-A-
-L-
ACS Publications Division Home Page
American Society for Microbiology
Agricultural Research Service
American Association for the Advancement of Science
-M-
American Chemical Society Maize Genetics Cooperation - Stock Center
American Phytopathology Society
Anchor Probes-- Cornell
-N-
Arabidopsis Servers National Corn Growers Association
ASPP Plant Gene Register NCBI (GenBank)
Arabidopsis Genome Intitiative NetCenter for Plant Genomics
North American Barley Mapping Project
-B-
Barley Genome Mapping Project
-O-
Bioinformatics News Service
BioInformer, The
Biology @ Yahoo!
BIOSCI International Newsgroups
-P-
Biotechnology Information Center @ USDA PIR: Protein Information Resource
Biotechnology Software Pedro's BioMolecular Research Tools
Blocks, protein sequence homology PiGMaP @ Roslin
BovMaP @ Roslin ProDom, The Protein Domain Database
Plant, Animal and Microbe Genomes
Purdue University Genomics
-C-
Caenorhabditis elegans
-Q-
ChickMap @ Roslin
Cold Spring Harbor Laboratory
-R-
CornCam @ iowafarmer.com RGP Rice Genome Research Program
CropNet - UK Roslin Institute
Cornell Small Grains Breeding and Genetics The Royal Society of Chemistry
-D-
dbEST @ NCBI
Dendrome Project - Inst. of Forest Genetics
-S-
Diseases of Corn or Maize Saccharomyces Genomic Information Resource
Scottish Crop Research Institute
Science @ Yahoo!
-E-
 Sugar Cane EST Genome Project
EcoCyc --Metabolic Pathways
E. coli Stock Center
-T-
EMBL European Molecular Biology Laboratory Triticeae Mapping Initiative
ExPASy Molecular Biology WWW Server TIGR - Institute for Genomic Research
European Bioinformatics Institute
European Wheat Database
-U-
USDA
-F-
FlyBase
-V-
Virtual Barley
-G-
-W-
GenBank
GenomeWeb
Genetic Information Research Institute
-X-
GSDB Genome Sequence DataBase
GrainGenes
-Y-
GRIN Germplasm Resources Information Network
Genetic Resources Conservation Program - UC
-Z-
-H-
HarvEST
Harvard Biological Laboratories
HMS Beagle
Human Genome Database
-I-
IGGI-An International Grass Genome Initiative
ITEC
IUPAC Nomenclature
ITMI
IHAR
-J-
-K-
Kansas StateUniversity Wheat Page
KOMUGI Wheat Network of Japan
Klotho:Biochem Compounds Database

Other Projects:


2001 NSF Awards

What follows is a summary of other plant genome projects awarded NSF grants in FY 2001.


 PlantGDB - Plant Genome Database and Analysis Tools
Volker Brendel, Iowa State University

Abstract:
     PlantGDB is a database of plant genomic sequences, in particular Expressed Sequence Tags (ESTs) that correspond to fragments of genes that are actively transcribed under particular conditions. The database organizes the ESTs into contigs that represent tentative unique genes. The contigs are annotated and, whenever possible, linked to their genomic DNA origins. The PlantGDB web site includes a number of bioinformatics tools that facilitate gene prediction and cross-species comparisons. The database will provide snapshots of the current knowledge of plant gene composition and facilitate our understanding of plant genetics and evolution.

Web Resources
http://www.zmdb.iastate.edu/: Brendel Lab Homepage


1999 NSF Awards

What follows is a summary of other plant genome projects awarded NSF grants in FY 1999.


 High-Thoroughput Mapping Tools for Maize Genomics
Patrick Schnable, Iowa State University

Abstract:
     A greater understanding of the organization and function of the maize genome is essential if US agriculture is to be successful in meeting the growing needs for maize as food, feed and a source of industrial raw materials as the US moves towards a "plant-based" economy. A team of molecular, quantitative and evolutionary geneticists and bioinformaticists has been assembled to build upon existing NSF investments in plant genomics to develop the novel high-throughput genetic mapping technologies and resources needed to meet this challenge.
     IDPs (InDel Polymorphisms) are a new class of co-dominant, allele-specific, genetic markers suitable for high-throughput analyses. The project team will identify, develop and genetically map 500 IDP markers specific to two widely used inbred lines (B73 and Mo17). To identify efficient IDP isolation strategies, the rates of IDP identification will be compared from four sources: 1) GenBank genic sequences; 2) Mu transposon flanking sequences; 3) 3' UTRs from ESTs; and 4) previously mapped RFLP markers. In addition, computational and wet lab approaches for the high-throughput acquisition and mapping of IDPs will be developed and optimized.
     The Mapping Array is a novel chip-based technology designed to genetically map a large number of non-redundant, sequence-defined cDNAs. During Phase I, an existing nylon-based protocol will be adapted to DNA "chips"; hybridization conditions optimized; various sources of "target" sequences (e.g., 3' UTRs, exons, full-length cDNAs and RFLP markers) tested; experimental design parameters determined; and mapping software developed. Upon successful completion of Phase I, 10,000 ESTs will be genetically mapped (Phase II).
     The sequences of EST 3' UTRs are of great value in distinguishing members of gene families, as potential sources of IDPs and for producing the gene-specific probes needed for the Mapping Array. The project team will sequence the 3' ends of 20,000 of the ESTs being isolated by the NSF-supported maize genome project headquartered at Stanford University. In addition, the insert size associated with each of these 20,000 clones will be ascertained. Because the proposed research will occur at the interface between molecular and computational genetics, it will provide important cross-disciplinary training opportunities for graduate students and post-doctoral scientists.

