Associate Professor of Plant Biology
Ph.D., 1992, Utah State University, Logan, UT
Department of Plant Biology
Michigan State University
East Lansing, MI 48824-1312 USA
Phone: (517) 353-5597
Fax: (517) 353-1926
e-mail:buell@msu.edu
http://buell-lab.plantbiology.msu.edu
Plant Biology Department
College of Natural Science
Michigan Agricultural Experiment Station
Genetics Graduate Program
Quantitative Biology Initiative
Plant Breeding, Genetics, & Biotechnology Program
Research
My research activities are centered on genomic aspects of plant biology and plant pathogens. My research primarily involves projects focused on high throughput sequencing, functional genomics, comparative genomics, and bioinformatics.
Rice Genomics and Bioinformatics
Worldwide, rice is one of the world’s most important crop plants with 50% of the population dependent on rice as a food source. Furthermore, rice is a member of the grass family (Poaceae) and is considered a model species for the cereals as it has a near-complete finished genome and a wealth of resources for functional genomics studies. One important component of a genome sequence is accurate, uniform annotation of genes, gene models, and gene function. Using a suite of automated, semi-automated, and manual computational methods, my group has annotated the rice genome (http://rice.plantbiology.msu.edu/). We have generated pseudomolecules to represent the 12 rice chromosomes, modeled genes, incorporated experimental evidence into gene models, generated deep, rich functional annotation of the genome, and identified related sequences in other plant species (Yuan et al. Plant Physiol. 2005; Ouyang et al. 2007). We have deployed a genome browser for the rice genome in which >60 tracks of annotation are displayed (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/).
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We have identified nearly 42,000 non-transposable element related genes in the rice genome and have initiated analyses of the rice genome and its predicted proteome to provide insights into the biology of this model species. The large number of genes in rice is attributable to the substantial segmental duplication that involved nearly half of the genome (Lin et al. 2006). One impact of this duplication is the generation of large gene families and in providing new genes for diversity. Indeed, nearly half of the predicted rice proteome can be found in paralogous families. We have analyzed alternative splicing in rice and observed that alternative splicing is not only widespread but also that a surprising number of alternative splice forms result in a significant change in coding sequence, suggesting a potential pathway for non-sense mediated decay of mRNAs in rice (Campbell et al. BMC Genomics 2006).
Rice has an immense level of diversity that provides a genetic resource for improving germplasm. Using the Perlegen hybridization-based re-sequencing technology to identify single nucleotide polymorphism data (McNalley et al. Plant Physiol. 2006), we are collaborating with multiple scientists to generate a “hapmap” for rice (http://oryzasnp.plantbiology.msu.edu/). With access to sequence data from 184 plant species, we have been able to examine the conservation of predicted rice genes throughout the Plant Kingdom (Zhu and Buell, Genome Research 2007). Through these analyses, we have been able to identify core sets of conserved genes across not just the Poaceae but also angiosperms and the Plant Kingdom.
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Solanaceae Genomics and Bioinformatics
The Solanaceae family contains several species relevant to agriculture including potato, tomato, tobacco, petunia, and pepper. While selected for diverse morphological features such as fruit (tomato, pepper, eggplant), tubers (potato), leaves (tobacco), and flowers (petunia), the Solanaceae share a high extent of sequence similarity. Previous work in my group has focused on generation of genomic resources for potato (Ronning et al. Plant Physiol. 2003; Rensink et al. Genome 2005a), identifying disease resistance genes in wild potato species (Song et al. PNAS 2003), and expression profiling (Rensink et al. IFG 2005b). We have also initiated comparative genomic analyses within the Solanaceae (Rensink et al. BMC Genomics 2005) which confirmed earlier reports of conservation within the Solanaceae but also revealed a higher degree of species specific sequences within the Solanaceae than previously documented. My group is currently involved in the international Potato Genome Sequencing Consortium (http://solanaceae.plantbiology.msu.edu/). In this project funded by the National Science Foundation, we are generating sequence from chromosome VI of potato. We are creating a suite of genomic and bioinformatic tools and resources for the potato community. This involves annotation of potato genome sequences and development of a “web portal” so that potato breeders and geneticists, along with other Solanaceae researchers, can access the genome sequence, annotation, and expression data in a meaningful, user-friendly manner.
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Genomics and Bioinformatics of Plant Pathogens
My work on plant pathogens involves genome sequencing, comparative genomics, and bioinformatics. We have generated a plant pathogen genome sequence and annotation resource (http://cpgr.plantbiology.msu.edu), termed the Comprehensive Phytopathogen Genome Resource (CPGR), which is populated with all plant pathogen genome sequence data including viruses, bacteria, fungi, stramenopiles, and nematodes and provides genome/annotation data-mining and visualization tools. In this collaborative project (Jan Leach (Colorado State University), Ned Tisserat (Colorado State University), Tom Powers (University of Nebraska) and Andre Levesque (Agriculture and Agri-Food Canada)), we are developing diagnostic markers for three pathogens using genomics-based methods. These three “proof-of-concept” sub-projects will allow for the development and deployment of genomic and bioinformatic tools that will enable the broader plant pathology community, including diagnosticians and extension agents, to employ genomics in diagnostics.
We are also currently sequencing two strains of the ubiquitous plant pathogen, Pythium ultimum, and will be performing a comparative genomics analysis between the two isolates and with other oomycetes (http://pythium.plantbiology.msu.edu/).
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Project Web Sites
Rice Genome Annotation
OryzaSNP Database
Pythium Genome Database
Comprehensive Pythopathogen Genome Resource
SolCAP
Solanaceae Genomics Resource
Biofuel Feedstock Genomics Resource
MSU Plant Repeats Database
Buell Lab Website
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Current Funding Support
An annotation resource for the rice genome; NSF; 9/27/07-8/31/10
Whole Genome Sequencing of Pythium ultimum; USDA; 1/15/08-4/14/10
A comprehensive genome-based diagnostics resource and pipeline for identification of threatening plant pathogens; USDA; 10/01/07-2/28/10
Generation of potato sequence and annotation resources; NSF; 9/28/07-9/30/10
Comparative genomics resources for the Solanaceae: Tools and resources for cross-species translational genomics; USDA; 11/30/07-12/31/10
Computational Resources for Biofuel Feedstock Species; DOE & USDA; 8/15/08-8/14/11
Biochemical Pathway Mapping of Genes within Biofuel Feedstock Species; Michigan Agricultural Experiment Station;7/18/08-6/30/10
SolCAP: Translating Solanaceae sequence diversity and trait variation into applied outcomes through integrative research, education, and extension; USDA; 10/01/08-9/20/12
High throughput sequencing for comparative genomics of the Solanaceae; MSU Foundation; 7/1/08-6/30/12
