable traits using marker-aided selection. Another widely used approach is the generation of Expressed Sequence Tags (ESTs). These short, randomly selected sequences are a very cost effective way of identifying a large number of genes expressed in a tissue. This award supports: (1) Identification, isolation and sequencing of regions of wild potato genomes bearing disease resistance (R) genes and quantitative trait loci (QTLs) for P. infestans resistance. The genome sequences of these important regions will be determined, annotated, compared to each other and made publicly available. These sequences will facilitate the cloning of the significant resistance genes and other traits to combat late blight disease, provide tools to readily isolate and characterize functionally similar regions from other wild Solanum genomes to combat late blight, and provide substrates for evolutionary studies; (2) Generation of 55,000 ESTs from a variety of potato tissues and from disease-challenged tissues, to construct an annotated, publicly available Potato Gene Index and establishment of a potato Expressed Sequence Tag (EST) database including sequences expressed during response to late blight pathogen infection; (3) Specific ESTs will be selected and arrayed to fabricate potato cDNA microarrays, and used for genome-wide analyses during responses to pathogen infection and other plant processes; (4) Refinement of the syntenic relationship between potato and tomato and to base the linkage between these two genomes on orthologous sequences, which are also being anchored in the Arabidopsis genome. Tools and information will be made available to the scientific community for studies on late blight disease and will provide materials and information pertinent to the investigation of other pathogen diseases and critical plant processes.