Web Resources
http://maize.math.iastate.edu/isumaize/homepage.html: ISU Maize Genome Homepage
http://www.public.iastate.edu/~schnable: Schnable Lab Homepage


Tools for Potato Structural and Functional Genomics
Barbara Baker, University of California Berkeley & Catherine Ronning, The Institute for Genomic Research

Abstract:
     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.

Web Resources
http://www.tigr.org/about: About TIGR and Contact Information
http://plantbio.berkeley.edu/~baker/index.html: Baker Lab Home
http://genome.cornell.edu/solgenes/welcome.html: The SolGenes Webserver


Functional Genomics of Maize Centromeres
Kelly Dawe, University of Georgia

Abstract:
     Centromeres are long stretches of DNA that, along with a set of proteins known as kinetochore proteins, are responsible for ensuring that chromosomes are accurately segregated and passed on to the next generation. Previous work has demonstrated that centromeres are composed primarily of repeated DNA sequences. Not all of the repeats are required because large sections of a centromere can be removed without affecting chromosome segregation. Research carried out under this award is designed to identify which of the DNA sequences in the maize centromere are directly responsible for chromosome segregation. Towards this end, a sample of ~400,000 base pairs of centromeric DNA will be sequenced to determine the basic organization of the centromere. Each unique class of DNA sequence (either repetitive or single-copy) will be analyzed with respect to its distribution among the ten maize chromosomes and its interaction with a maize kinetochore protein. Based on these data, artificial centromeres will be created from selected portions of natural centromeres to test their activity in transgenic maize plants. In the final stages of the project, artificial centromeres will be used to create fully autonomous artificial chromosomes. Such artificial chromosomes could be used as vehicles for carrying agronomically important genes and could greatly improve existing methods for transferring genes into plants.

Web Resources
http://dogwood.botany.uga.edu/maize/centromeres.html: The Maize Centromere Page


Collinearity of Maize and Sorghum at the DNA Sequence Level
Joachim Messing, Rutgers University

Abstract:
     Comparative analysis of aligned plant chromosomal regions have exceptional, but largely untested, potential for the discovery of genes, new classes of mobile DNAs, and the nature, rates and mechanisms of evolutionary change. Moreover, comparative analysis of closely-related genomes that differ greatly in size can indicate both the origin(s) of that genome size difference and, equally important, determine whether the small genome could be used instead for map-based cloning of significant genes in the large genome species. In this project, maize and sorghum have been chosen for such an analysis because of their importance as crop plants and as model genetic systems. In particular, it is sought (1) to uncover basic genomic composition of several gene-rich regions, (2) to use this two genome approach to improve and test annotation (including gene prediction) programs, (3) to determine whether the compactness of the sorghum genome can be used to physically link maize genes that have been genetically mapped to be as close as one map unit, and (4) to characterize the chromosomal composition of maize and its relationship to the origin of the sorghum genome for gene clusters and intergenic regions. The content of contiguous DNA sequence from 10 different chromosomal locations in maize and sorghum will be characterized. The size of these regions will differ between the two genomes because of their differential gene density. In maize, a minimum pathway of clones to link two BAC clones whose overlap hybridizes to a designated nucleation probe sequence will be used, whereas in sorghum, the probe will be centered within a single BAC. By selecting gene sequences as probes to genic regions of the respective genomes, 10 clusters, each with a predicted 20-25 genes and their intergenic regions will be obtained. By comparing gene clusters in a bi-genomic fashion, better computational programs for predicting gene boundaries and repeat elements will emerge. In a number of cases, gene sequences will be discovered with known phenotypes because of the integration of genetic and DNA sequence data. Current projects to increase the density of DNA markers and phenotypes on both maize and sorghum maps will also benefit from this analysis because it will provide extensive evidence on the feasibility/difficulty of positional cloning in maize or its relatives. Evolutionary studies of cereal genomes based on gene islands will now be enhanced by the analysis of gene clusters and intergenic regions.

