An Update on Generation and Use of Microarray Resources for Soybean
Authors:
Lila Vodkin, Delkin Orlando Gonzalex, Garcia Zabal, Sarah Jones-Dept. of Crop Sciences, University of Illinois, Urbana, IL 61801
Abstract:
Both spotted cDNAs and 70-mer oligo arrays are available for global gene expression analyses and represent over 36,000 members of the soybean (Glycine max) unigene set. The cDNA resources have been described (Vodkin et al., 2004; http://soybeangenomics.cropsci.uiuc.edu) and used to investigate many biological questions including the processes of somatic embryogenesis (Thibaud-Nissen et al., 2003), soybean seed development and germination (Jones et al., 2006; Gonzalez et al., 2006), and the responses to pathogen challenge (Zho et al., 2005) and to elevated carbon atmospheric conditions (Ainsworth et al., 2006). In addition, they proved useful for identifying single gene differences between isogenic lines (Zabala and Vodkin, 2005). Both cDNA and oligo microarrays are distributed to the community on a cost recovery basis. Contact Lila Vodkin, Department of Crop Sciences, University of Illinois for availability of slides of either the GmcDNA or GmOLIGO microarrays sets for Glycine max.
SoyCAP: Roadmap for Soybean Translational Genomics
Authors:
Gary Stacey1, Anne Dorrance2, Henry Nguyen1, Vince Pantalone3, Wayne Parrott4, Randy Shoemaker5, and David Sleper1
Abstract:
Executive Summary Soybean is the most valuable legume crop, with numerous nutritional and industrial uses due to its unique chemical composition. Recently, a group of legume specialists voted soybean as the representative species of the phaseoloid legumes, the group that contains most legume crop species. Elucidating the genome sequence of soybean was chosen as the top priority. Through a series of past workshops and discussions, the soybean community developed and refined a cogent plan for soybean genomics. Many of the preliminary goals identified have already been accomplished. Thus, soybean is well positioned as a key model for translational genomics. With this in mind and with funding from the USDA National Research Initiative, a SoyCAP planning conference was held in St. Louis, MO, from December 16-17, 2004. A largely elected steering committee organized the meeting, which was attended by 30 soybean experts, as well as observers representing industry, commodity groups and the USDA. Attendance at the conference was purposely slanted toward soybean breeders, since it is this group that will ultimately develop improved soybean germplasm, aided by genomic tools and information. Over a two-day period, with much give and take, the following three objectives, in order, were chosen as representing the most critical needs, as well as the areas to which translational genomics could be effectively applied: I. Biotic Stress: Efforts should be mounted to develop breeder-friendly molecular markers to identify QTL regions encoding resistance to a variety of soybean diseases and pests. A special focus should be placed on developing markers to aid breeders in developing soybean germplasm with decreased susceptibility to Asian soybean rust. Finally, transgenic approaches should be considered to develop soybean germplasm resistant to priority pathogens and pests, especially in those cases where genetic resistance has proved elusive. II. Seed composition: Breeder-friendly molecular markers also should be developed towards seed target traits, in order to increase seed protein quality and quantity, without reducing seed yield or oil. Given the growing importance of biodiesel and the importance of oil quality in nutrition, efforts should be made to develop markers to allow breeders to engineer soybean with optimal oil composition. Finally, since soybean farmers are paid based on soybean seed yield, there is a need to broaden the soybean genetic base and foster technological innovations for sustainable yield improvements. III. Abiotic stress: Environmental stress is among the leading causes of soybean yield reduction. Drought, iron limitation, heat and cold stress, and flooding were identified as key areas in need of additional research with the goal of developing breeder-based tools for soybean improvement. Among these, increased drought tolerance was chosen as the top priority for soybean improvement through translational genomics. In addition to these research priorities, participants at the SoyCAP planning conference also set priorities with regard to information transfer, outreach, education and extension. Perhaps most notable, the participants called for the development of a novel, Web-based Soybean Breeder's Toolbox. This resource in envisioned as an interactive database to deliver genomic and genetic information in a manner targeted for and conducive to breeding and crop improvement strategies. The Toolbox also will play an educational role. Specific timelines were set to achieve the consensus goals identified. A management plan was developed, as well as policies on public release of information and intellectual property. A coordination committee was chosen and charged with preparing a SoyCAP grant proposal following the guidelines set during the planning conference.
James E. Specht Charles E Bessey Professor of Agronomy & Horiculture 322 Keim Hall East Campus- Fair Street University of Nebraska Lincoln, NE 68583-0915 jespech@unlnotes.unl.edu Since 2004, the Soybean Genetics Executive Committee (SoyGEC) has had the responsibility of representing both the soybean genomics and soybean breeding research communities. This has been accomplished in a number of ways. For example, the first GEC brought together members of the broader soybean research community together for a July 2005 meeting at St. Louis, at which the attendees developed a draft plan for future strategic research thrusts and then specific goals to achieve the strategic objectives. That draft plan, which was subsequently reviewed/revised by the broader research community, is now available at SoyBase. Another example is the many efforts by the GEC to work with federal, state, and other research funding agencies relative to enhancing soybean research funding. The GEC also attempts to assist and encourage collaboration among soybean researchers when large research grant proposals, such as SoyCAP are developed by the community. More about SoyGEC can be found on the SoyBase web site. The current SoyGEC is comprised of Jim. Specht (Chair) and Randy Nelson (both have one year left of a 3-year term); Gary Stacey and Brian Diers (both have two years left), and Tommy Carter (recently elected to a 3-year term). A proposal was just put forth for a soybean research community vote to expand the GEC to six members, such that a each year two persons would be elected to 3-year terms, one from the breeding and genetics research community and one from the genomics research community, to replace members concluding their 3-year terms. If approved, the SoyGEC will have six members by the time you read this article. Past SoyGEC members have included Randy Shoemaker (3-year term ended in 2006), Perry Cregan & Roger Boerma (2-year terms ended in 2005), and Wayne Parrot & Jim Orf (1-year term ended in 2004). The shorter terms of the initial GEC members were purposeful, allowing two member positions on the GEC to come up for election on an annual basis. Elections to fill two open SoyGEC membership slots each year are held in late July. Next July, we will be asking you to nominate individuals for membership in the SoyGEC (self-nominations are also OK!). Once the new members are on board, the election of a SoyGEC Chair will then occur (usually in August or early September). If you desire more information, or have questions, or simply desire to purse an issue relevant to the SoyGEC, please feel free to contact any current SoyGEC member.
SoyMap: an integrated map of soybean for resolution and dissection of multiple genome duplication events
Authors:
Scott A. Jackson1, Rod A. Wing2, Gary Stacey3, Gregory May4 and Randy C. Shoemaker5
Abstract:
SoyMap is an NSF-funded project to create an integrated genetic and physical map of soybean as a community resource for gene cloning, evolutionary/structural genome studies and as a predicate to determine an intelligent genome sequencing approach. Although determination of sequencing approach has to some extent been obviated by the DOE-JGI soybean genome initiative (whole genome shotgun approach), the integrated map is important nonetheless to anchor the sequence map to the chromosome and linkage maps, making the sequence map functional for the community. The SoyMap project is an outgrowth of a commodity board-funded physical map of soybean: two BAC libraries were fingerprinted using high information content fingerprinting (HICF) and genetic markers were placed on the physical map. SoyMap continues this effort by expanding the library coverage with a third library, additional makers placed on the physical map to further integrate the genetic and physical maps, and preliminary sequencing to understand genome structure at duplicated regions and as quality control for the current shotgun sequencing approach.