Progress 07/01/03 to 06/30/08
Outputs
OUTPUTS: No further research to report since 2007 report due to resignation of principal investigator. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
No further research to report since 2007 report due to resignation of principal investigator.
Publications
- No publications reported this period
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Progress 01/01/07 to 12/31/07
Outputs
OUTPUTS: Results from research have been made publicly available through the Clemson Univ Genomics Institute's web site at www.genome.clemson.edu. Users of the web site will find searchable databases with user friendly interfaces for the uploading or cutting and pasting of data, downloadable data and analyses in a variety of common formats, and the ability to also order DNA products related to electronic information associated with each project. Major findings have also been published in journals within the area of research containing links to the web site and DNA resources.
TARGET AUDIENCES: Our target audience is the agricultural research community. We provide critical key genomic data that is subsequently used by applied researchers for biotechnology-based improvement of a wide variety of plant species important to agricultural production.
Impacts
Physical frameworks or genome maps for DNA sequencing of plant genomes are developed by fingerprinting large DNA fragments (clones) and then aligning the clones based on shared bands into contiguous overlapping sets called contigs. Entire chromosomes and sections of chromosomes can be reconstructed this way for the purpose of mapping the genome and identifying and cloning genes that are important for the improvement of plant growth, yield and quality traits. This past year we have completed work on a genome map for American chestnut, a model genome for the Fagaceae family of hardwood tress which also include the birches, beeches, and oaks. The sequencing of cDNA clones which represent expressed genes, is also a critical component in developing a framework for plant genomes because it provides expressed sequence tags for genes throughout the genome. We have sequenced about 18,000 American chestnut ESTs to add to the genome map which will show the location of important
genes throughout the genome. All of the genome map data we generate is housed in a publicly accessible database on the CUGI website (www.genome.clemson.edu). Our genomics work combined with the rapid and effective dissemination of data and other resources in American chestnut and the ecological plant model systems Aquilegia and Mimulus is having a significant impact within the research community. Areas of research that have significantly benefited from our work include; plant speciation mechanisms, abiotic stress responses, pathogen resistance, and novel gene discovery related to all of these fields. New gene sequences underlying a wide variety of traits expressed by ecologically studied model plants adapted to extreme environments will greatly aid our efforts in agricultural plant improvement through transgenic research. This is especially relevant given that climactic conditions are forecasted to become more unstable and inhospitable to agricultural production for food and fiber.
Publications
- Liang, H., E.G. Fang, J.P. Tomkins, M. Luo, D. Kudrna, K. Arumuganathan, S. Zhao, S.E. Schlarbaum, , J.A. Banks, C.W. dePamphilis, D.F. Mandoli, R.A. Wing, and J.E. Carlson, 2006. Development of a BAC library resource for yellow poplar (Liriodendron tulipifera) and the identification of genomic regions associated with flower development and lignin biosynthesis. Tree Genetics and Genomes http://www.springerlink.com (DOI 10.1007/s11295-006-0057-x).
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Progress 01/01/06 to 12/31/06
Outputs
Physical frameworks for DNA sequencing of plant genomes are developed by fingerprinting large DNA fragments (clones) and then aligning the clones based on shared bands into contiguous overlapping sets called contigs. Entire chromosomes and sections of chromosomes can be reconstructed this way for the purpose of mapping the genome and identifying and cloning genes that are important for the improvement of agricultural production. This past year we have completed work on a physical framework for Mimulus guttatus, a model plant species with genes conferring environmental stress adaptation, particularly drought stress. We also completed physical map work on Aquilegia, another model plant species containing valuable genes for adaptation to environmental stress. Plant genes conferring resistance to various types of environmental stress are important tools in the biotechnological improvement of crop yield. BAC end sequencing is a critical component in developing a framework
for plant genomes because it provides sequence tagged sites (STSs) throughout the genome. For both Mimulus and Aquilegia, we have finished sequencing the ends of the DNA clones used to make the physical maps. These DNA sequences or STSs are housed in a publicly accessible database on the CUGI website (www.genome.clemson.edu). An STS database for the cotton genome was also recently completed this past year in my lab. Cotton is the most important fiber crop in the USA and we are using these DNA sequences to develop new genetic markers for cotton breeders and geneticists.