Web Resources
http://pgir.rutgers.edu: The Plant Genome Initiative at Rutgers


The Structure and Function of the Expressed Portion of the Wheat Genomes
Calvin Qualset, University of California Davis

Abstract:
     This award supports a project to generate and map a large number (target is 10,000) of unique DNA sequences from the genetic code (genome) of bread wheat. The assumption is that these unique DNA sequences will correspond to individual genes of wheat and their identification is a first step in determining the function of these genes. The ultimate goal is to use this information to improve the quality and yield of wheat and enable successful adaptations to new and marginal environments, thus increasing production. Wheat belongs to a group of closely related species (termed a tribe, named Triticeae) in the grass family which includes more than 300 species, including several very important crops (bread and durum wheats, barley, rye, triticale) and several forage-grass species. World-wide, wheat is the most widely grown crop and the third in economic significance for the United States. The US is the largest wheat exporter in the world and, to maintain this market continuous genetic improvement of the crop is required.
     Recent advances in plant genetics and genomics offer unprecedented opportunities for discovering the function of genes and potential for their manipulation for crop improvement. Because of the large size of the wheat genome (the total DNA or genetic information of the species), it is unlikely that the actual base pair sequences of the DNA molecules will be learned completely in the near future. This project takes an alternative strategy to realize the benefits of new techniques for discovering genes and learning their function (functional genomics). Following the identification of 10,000 unique wheat DNA sequences (termed ESTs, Expressed Sequence Tags), they will be mapped to their physical location on the chromosomes of wheat. This process utilizes a unique feature of the wheat chromosomes, their ability to tolerate deletions of portions of the chromosomes and still produce a viable plant. The mapping logic is direct: if an EST is present in a plant with complete chromosomes, but absent in a plant missing a known part of a single chromosome, then it can be inferred that the DNA sequence that corresponds to that EST is located in that segment of the chromosome. By the end of the mapping component of this project, a most valuable tool will have been produced: 10,000 unique DNA sequences, likely corresponding to genes, whose physical location in the chromosomes of wheat are known. This sets the stage for the next phase of the project, the analysis of this array of mapped ESTs to determine function. The project will focus on characteristics of the wheat reproductive stages, from flowering signals through seed development and dormancy. The information gathered on the sequence, function, and position of these genes in the wheat chromosomes will be collected and distributed by means of a USDA public database of genomics information (known as GrainGenes). Because of the close relationship of wheat to other species in the Triticeae tribe and other grass species, especially corn and rice, the results from this project will be immediately applicable to other crops in the Triticeae. Most of the collaborating investigators are already collaborating members of the International Triticeae Mapping Initiative which has produced molecular genetic maps of the chromosomes of wheat and related species. The diversity of experimental techniques and traits pursued in the individual laboratories collaborating on this project will be an ideal training ground for graduate students and postdoctoral scientists. The large pool of well-characterized and mapped unique DNA sequences, available in the public domain will be an exceedingly important resource for future Triticeae research and basic functional genomics research.

Web Resources
http://www.grcp.ucdavis.edu: Genetic Resources Conservation Page
http://wheat.pw.usda.gov/wEST/: GrainGenes: Expressed Sequence Tags


Functional Genomics of Plant Phosphorylation
John Walker, University of Missouri

Abstract:
     Reversible protein phosphorylation is a key component of virtually every regulated biological process. Approximately 5% of the genes in higher plants are directly involved in signaling by protein phosphorylation. The goal of this project is to integrate bioinformatics and genetics to investigate phosphorylation-dependent signal transduction in plants. Bioinformatics will be used to mine plant sequence databases to gain new insights into the structural and functional relationships of the genes and proteins involved in post-translation modification by phosphorylation. Annotation of every protein kinase and phosphatase in Arabidopsis thaliana will be complemented with enhanced annotation for genes with published information. A community interface for data submission (published and unpublished) will be created and bioinformatics training will be provided to plant scientists who can then directly access and modify the data base from their home institution. A network of laboratories will both identify knockouts in genes encoding protein kinases and phosphatases and characterize the phenotypes of knockouts. Each of the network laboratories will focus on a group of proteins in which they are knowledgeable or expert. The network laboratories will also contribute to the database annotation for the groups of proteins for which they are experts. This project will yield significant advances in understanding the molecular mechanisms controlling cellular function in plants and will ultimately facilitate the development of improved crops.

Web Resources
http://www.sdsc.edu/mpr/plant_p/: Plant Phosphoprotein DB


1998 NSF Awards

What follows is a summary of other interesting and useful plant genomic projects awarded NSF grants in FY 1998.


