Be sure to visit the NCSB soybean genomics portal: http://soybeangenome.org

Scientists at the National Center for Soybean Biotechnology are committed to developing modern genomic tools to support soybean research. NCSB scientists are working on a number of projects, in collaboration with other members of the soybean community. The number of projects underway are too numerous to describe in detail. A few key examples are given below.

Development of a high resolution physical map of Glycine max cv. Williams 82.  NCSB scientists are participating in a collaborative project funded by the United Soybean Board to develop a high resolution physical map of soybean. We are collaborating with scientists at the Washington University Genomics Center to manual annotate the physical map based on restriction fingerprinting of BAC clones.

Anchoring the physical map to the genetic map.  NCSB scientists created a six-dimensional pool of BAC clones representing 5-fold redundancy of the soybean genome. Using PCR, these pools can be used to place any gene or marker onto the physical map. These same genes/ markers are being used for mapping onto the genetic map. In this way, the physical map is being anchored to the genetic map. This will greatly increase the utility of the physical map for locating genes and for development of additional markers for molecular assisted breeding. Progress has been made on anchoring genetically mapped SSR and STS markers developed from known genes and or EST unigenes associated with stress responses and seed composition in soybean. In collaboration with Dr. Scott Jackson ( Purdue University), this project will receive funding from the National Science Foundation beginning in summer, 2005.

Survey sequencing of the soybean genome.  (Funded by the National Science Foundation) NCSB scientists collaborated with the Washington University Genomics Center and Orion Genomics, Inc. in a pilot study to explore the feasibility of methylfiltration as a means to enrich for the gene-encoding segments of the soybean genome. This method takes advantage of the fact that repetitive regions of plant genomes are hypermethylated. Therefore, cloning of such regions in E. coli strains that restrict methylated DNA leads to an enrichment in gene-encoding regions, which tend to be hypomethylated. Methylfiltered and unfiltered library were constructed and over 25,000 random DNA sequences generated. These data showed an ~3.2-fold enrichment of genic sequences by methylfiltration. The data predict that 340 Mbp of the 1.1 Bbp soybean genome are gene-rich. In addition, >21,000 BAC end sequences were generated. These sequences will be added to the physical map (see 1 above) resulting in the placement of many genes onto the physical map. All of these sequences were used to develop a DNA repeat database for soybean that can be used for masking repeats for future sequence annotation. A publication describing this work in in preparation. The DNA repeat database can be downloaded at the NCSB genomics website ( http://soybeangenome.org/).

EST sequencing of root libraries. We constructed a normalized and subtracted library from root tips exposed to drought stress and sequenced 15,000 ESTs. The data was submitted to GenBank. This information was provided to Dr. Lila Vodkin at the University of Illinois for including in a USB-supported soybean oligo array development.

Functional analysis of soybean genes through transposon mutagenesis. (supported by the United Soybean Board) Over the past several years, substantial progress has been made to develop soybean, Glycine max (L.) Merr., as a model plant for genetic/genomic studies. A major challenge in the future will be to define the function of the 30-50,000 genes present in soybean. Mutants offer one avenue for relating a gene to its function. Among several methods to produce a mutant library, transposon tagging has been used for a number of plants to develop a simple, large-scale, and reproducible mutagenesis system, with the ease of analysis after mutation. NCSB scientists are using two transposons systems, the retrotransposon Tnt1 originally isolated from tobacco and the Ds element originally from maize. Twelve, activation-tagging Ds vectors were constructed, each containing various combinations of either the CaMV 35s promoter or individual seed-specific promoters (e.g., phaseolin, soybean seed lectin, or glycinin). These vectors were subsequently used to construct transgenic soybean plants by Agrobacterium-mediated transformation. The project is at an early stage. However, thus far, around 500, independent transgenic soybean lines have been developed using the different Tnt1 and Ds element constructs. In order to ascertain the insertion site, flanking DNA sequences were isolated by PCR walking and sequenced. Primers developed from these flanking sequences will be used to localize the insertion sites on the soybean physical map, which is anchored to the genetic map. A Soybean Transposon Insertion Mutant Database is under development to serve as a resource to the community. The goal of the project is the development of sufficient transposon insertions so as to target any soybean gene.

Bioinformatics development for soybean research.  We have developed an infrastructure for storing, managing, and analyzing soybean data. We installed gene expression data management tool BASE and physical map viewer WebFPC, populated with internal experimental data. We performed computational analyses for the ESTs from soybean root samples under drought stress. Out of total 15,168 EST sequences collected by NCSB scientists, 13,430 EST sequences passed the quality control and have been submitted to GenBank. We performed Unigene analysis and identified 1331 novel genes in these ESTs. We also carried out the Gene Ontology classification and biological pathway projection in the KEGG database for the ESTs.