Impacts
The impact of our efforts is evidenced by the popularity of the genomic resources that have been developed for a wide variety of plant species. Electronic data is freely available to researchers through the Clemson University Genomics Institute (CUGI) user-friendly web interface (www.genome.clemson.edu)that provides integrated access to a variety of DNA sequence databases. Physical resources related to the research are also publicly available in the form of DNA clones, whole libraries, and high-density colony filter arrays for many plant species that are important to agriculture (e.g. soybean, rice, maize, barley, cotton, sugarcane, tomato, sorghum). These resources are sold through the CUGI web interface on a cost-recovery basis for crop improvement research. The ultimate impact of these tools is the biotechnology-based improvement of crops for a variety of important traits. On a regional basis, our activities provide incentive to agricultural biotechnology companies
to invest in the State of South Carolina, thus directly influencing the state's economy in the agricultural technology sector. It is hoped that new biotech companies will add highly technical job opportunities to the economy, increase skill levels in the state work force, and produce cutting edge agricultural crop improvements that will benefit the farmers.
Publications
- Blenda, A., J. Scheffler, B. Scheffler, M. Palmer, J. Lacape, C, Jesudurai, Sook Jung, S, Muthukumar, P. Yellambalase, S. Ficklin, M. Staton, R. Eschelman, M. Ulloa, S. Saha, B. Burr, S. Lui, T. Zhang, D. Fang, J. Yu, A. Pepper, S. Kumpatla, J. Jacobs, J. Tomkins, R. Cantrell, and D. Main. 2006. CMD: A Cotton Microsatellite Database Resource for Gossypium Genomics. BMC Bioinformatics http://www.biomedcentral.com/1471-2148/6/32
- Jansen R.K., C. Kaittanis, S.B. Lee, C. Saski, J. Tomkins, A.J. Alverson, H. Daniell. 2006. Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evolutionary Biology. http://www.biomedcentral.com/1471-2164/7/132
- Daniell, H., S. Lee, J. Grevich, C. Saski, Quesada-Vargas T. Guda, J. Tomkins, and R. Jansen. 2006. Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theoretical and Applied Genetics. 112:1503-1518
- Frelichowski, J.E., Jr, M. Palmer, D. Main, J.P. Tomkins, R.G. Cantrell, D. Stelly, J. Yu, R.J. Kohel, M. Ulloa. 2006. Cotton genome mapping with new microsatellites from Acala ?Maxxa? BAC-ends. Molecular Genetics and Genomics 275:479-491
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Progress 01/01/05 to 12/31/05
Outputs
In 2005, we made significant progress in mapping and characterizing the genes that control senescence in plants using the Hemerocallis model system. Senescence is an important physiological process affecting yield and harvesting operations for many crop species. We also mapped the genome of maize with a focus on the centromere and telomere regions. These genomic regions are important for chromosome stability, especially in regard to artificial chromosome engineering experiments. The genomes of two ecologically important plant species (Aquilegia formosa and Mimulus guttatus)that contain important genes for environmental stress tolerance were mapped to provide a rich new resource for novel transgenes in crop plants. In addition, a number of new plant DNA libraries were constructed for peach, blackberry, chestnut, and rye. For cotton, four new DNA BAC libraries were made from different wild species that will provide a rich new resource for novel genes in cotton
transgenic research.
Impacts
The impact of our efforts is evidenced by the popularity of our DNA resources which are distributed through our BAC/EST Resource Center (www.genome.clemson.edu). Clones, whole libraries, and high-density BAC colony filter arrays for all of the major agronomic crops (e.g. soybean, rice, maize, barley, cotton) and most other crop taxa as well (e.g. sugarcane, barley, bean, tomato, sorghum) are provided by our facility. These resources are sold on a cost-recovery basis to researchers all over the USA for crop improvement research. The ultimate impact of these important genomic tools is the agronomic improvement of crops for many types of important traits. The electronic genomic data (DNA sequence)that we freely release over the internet via our website (www.genome.clemson.edu) for the various crop genome frameworks also adds to the impact factor of the research and ultimately benefits the agricultural community. On a regional basis, our activities provide incentive to
agricultural biotechnology companies to invest in the State of South Carolina, thus directly influencing the state's economy in the agricultural technology sector. It is hoped that new biotech companies will add highly technical job opportunities to the economy, increase skill levels in the state work force, and produce cutting edge agricultural crop improvements that will benefit the farmers.