 Center for Maize Targeted Mutagenesis
Robert A Martienssen , Cold Spring Harbor Laboratory

Abstract:
The genetic makeup of crop plants is the fundamental basis for yield, grain quality, plant breeding and crop improvement. In principle, this genetic makeup can be determined by sequencing plant DNA, and in this way identifying most if not all of the genes encoded by a given plant genome. Sophisticated software tools are becoming available that allow a great deal of information to be extracted from sequence data, but ultimately the function of a gene can only be determined by genetic analysis. Classically, this has been achieved by subjecting plants to mutagenizing agents, such as chemicals or X-rays, and then searching for those mutants that have a desired property or trait. The gene mutated in each case can then be identified by a laborious genetic procedure to ultimately isolate the corresponding sequence of DNA. The availability of large amounts of methodically determined DNA sequence information, however, allows a novel, systematic approach to be taken to determine gene function. This approach, first pioneered in model animal genomes such as the fruitfly Drosophila and the nematode worm, C. elegans, involves first constructing a library of thousands of organisms, each of which has a different spectrum of mutations. This library is then screened directly with a DNA sequence to identify mutations in a given gene. Two technological advances make this possible. The first is the use of transposable elements as the mutational agent. Transposable elements were first discovered in maize at Cold Spring Harbor Laboratory by Dr. Barbara McClintock in the 1940s. These elements have a conserved DNA structure enabling them to be readily identified in the genome. They disrupt genes at random, simultaneously providing the mutation of interest, and labeling the gene with the conserved DNA sequence. The second technology is the polymerase chain reaction (PCR), which allows such DNA sequences to be amplified from individual plants giving immediate access to a plant carrying a given mutation. Scientists at Cold Spring Harbor Laboratory have combined these advances to develop a systematic method for determining gene function in maize. Robertson's Mutator transposable elements, first characterized at the DNA level at the University of California at Berkeley, are uniquely suited for this purpose, and a sophisticated genetic strategy has been developed allowing large populations of plants to be screened for mutations in pools. In partnership with Novartis AG, geneticists at Cold Spring Harbor and Berkeley are developing a population of 40,000 plants, and DNA samples are being extracted. Seed from each plant will be cataloged and stored. The PCR reaction will be performed on DNA pools derived from this population so that seed corresponding to mutations in a given gene can be readily identified. Individual geneticists from the maize community will be able to send in sequence information for targeted disruption of genes of interest to them. The information will be entered into a database, and seed corresponding to the mutation will be distributed to interested researchers to allow them to determine the function of each gene chosen in this way. The Mutator Targeted Mutagenesis (MTM) system can thus be used to build up a database of gene function in maize, eventually comprising a significant proportion of the genetic makeup of this crucial crop plant.

Web Resources
http://mtm.cshl.org: Maize Targeted Mutagenesis Database

Genomics of Plant Stress Tolerance
Hans Bohnert, University of Arizona

Abstract:
     The long-term goal of this proposal is to identify and determine the role of all the genes involved in a plants response to salt and water stress. Over the last decade, it has become clear that responses to water deficit and ion imbalance are governed by complex molecular and biochemical signal transduction processes, which coordinately act to determine tolerance or sensitivity at the whole-plant levet. Within the last five years, however, advances in genomics, informatics, and functional genomics have made it technically feasible to gain a global understanding of the gene complement or set that becomes integrated to effect abiotic stress tolerance. To tackle the genetic basis of this tolerance in higher plants in the most efficient, comprehensive, and integrative way possible Drs. R. Bressan, P. Hasegawa ( Purdue University), R. Burnap, J. Cushman, R. Prade (Oklahoma State University) and H. Bohnert, D. Gaibraith, J-K. Zhu (University of Arizona) have formed a consortium. Each participant has a documented and extensive experience in this research area with a proven record of productivity and in many instances past or present collaborations.
     This team will employ three distinct, yet complementary approaches to isolate, characterize, and assess the function of the core set of stress-related genes that provide the basis for the water and salt stress tolerance phenotype in plants.
     The first approach will encompass the functional identification of genes important to stress tolerance by random and targeted mutagenesis strategies in well-studied model organisms (Synechocystis PCC6803, Saccharomyces cerevisiae, Aspergillus nidulans, and Arabidopsis thaliana). For Arabidopsis, they will identify, map and clone genetic Ioci from a large set of mutants defective in stress tolerance or signaling. The resulting sets of mutants will be used for complementation studies using genes from higher plant sources.
     The second approach aims to define the core set of stress-related transcripts from both sensitive plants (Arabidopsis thaliana and rice) and resistant plants (Dunaliella salina and ice plant) using EST sequendng and microarray analysis. This approach will focus on the comparative study of gene expression patterns in salt and drought sensitive and resistant organisms, since recent studies of resistant organisms have revealed the existence of mechanisms of stress tolerance not present or not appropriately expressed in sensitive organisms.
     The third approach will extend the functional analysis of stress-related transcripts by monitoring in situ Iocalizations by using promoter trapping approaches and gain-of-function studies.
     These approaches represent logical extensions of ongoing work in individual groups within this center. They will foster interaction and integration of Consortium activities through daily interactions, workshops/meetings and extended work periods in member laboratories for their students and postdoctoral fellows to ensure a new generation of researchers trained in multi-faceted and interdisciplinary problem solving. The impact of abiotic stress on crop productivity is remarkable according to USDA statistics and amounts to two-thirds of all yield reductions in agriculture. This proposal is exceptionally timely, combines unique expertise, is hypothesis-driven and culminates in a dearly defined goal - understanding the number, nature and networking of genes and physiological mechanisms that constitute plant abiotic stress tolerance.

