Current Projects

Blueberry Medicinal Genomics

A NIH-funded project to investigate the biosynthesis of iridoid compounds in blueberry, a class of pharmacologically important compounds that have positive human health benefits.

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Climate Change and Potato

As part of the MSU Project GREEEN we are investigating how potatoes produced in Michigan will be impacted by altered CO2 and temperature conditions anticipated in the mid-21st century.

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Cold Tolerance in Switchgrass

As part of the DOE USDA Feedstock Genomics for Bioenergy Project and in collaboration with USDA-ARS, we are examining genomic variations from exome capture and transcriptome sequencing of switchgrass populations to improve the efficiency of breeding switchgrass cultivars with high biomass and cold hardiness.

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Genome Editing

The recent evolution of genome editing technologies has transformed the field of plant biotechnology and provided the opportunity for crop improvement. With funding from USDA-Biotechnology Risk Assessment Grans Program (BRAG) we explore the impact of genome editing technologies in potato at the whole genome and transcriptome levels.

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Genomic Tools for Sweetpotato (GT4SP) Improvement Project

A multi-institutional collaboration supported by The Bill and Melinda Gates Foundation whose primary aims are to develop new genomic, genetic, and bioinformatics tools for improvement of hexaploid sweetpotato. See Sweetpotato Genomics Resource and the GT4SP website for more information.

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Maize Genetic Diversity

As part of the Great Lakes Bioenergy Research Center, we are examining natural diversity in maize and associating genes and alleles with traits important to use of stover in biofuel feedstock production.

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Maize Nutrigenomics

We are participating in a collaborative project funded through the National Science Foundation Plant Genome Research Program to determine the genetic architecture of vitamin biosynthesis in maize.

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Medicinal Plant Genomics

Building upon past accomplishments from our Medicinal Plant Transcriptomics project we have continued our work on generating genomic resources and functional annotation of several medicinal plants with the target of functionally characterizing genes involved in natural product biosynthesis and facilitating the artificial synthesis of economically pivotal specialized metabolites in heterologous organisms.

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Mint Genomics

A new NSF-funded project on evolution of chemical diversity in the mint family started in collaboration with scientists at the University of Florida, Purdue University, and the John Innes Centre.

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Pack-MULEs and Genome Evolution in Rice

Pack-MULEs are transposable elements that carry fragments of normal protein-coding genes. An NSF funding supports a project on the impact of Pack-MULEs on plant genome evolution and mechanisms of sequence acquisition by Pack-MULEs.

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Plant Resilience Institute

As part of the MSU Plant Resilience Institute, we will be interrogating the genome of tepary bean (Phaseolus acutifolius), a species native to the southwestern U.S. and extremely heat tolerant.

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Potato Genome Variation

We are continuing work on an NSF-funded project to understand the contribution of intra-genome variation to potato fitness through the study of tetraploid, diploid, and dihaploid potato.

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Sweet Potato Genomics

We are participating in a consortium led by North Carolina State University funded by the Bill & Melinda Gates Foundation to develop genome resources for improved breeding efficiencies in sweet potato.

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Switchgrass Genetic Diversity

As part of the Great Lakes Bioenergy Research Center, we are examining natural diversity in swithgrass to enable improved breeding efforts for biofuel feedstock production.

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Former Projects

Biofuel Feedstock Genomics Resource

The Biofuel Feedstock Genomics Resource is a database that provides fully integrated and uniform annotation to a large collection of plant species that are being examined for possible use as ligno-cellulosic feedstocks for biofuel production.

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Comprehensive Phytopathogen Genomics Resource

The Comprehensive Phytopathogen Genomics Resource (CPGR) is a comprehensive plant pathogen genomics and annotation resource funded by USDA CSREES. A focus of the project is the development of plant pathogen diagnostic markers using genomics data.

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Medicinal Plant Transcriptomics

This project, funded by the NIH, addresses the gap in our knowledge base of species-specific plant metabolism. Data generated through this project will accelerate the identification and functional analysis of genes involved in natural product biosynthesis in 14 widely used medicinal plant species.

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Oryza SNP Project

As part of an international collaboration, we have been involved in the discovery and annotation of SNPs in the rice genome. This project is funded by USDA CSREES.

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Plant Repeat Database

We have created the Plant Repeat Database to assist in the compilation and identification of repeat sequences in plant genomes.

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Pythium Genomics

We have been funded by the U.S. Department of Agriculture to sequence and annotate two strains of Pythium ultimum, an important plant pathogen.

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Rice Genome Annotation Project

The Rice Genome Annotation Project is an NSF funded effort to provide high quality annotation of the rice genome to the research community.

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Solanaceae Coordinated Agricultural Project

In this collaborative project, we are using high throughput sequencing and bioinformatics to identify variation in elite potato and tomato germplasm for the identification of candidate genes of high value traits such as carbohydrate, sugar and vitamin content. These resources will ultimately be used to develop improved varieties through genotyping and phenotyping panels to associate genes with phenotypes.

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