Breeding Tools

A Whole-Genome Approach to Characterizing Genes in Pepper
California grows 40% of the peppers in the United States. The SBC, James Prince (California State University, Fresno), Alex Kozik (UC Davis) and a consortium of seed companies have developed a comprehensive Affymetrix microarray to discover and apply DNA markers (Single Feature Polymorphisms) in pepper. In 2009, the SBC genetically mapped more than 6,000 genes in pepper. These genes are being correlated with data collected for physiological and quality traits in hot peppers. Additional collaborators are Molly Jahn (University of Wisconsin) and Michael Mazourek (Cornell University). This research is funded by the UC Discovery program, Rijk Zwaan B.V., Enza Zaden B.V., Nunhems, DeRuiter Seeds, Syngenta Inc., Seminis Vegetable Seeds Inc. and Harris Moran/Vilmorin.

A Whole Genome Approach to Marker Discovery in Lettuce
The California lettuce industry is worth over $2 billion annually. The SBC and Maria Jose Truco, Alex Kozik and Richard Michelmore (UC Davis) have partnered with an industry consortium to develop and apply microarray- based tools for DNA marker discovery and application. In 2009, using this technology, the resolution of the genetic map for lettuce was expanded from 114 to 214 segregating lines and 12,000 genes have been mapped. The genetic map serves as the basis to define and track traits in lettuce breeding. Several high quality target traits have already been identified. This project is co-funded by the UC Discovery program, Harris Moran/Vilmorin, Rijk Zwaan B.V. and Enza Zaden B.V.

An Integrated Approach to Breeding Resistance to Phytophthora capsici in Pepper
Resistance to Phytophthora capsici, the most devastating disease worldwide, is critical for pepper varieties to grow in the United States. Breeding for resistance is complicated by the large number of races found, the dynamic preponderance of races in fields and the differential genetic control of resistance across specific tissues and races. Taking advantage of the genomic and genetic tools that we previously developed, the SBC will integrate the high-density genetic map to pyramid genetic loci determining resistance
to root rot and leaf blight in pepper. The SBC is collaborating with James Prince (California State University, Fresno), Raoul Adamchak and Carol Hillhouse from UC Davis on this project funded by the USDA, National Institute of Food and Agriculture. For more information, see A Pepper Primer: Introducing the Capsicums

Solanaceae Coordinated Agricultural Project
The SBC is working with David Douches and Robin Buell (Michigan State University), David Francis (The Ohio State University), Walter DeJong and Lukas Mueller (Cornell University) and Alexandra Stone (Oregon State University) on a $5.45 milllion Solanaceae Coordinated Agricultural project (http://msu.solcap.edu) to translate genomic research to breeding in potato and tomato. In its first year, the SBC sequenced expressed genes in six relevant tomato breeding lines and three relevant potato lines. From these, DNA marker assays are being developed to scan the diversity of 480 tomato and 1,200 potato breeding lines. A subset of 480 lines, per crop, were tested in replicated trials for production and quality traits to associate DNA regions and understand population structure in U.S. breeding programs. Concurrently, breeding modules are being developed for the Solanaceae Genomics Network database and extension classes have been delivered (see Education). The project is funded by the USDA, National Institute of Food and Agriculture. For more information, see SolCAP.

Improving Genetic Resources in Carrot
Although carrot is an important source of nutrients, few genomic resources are accessible for breeding. The SBC is partnering with Phil Simon (USDA/ ARS, Wisconsin) Rijk Zwaan B.V., Bejo, Nunhems, Takii and Vilmorin, to develop a genomics database containing sequences for over 10,000 genes expressed in carrot roots and leaves. This resource is being developed to further define diversity and genetic traits for improving carrot.

Genetic Diversity of Cotton
The SBC is continuing to integrate second generation sequencing of genes and high-throughput genotyping to expand molecular tools for cotton breeding. The SBC is working with David Stelly (Texas A&M), Chris Towne, Foo Cheung (J. Craig Venter Institute) and Jeffrey Chen (University of Texas) to characterize the genetic diversity in four cotton varieties and four crossable species, Gossypium barbadense, G. mustelinum, G .longicalyx, G. armourianum and G. tomentosum. By working in select breeding germplasm, DNA markers to manipulate agronomic and quality traits are being rapidly identified and validated. The research is supported by Cotton Incorporated.