Web Resources
http://stress-genomics.org: Stress Genomics Team Website


An Integrated Map of Cytological, Genetic and Physical Information of Maize
W. Zacheus Cande, University of California Berkeley

Abstract:
     The goal of this proposal is to generate a map of the chromosomes of maize based on cytological features that will integrate information from existing genetic maps with new cytological and physical data. In general, this new map will be created by using three dimensional fluorescent in situ hybridization (3-D FISH), deconvolution light microscopy, and computerized image analysis to place genetically mapped genes onto the cytological map of maize. Genetic maps are based on the percent recombination between genes. Genetic maps report the linear order of genes and the amount of recombination between linked genes, but do not contain information on cytological distance or number of base pairs between genes. Cytological maps are created by determining the position of any visible structure on a chromosome as viewed through a microscope. The position is usually reported as a percentage of total chromosome arm length. Physical maps reflect DNA sequence data, and show the position of DNA motifs relative to an absolute scale in base pairs. For example, a map of overlapping sequenced clones forming a contig is a physical map.
     The cytogenetic map will be created by using 3-D FISH to place genetically mapped genes onto the cytological map of maize. Meiotic pachytene chromosomes will be utilized as the basis of the map since they are 10X longer than mitotic chromosomes and display excellent cytology. Several cytological features such as the heterochromatic knobs and prominent chromomeres will be genetically mapped. Chromosome specific bar codes, based on repetitive sequences, that will allow unambiguous determination of each region on every chromosome, will also be developed. The cytological position of highly repetitive DNA elements, as well as the gene positions, will be determined to allow the discovery of regions of the chromosomes that are gene rich or gene-poor. To utilize sequence data in the map, base pair distances between markers will be integrated into the map as these data are determined by other groups. This will make it possible to determine relationships between physical, cytological and genetic distances; i.e., the relationships of base pairs to microns to centimorgans in different parts of the genome.
     This map will provide biological information about the global positions of genes, the global organization of repetitive elements, position of recombination events, and will possibly shed light on the process of meiotic homologous pairing. It could be used for ordering large insert clones, for integration of the several genetic maps of maize, and for the genetic placement of markers that cannot be mapped genetically. This technology will be generally applicable to other grasses and could be used in a comparative approach to study grass genome evolution. In general, this publicly available map will be used to arrange and manage a large amount of genome data, and will provide biologically relevant information to the plant genome community.

Web Resources
http://mcb.berkeley.edu/labs/cande: Cande Lab Homepage


Comprehensive Genetic, Physical, and Database Resources for Maize
Edward H. Coe, University of Missouri

Abstract:
     The US is a recognized world leader in the production and trade of agricultural commodities and US corn exports represent 80% of the total world trade in corn. While the yield of corn in the US has steadily increased over the last 40 years, it is beginning to level off. With the expected increase in world population combined with concerns over the environmental effects of chemical intensive agricultural practices, it is clear that a new way to increase corn yield is needed. According to some experts, 50% of the increase in corn yield can be attributed to genetic improvements made to corn with the other 50% coming from use of agrochemicals. With the advent of genomics, the scientific community has an unprecedented opportunity to make significant genetic improvements in corn.
     The primary goal of this project is to take the first step toward understanding the structure and function of the Maize Genome by developing and disseminating a comprehensive integrated physical and genetic map of the Maize genome. This will involve the preparation of Maize Genome fragments inserted into a Bacterial Artificial Chromosome library, and the development and use of an array of markers (Expressed Sequence Tags, Single Sequence Repeats and Radiation Hybrids) to help determine the map. In all cases the results (the map) and the reagents (the markers) will be made available to the scientific community at large.
     A consolidated physical and genomic map of maize, and the molecular mapping markers to be developed will enable the use by basic scientists for gene discovery, studies of gene functions, and comparative genomics among others. The information and resources that will result from this activity will be invaluable to basic research, the corn industry, and, ultimately, US consumers.

Web Resources
http://www.agron.missouri.edu: MaizeDB - Maize Genome Database
http://www.genome.clemson.edu: Clemson Genomics Institute
http://cafnr.missouri.edu/mmp/index.htm: Missouri Maize Project


Medicago truncatula as the Nodal Species for Comparative & Functional Legume Genomics
Douglas Cook, Texas A & M University