Publications
- Horn R, Lecouls AC, Callahan A, Dandekar A, Garay L, McCord P, Howad W, Chan H, Verde I, Main D, Jung S, Georgi L, Forrest S, Mook J, Zhebentyayeva T, Yu Y, Kim HR, Jesudurai C, Sosinski B, Arus P, Baird V, Parfitt D, Reighard G, Scorza R, Tomkins J, Wing R, Abbott AG. 2005. Candidate gene database and transcript map for peach, a model species for fruit trees. Theoretical & Applied Genetics. 110(8):1419-28.
- Jung S, Abbott A, Jesudurai C, Tomkins J, Main D. 2005. Links Frequency, type, distribution and annotation of simple sequence repeats in Rosaceae ESTs. Functional & Integrative Genomics. 2005 5(3):136-43.
- Cuthbertson, B., J. Rickey, Y. Wu, G. Powell, and J. Tomkins. 2005. Exploitation of the daylily petal senescence model as a source for novel proteins that regulate programmed cell death in plants. Y. Blume (editor). In NATO Cell Death Monograph. NATO ASI Series in Cell Biology (In Press).
- Wang, W., M. Tanurdzic, M. Luo, N. Sisneros, H. Kim, J. Weng, D. Kudrna, C. Mueller, K. Arumuganathan, J. Carlson, C. Chapple, C. dePamphilis, D. Mandoli, J. Tomkins, R. Wing, and J. Banks. 2005. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: A resource for plant comparative genomics. BMC Plant Biology. 5(1):10
- Margulies, E.H. NISC Comparative Sequencing Program, V.V. Maduro, P. J. Thomas, J.P. Tomkins, C.T. Amemiya, M. Luo, and E.D. Green. 2005. Comparative sequencing provides insights about the structure and conservation of marsupial and monotreme genomes. Proceedings of the National Academy of Sciences USA (PNAS). 102:3354-3359.
- Tomkins, J.P., T.C. Wood, and D. Main. 2005. DNA Sequencing for Genome Analysis. In Analytical Techniques in DNA Sequencing. B.K. Nunnally editor). Pp. 157-176. Taylor & Francis Books Inc, Boca Raton, FL.
- Saski C, Lee S, Daniell H, Wood T, Tomkins J, Kim H-G, Jansen RK. 2005. Complete chloroplast genome sequence of Glycine max and comparative analyses with other legume genomes. Plant Molecular Biology 59:309-322.
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Progress 01/01/04 to 12/31/04
Outputs
Physical frameworks for sequencing are developed by fingerprinting BAC clones and then aligning the clones based on shared bands into contiguous overlapping sets of clones. Entire chromosomes and sections of chromosomes can be reconstructed this way. In 2003, we aquired specialized DNA analysis instrumentation to utilize new fingerprinting technologies which are more robust than previous methods. We also began work in Oct, 2003 on developing a physical framework for Mimulus guttatus, a model plant species with genes conferring environmental stress adaptation, particularly drought stress. In Oct 2004, we began work on Aquilegia, another model plant species containing valuable genes for adaption to environmental stress. Both of these physical map projects are still ongoing. Plant genes conferring resistance to various types of environmental stress are important factors in crop yield. BAC end sequencing is a critical component of developing a framework for a crop genome
because it provides sequence tagged sites (STSs) throughout the genome. We have continued our development of an STS database for the cotton genome by BAC end sequencing the cotton BAC library which was made at Clemson University. Cotton is the most important fiber crop in the USA and we are using these DNA sequences to develop new genetic markers for cotton breeders and geneticists. BAC library production which produces the substrates for making physical maps to sequence the genomes of crop plants was also accomplished for new strains/varieties of the following crops: sunflower, soybean, rape seed, and cotton.
Impacts
The impact of our efforts is evidenced by the popularity of our resources which are distributed through our BAC/EST Resource Center (www.genome.clemson.edu). Clones, whole libraries, and high-density BAC colony filter arrays for all of the major agronomic crops: soybean, rice, maize, barley, cotton, and tomato were sold on a cost-recovery basis to researchers all over the USA. These resources will be used for crop improvement research at many locations throughout the USA and the ultimate impact of these important tools is the agronomic improvement of crops for many types of traits. The public data that we freely release over the internet via our website (www.genome.clemson.edu) for the various crop genome frameworks also adds to the impact factor of the research and ultimately benefits the agricultural community. On a regional basis, our activities are beginning to draw agricultural biotechnology companies to the State of South Carolina, thus directly influencing the
state's economy in the agricultural technology sector. It is hoped that these companies will add jobs to the economy, increase skill levels in the state work force, and produce cutting edge agricultural crop improvements that will benefit the farmers.
