The Solanaceae Coordinated Agricultural Project (SolCAP) The SBC will play a role in a $5 million for a Coordinated Agricultural Project (CAP) to study specialty crops within Solanaceae, including potato and tomato. The Solanaceae Coordinated Agricultural Project (SolCAP) brings together an integrated team of researchers, educators and extension specialists at Michigan State University, The Ohio State University, Cornell University, University of California, Davis and Oregon State University to incorporate emerging DNA-sequence data into efforts to improve vegetable crops. Potato and tomato are the two most important vegetable crops in Solanaceae, a taxonomic family that includes pepper, eggplant, and petunia. The project will identify DNA sequence variation in genes associated with high value traits, such as carbohydrate and vitamin content and link these traits with breeder friendly markers. The SolCAP project is supported by the National Research Initiative Plant Genome Program of USDA’s Cooperative State Research, Education and Extension Service. For more information go to: SolCAP.
Deletion-Mutant Populations for Breeding and Functional Genomics
The SBC is working with the McClellan Nuclear Research Center (MNRC) in Sacramento and UC Davis researchers to determine the feasibility of using mutations induced by irradiation, in conjunction with sensitive screening techniques, to develop improved traits for California crops. Mutations offer an alternative method to transgenics for developing new traits. Modern techniques allow the efficient screening of large populations to identify mutations in specific genes. The SBC has established a mutation population resource in tomato and is testing the feasibility of using this approach to identify mutations in specific target genes having known functions. This project is funded by the MNRC and the California Tomato Research Institute.
Testing Genes from Model Systems in Tomato
The SBC is continuing to work on a project with a California-based genomics company to evaluate genes that have been identified in the model plant, Arabidopsis, for their potential to improve yield and fruit quality in tomato. The project was extended an additional three years to also evaluate genes previously characterized in Arabidopsis to improve tolerance to stress and nutrient utilization. The Ralph M. Parsons Foundation Plant Transformation Facility is also involved in this project, which is funded jointly by the participating company and the UC Discovery Grants program. The project will run through July 2007. This venture is co-funded by the UC Discovery Grants prorgram. Click for more Information about UC Discovery Grants. For additional information go to Traits.
Sampling Nucleotide Diversity in Cotton
Cotton breeding germplasm has a relatively narrow genetic base. The SBC worked with Cotton Inc. and major cotton seed companies to determine the best method to develop DNA-based genetic markers (single nucleotide polymorphisms or SNPs) in this crop. The SBC is now applying this knowledge to discover SNPs that are useful for cotton breeding. The availability of such markers could assist cotton breeders in introducing new germplasm into commercial cotton varieties to improve fiber quality or other traits. The grant program provides UC funding to match contributions from private collaborators. Click for more Information about UC Discovery Grants.
Characterizing Lettuce for Novel Traits
The SBC is partnering with a California-based lettuce company and the USDA-ARS Salinas Agricultural Research Center to characterize a diverse lettuce genetic population for seed germination and disease traits. DNA-based markers will be developed for the novel traits so that they can be efficiently incorporated into commercial lettuce varieties. This project is co-funded by the UC Discovery Grant Program and will run from August 2004 through July 2006.
Development and Application of an Informative Set of Anchored Markers for Tomato Breeding
In cooperation with David Francis and Esther van der Knaap (OSU/OARDC) the SBC is developing Single Nucleotide Polymorphisms (SNPs) based on sequence variation within the introns of Conserved Orthologous Set (COS) genes. These COS intron (COSi) markers have a rate of polymorphism that is ~5 fold higher than the coding regions found in the EST databases.
The project targets the most variable portion of genes and prescreen approximately 1500 marker loci for variation specifically in breeding germplasm prior to developing the markers. Markers are being developed and evaluated on a set of 48 breeding lines and genetic mapping populations. They will also be used directly in identifying genetic loci related to fruit shape and quality. The information will be made available through an interactive database. The purpose of the project is to develop DNA markers that are useful to manipulate traits and germplasm in tomato breeding.
OBJECTIVES: 1) Develop bioinformatics to predict intron position, design primers, and display annotated sequences. 2) Develop a pre-screen for SNPs among L. esculentum lines, based on Single-Stranded Conformation polymorphism. 3) Characterize, and display in an interactive database, SNP variation among tomato varieties and species. 4) Apply SNPs to the analysis and characterization of elite breeding populations and wide crosses of tomato for nutritional quality. Link to abstract of the USDA/NRI grant supporting this work beginning August 2004 through July 2007.
See: Diversity in conserved genes in tomato published by BMC Genomics.
A Whole-Genome Approach to Characterizing Genes in Pepper
Allen Van Deynze and Alex Kozik (Genome Center) received a $1.1 Million grant from UC Discovery and a consortium of seed companies including: Rijk Zwaan, Enza Zaden, Bayer, DeRuiter seeds, Syngenta Inc. Seminis Inc and Harris Moran/Vilmorin to develop a comprehensive Affymetrix Array to discover and genotype DNA markers, Single Feature Polymorphisms, in pepper. This 3-year project will take advantage of the current EST resources in pepper representing >30,000 unigenes to design a massively-parallel microarray to define and map the variation in pepper breeding germplasm and genetic populations. This resource will also serve as a highly redundant microarray for expression analysis in pepper. In collaboration with Dr. James Prince, Fresno State University, we will phenotypically characterize a population segregating for resistance to Phytophthora blight on pepper, one of the most serious diseases in pepper. Additional collaborators are Dr. Molly Jahn, University of Wisconsin and Dr. Shanna Moore, Cornell University. This project will enable genetic and functional studies on a whole genome scale, as well as rapidly link markers to traits and candidate genes for breeding.
A Whole Genome Approach to Marker Discovery in Lettuce The SBC and Dr. Richard Michelmore (UC Davis) are partnering with an industry consortium to develop microarray-based tools for DNA marker discovery. With these tools approximately 25,000 lettuce genes will be simultaneously screened for diversity in breeding germplasm. The resulting markers will be validated to develop high density maps to identify and manipulate loci linked to important traits in lettuce. This project will directly benefit the lettuce industry by providing new tools (high throughput molecular markers, SNPs) to improve lettuce. This project is co-funded by the UC Discovery Grant Program. See the Lettuce SFP Chip Project for more information.