Abstract:
     The legume family is one of the most important groups of plants worldwide, as an important source of protein in the human diet, of fodder and forage crops for animals, of oil crops, and for available nitrogen in the biosphere. Moreover, several crop legumes are among the best characterized plant genetic systems, with numerous classical genetic markers, well developed DNA marker maps, and basic tools for genome analysis. Nevertheless, despite the investment of considerable resources from private and public sources, features such as large and complex genomes, and difficulties with introduction of foreign genes have severely limited the pace of molecular analysis in crop legumes. In response to the need for a simple genetic system in legumes, investigators selected Medicago truncatula as a model species for legume biology. Unlike the major crop legumes, Medicago truncatula is amenable to efficient molecular and genetic analyses and it is well suited for study of biological issues important to the related crop legume species.
     This project will undertake the large scale analysis of Medicago truncatula's total DNA, called its "genome". In particular, a map of the organization of genes (comparative genomics), and of their functions in plant biology (functional genomics), are the emphases of this project. Recent results from this research team document the first indications of conserved genome structure between Medicago truncatula and crop legumes and between Medicago truncatula and the well-characterized model plant Arabidopsis thaliana. Conserved genome structure between model plants and related crop species is significant because it is expected to accelerate the pace of cloning and characterization of agronomically important genes and traits.
     Research activities conducted under this program will encompass the following approaches: (1) comparative genomics, which will involve comparing the organization of genes between Medicago truncatula the crop legumes pea, alfalfa, and soybean, and the well-characterized model plant Arabidopsis thaliana; (2) functional genomics, which will involve constructing and characterizing a library of expressed gene sequences, and conducting large scale gene expression analysis to study gene function, and (3) bioinformatics, which will involve developing a database and database resources for analysis and dissemination of Medicago truncatula genome information.
     The long term impact of this research will be to integrate genetic and functional information across legumes, and thereby expand opportunities for basic and applied research in economically important legume species. This research will allow scientists to compare genes of agronomic and scientific interest in Medicago truncatula and the related crop legumes. This knowledge will enable more efficient cloning and characterization of valuable genes and traits, such as disease resistance and crop productivity, and it will ultimately facilitate the development of improved crop varieties. The database of expressed genes generated by this research will enable the detailed analysis of the role of specific genes in plant growth and development. Many of the genes identified in the course of this research will become the focus of crop improvement strategies and of continued scientific investigation by legume biologists. The proposed work benefits enormously from previous NSF-sponsored research on the model plant Arabidopsis thaliana. Likewise, completion of the project will benefit not only research on legumes, but the broader scientific community as well.

Web Resources
http://chrysie.tamu.edu/medicago: Medicago truncatula


Evolutionary Genomics of Maize
John F. Doebley, University of Minnesota

Abstract:
     The complete DNA sequence of crop genomes will dramatically change the landscape in which plant breeders, biotechnologists, and biologists in general operate. Among the wealth of new opportunities will be one to exploit genomic sequence data to better utilize naturally occurring variation for agronomically important traits in crops. As new genes of biological and agronomic importance are determined, we need to identify the amount, distribution and nature of functional variation in these genes that exist in the germplasm pools of crop species. The proposed research will create the necessary infrastructure to do this in maize. These investigators will define where in the maize germplasm pool and where in the maize genome useful variation is most apt to be found. They will examine nucleotide diversity in a set of candidate genes for agronomic traits and test whether specific DNA sequence polymorphisms can be associated with variation in the phenotype for these traits. The overall goals of this project are to better understand the distribution of genetic diversity within the maize genome and to facilitate the identification of polymorphisms at the nucleic acid level in candidate genes that control variation at the phenotypic level in agronomically and biologically important traits.
     The project has four components: (1) To examine how diversity is distributed among breeding lines, landraces and wild relatives of maize. Genetic diversity in the maize germplasm pool will be assayed using microsatellites (simple sequence repeats; SSRs). Agronomic trait data for maize germplasm will be organized and published. This portion of the project will help to define the degree of genetic similarity among maize lines, to estimate the level of genetic diversity in different segments of the germplasm pool, and to identify a core set of accessions that amply represent diversity in maize. (2) To examine how genetic diversity is distributed across the maize genome. Forces such as recombination rates, chromosomal position, linkage relationships, past selective sweeps, and nucleotide composition can all influence the level of nucleotide polymorphism in particular genes such that genes in different contexts in the same genome can exhibit vastly different levels of polymorphism. These investigators will measure how the above forces have shaped diversity across the maize genome. (3) To develop and test methods to associate phenotypic variation for specific agronomic traits with sequence variation in candidate genes. Association analyses of this type are now being widely used in the study of the inheritance of complex diseases in humans. Association analyses have yet to see significant use in agronomic research, despite their potential to provide more rapid and more specific results than quantitative trait locus mapping. (4) Because each of the first three sections involves extensive statistical analyses of multilocus genotypic data, the project includes a Biostatistics/Informatics Group that will devise new or refine existing statistical procedures for the analysis of the data collected. This group will also oversee World Wide Web publication of the information produced.