Publications
- Tomkins, J., M. Fregene, D. Main, H. Kim, R. Wing, and J. Tohme. 2004. Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in Cassava (Manihot esculenta Crantz). Plant Molecular Biology 56:555-561.
- Jung, S., C. Jesudurai, M. Staton, Z. Du, I. Cho, J. Tomkins, A. Abbott and D. Main. 2004. GDR: Genome Database for Rosaceae: integrated web resources for Rosaceae genomics and genetics research. BMC Bioinformatics 5:130 (http://www.biomedcentral.com/1471-2105/5/130)
- Sajjaphan, K, N. Shapir, L. Wackett, M. Palmer, B. Blackmon, J. Tomkins, and M. Sadowsky. 2004. Arthrobacter aurescens TC1 atrazine catabolism genes trzN, atzB, and atzC are linked on a 160-kilobase region and are functional in Escherichia coli. Applied and environmental Microbiology 70:4402-4407.
- Wood, T.C. and J.P. Tomkins. 2004. Genomic Sequencing (Core Article). In Encyclopedia of Molecular Cell Biology and Molecular Medicine. R.A. Meyers (editor). Vol. 5. Pages 513-536. Wiley-VCH Verlag Publishing. Weinheim, Germany.
- Tomkins, J.P. 2004. Cloning the daylily genome. Daylily Journal. 59:245-250.
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Progress 01/01/03 to 12/31/03
Outputs
Physical frameworks for sequencing are developed by fingerprinting BAC clones and then aligning the clones based on shared bands into contiguous overlapping sets of clones. Entire chromosomes and sections of chromosomes can be reconstructed this way. In 2003, we aquired specialized DNA analysis instrumentation to utilize new fingerprinting technologies which are more robust than previous methods. We also began work on developing a physical framework for Mimulus guttatus, a model plant species for environmental stress adaptation and flower development. These traits are important factors in crop yield. BAC end sequencing is a critical component of developing a framework for a crop genome because it provides sequence tagged sites (STSs) throughout the genome. We have continued our development of an STS database for the cotton genome by BAC end sequencing the cotton BAC library which was made at Clemson University. Cotton is the most important fiber crop in the USA and we
are hoping to make a complete physical framework for the cotton genome in anticipation of sequencing. BAC library production which produces the substrates for making physical maps to sequence the genomes of crop plants was also accomplished for new strains/varieties of the following crops: phaseolus, maize, soybean, and cassava.
Impacts
The impact of our efforts is evidenced by the popularity of our resources which are distributed through our BAC/EST Resource Center (www.genome.clemson.edu). Clones, whole libraries, and high-density BAC colony filter arrays for all of the major agronomic corps: soybean, rice, maize, barley, cotton, and tomato were sold on a cost-recovery basis to researchers all over the USA. These resources will be used for crop improvement research at many locations throughout the USA and the ultimate impact of these important tools is difficult to determine. One thing is for sure, it will be enormous. The public data that we freely release over the internet for the various crop genome frameworks also adds to the impact factor of the research and ultimately benefits the agricultural community. On a regional basis, our activities are beginning to draw agricultural biotechnology companies to the State of South Carolina, thus directly influencing the state's economy in the
agricultural technology sector. It is hoped that these companies will add jobs to the economy, increase skill levels in the state work force, and produce cutting edge agricultural crops that will benefit the farmers.
Publications
- Wood, T.C. and J.P. Tomkins. 2003. Genomic Sequencing (Core Article). In Encyclopedia of Molecular Cell Biology and Molecular Medicine. R.A. Meyers (editor). Wiley-VCH Verlag Publishing. Weinheim, Germany. (invited manuscript, in press).
- Tomkins, J.P. 2003. Plant Bacterial Artificial Chromosome Libraries: Advances in Their Development and Application. In Recent Research Developments in Plant Molecular Biology. Pp. 139 to 156. Research Signpost Publishers, Kerala, India.
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