Web Resources
http://peppercat.stat.ncsu.edu/maize/maize.html: Evolutionary Genomics of Maize


A Functional Analysis of the Arabidopsis Genome via Gene Disruption and Global Gene Expression Analysis
Pamela Green, Michigan State University

Abstract:
     In the near future, the complete sequence of the Arabidopsis genome will be known, which will lead to the identification of nearly all Arabidopsis genes. Most of these genes will have similarity with genes in other plants and many will have unknown function. The overall goal of this project is to provide plant biologists with a set of powerful tools that can be used in their efforts to understand the function and interrelationships of the 20,000 or more genes in this and other plants. The project has three components: technology development, service to the community, and biological application.
     Two synergistic technologies to investigate gene function will be developed and provided at service facilities. The first will be to assemble DNA microarrays of the genes of Arabidopsis. By hybridizing these arrays with probes corresponding to mRNA from different tissues and organs of wild type and mutant plants, global gene expression patterns under a variety of conditions can be investigated. Database and software support will facilitate sophisticated searching and comparisons among these global expression patterns. In parallel with the microarray experiments, the second technology development effort will be to optimize screening of Arabidopsis plants for mutations ("gene knockouts"). This will enable establishment of a gene knockout facility. A long-term goal of this facility will be to knock out all the genes of Arabidopsis. The PIs will use their microarrays to speed up the identification of gene knockouts from pools of candidates. The gene knockout facility and the microarray facility will comprise the service component of this project. The community will also be provided access to project databases and boinformatics tools through the existing Arabidopsis thaliana DataBase (AtDB) so that microarray and gene knockout data can be analyzed and cross-referenced with other plant genome data most effectively.
     The synergy between the microarray and gene knockout technologies will be most fully realized within the biological application component of this proposal. This component will focus on enhancing understanding of plant-specific genes of unknown function, but it will generate a large amount of data on the other Arabidopsis genes as well. Plant-specific genes (i.e., genes found in Arabidopsis and other plants but not in yeast, bacterial, or animal systems) are of great interest because they may be involved in plant-specific processes such as plant-pathogen interactions, cell-wall biosynthesis, and others. The PIs will identify knockout mutations in a large number of these genes and then examine the mutant plants for altered phenotypes under a variety of conditions. This will allow members of the community to formulate and test hypotheses about the function of these plant-specific genes.
     The impact of this project is expected to extend far beyond Arabidopsis. This is particularly true for the information obtained about plant-specific genes, many of which will be of general significance to crop plants and other plants of commercial value.

Web Resources
http://www.biotech.wisc.edu/Arabidopsis/: Arabidopsis KO Service Facility


Genomic Analysis of Seed Quality Traits in Corn
Bertrand Lemieux, University of Delaware

Abstract:
     About 85% of the U.S. corn harvest is used as animal feed, therefore the development of "high energy feeds" is highly relevant to the economy of the United States. Fats are the most concentrated source of energy in the cell. The long term effort conducted at the University of Illinois has resulted in lines with about 20% oil (Illinois High Oil or IHO) as well as lines with less than 2% oil (Illinois Low-Oil or IHO). These lines have retained a very high level of genetic diversity and preliminary mapping studies suggest that a large number of genes are involved in this important trait. The goal of the research is to identify all of the genes that are involved in this genetic trait.
     This research program will use a "candidate gene approach" to identify genes that may play a significant role in oil deposition in corn. The first step of this approach consists of using parallel gene expression analysis as a tool to identify genes whose expression levels are altered in IHO vs ILO maize. By using the large collection of maize mutants with defects in embryo and endosperm development it should be possible to identify a large number of genes that share common developmental expression programs. A number of maize lines have also been found that can "modify" the amplitude of the IHO trait (i.e., lines of corn that contain modifier genes for the IHO genes). These lines of maize could also be useful in finding candidate genes associated with components of the high oil traits.
     The aforementioned approach will identify many candidate genes. To reduce this number of candidates to a smaller number of "highly probable" candidates genes, a number of strategies will be used to map single gene mutations relative to the high oil trait. These will rely on cutting edge mutation detection technologies. Two strategies will be used to associate single nucleotide mutations and components of the high oil trait:
     The first will consist of a "direct association" between single nucleotide mutations and components of the high oil trait.
     The second will consist of an "indirect association" between single nucleotide mutations and IHO genes.
     Both of these strategies will exploit the plant genetic resources developed by the University of Illinois for high resolution mapping of DNA polymorphisms in IHO x ILO crosses.
     In addition to the research goal, this research program is designed to train graduate students and post-doctoral fellows in the science of genomics. The students will have the benefit of having two thesis advisors each and each PI will serve as a co-advisor to a minimum of 2 students.

Web Resources
http://bertrand.ags.udel.edu/: Bertrand Lemieux Home Page
http://genetics.mgh.harvard.edu/goodman/index.html: Goodman Lab


The Generation of a Tomato EST Database
Catherine M Ronning, The Institute for Genomic Research

Abstract:
     The tomato plant has long been a popular species for various aspects of plant biology research including genetics, development, physiology and pathology. Today much of the research on tomato concentrates on fruit development and pathogen response since in these areas tomato still stands out as an ideal model. In recent years, genomics has risen to the forefront of modern biological research and now provides great opportunities for plant biology. One of the most widely used genomics approaches is to generate Expressed Sequence Tags (ESTs) from an organism. These are short sequences obtained from cDNA clones selected at random and are a very cost effective way of identifying a large number of genes expressed in a tissue. Once generated these sequences are a valuable resource for a large number of experimental approaches including mapping, expression studies, and genome annotation. This project will generate 90,000 ESTs from a variety of tomato tissues including core tissues present in most plants (shoots, roots, developing anthers and ovules, and developing seeds), as well as tissues of particular interest to tomato researchers such as ripening fruits, and diseased tissues. These 90,000 sequences will be used to construct a tomato EST database in which the ESTs from the same gene are grouped together and treated as a single entity. These will then be annotated to identify possible functions of each gene. Information about the source of each EST will also be part of this database, and therefore it will be possible to identify tissue-specific genes, and genes switched on in response to attacking pathogens. It is expected that the sequences and the clones from this project will become part of the collection of tools used by tomato researchers, and indeed researchers working on any number of other species.

Web Resources
http://www.tigr.org/tdb/lgi/index.html: TIGR Tomato Gene Index
http://syntom.cit.cornell.edu: The Arabidopsis/Tomato Synteny Database


Structure and Function of the Cotton Genome: An Integrated Analysis of the Genetics, Development, and Evolution of the Cotton Fiber
Thea A. Wilkins, University of California Davis

Abstract:
     As the world's leading natural fiber, cotton is a major contributor to the U.S. and global economy, providing about 55% of the fiber used in textile manufacturing. The commercially-important cottons in the USA are allotetraploid ("AD") species that evolved from the interspecific hybridization of an Old World "A"-genome species of African-Asian origin with an endemic, New World "D"-genome diploid. The fibers themselves are actually single-celled hairs (trichomes) that range in length from ~17 to >50 mm, depending on the species. A vertically integrated, interdisciplinary team has been assembled to elucidate the organization, structure and function of genes that impart unique agriculturally-important properties to the fiber and to determine what role polyploidy has played in the evolution of the fiber.
     The specific research objectives are divided into three inter-related and complementary approaches: Functional Genomics, Structural Genomics, and Comparative Biology. In combination with the generation of fiber ESTs, the functional role of gene cascades and signaling pathways in developing cotton fibers derived from A or D diploid species will be assessed using DNA microarray technology. Global genetic and expression analyses will be performed in parallel using a unique collection of fiber developmental mutants and near-isogenic lines for fiber Quantitative Trait Loci (QTLs). For long-term gene function studies, parental lines for generating a gene knockout population in cotton will be developed. The structural genomics component will focus on linking fiber genes to the physical map by mapping novel fiber ESTs that are differentially expressed during fiber development in relation to fiber mutants and QTLs. Using a new technique tailored to polyploids, "alloBACs" containing the alleles from the individual subgenomes of the tetraploid will be identified for comparative analysis. Genes implicated in fiber development on the basis of expression patterns and the proximity to QTLs or mutant loci will be subjected to detailed comparative analysis to gain insight into the evolutionary basis of the fiber at the molecular level. The following null hypotheses will be tested: (1) homeologous sequences have evolved independently subsequent to allopolyploidization; and (2) rates of sequence evolution are equivalent in diploids and polyploids.
     The novel integration of structural, functional and evolutionary approaches to elucidate the molecular and evolutionary basis of the cotton fiber will generate vast new resources that will be available to the public sector for basic and applied research purposes. The scientific endeavors of this multi-disciplinary team are expected to provide new insight into fundamental cellular processes in plant growth and development, the evolutionary basis of morphological change, and the functional significance of polyploidy. Thus, enhanced understanding of this complex agricultural trait holds great promise for the genetic improvement of cotton and other important crop species in terms of production and quality.

Web Resources
http://cottongenomecntr.ucdavis.edu: Cotton Genome Center


A BAC Library Resource for Crop Genomics
Rod Wing, Clemson University

Abstract:
     Clemson University has established a Genomics Institute (CUGI) focusing on research, teaching and service in agricultural genomics. The service component of the CUGI has been to produce high-quality bacterial artificial chromosome (BAC) libraries from plants and plant pests and to provide convenient and affordable access to these products. With the assistance of several high-throughput robotic instruments, the CUGI has produced, acquired and distributed the majority of plant and fungal BAC libraries in use today. Because of the increasing demand on the service component of CUGI, funding is requested to support operations of the service facility. Funding of this project will expand services provided by CUGI to include: picking, arraying and rearraying of EST (expressed sequence tag) clones; arraying and rearraying of BAC and EST DNA onto filters; production of BAC DNA pools for library screening with primers; distribution of BAC and EST clones; BAC library screening by hybridization and PCR; fingerprinting of BAC clones identified by hybridization and PCR; BAC end sequencing; a centralized database for BAC fingerprints, hybridization and BAC end sequence data; training in BAC library construction and characterization through workshops at Clemson; and development of microarray technology for gene expression profiling and provision of this technology to the community. CUGI operates as a non-profit organization and will provide these services on a cost recovery basis. The service component of CUGI described here should be fully self-supporting by the end of the proposed funding period.

Web Resources
http://www.genome.clemson.edu: Clemson Genomics Institute



Comments? Suggestions? Email webmaster