Current Projects

Potato 2.0

Potato is an asexually propagated, cross-pollinated tetraploid crop for which breeding methods have not changed substantially in over 100 years. Current methods for generating new potato cultivars are genetically inefficient due to polyploidy, resource intensive due to vegetative propagation, and do not take full advantage of genomics resources. This project is focused on developing potato as a diploid, inbred-hybrid crop propagated by true seed.

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SweetGAINS (Genetic Advances and Innovative Seed Systems) Project

Key to genome-enabled breeding is access to a high quality, annotated genome assembly. We will be annotating the hexaploid Beauregard genome using Oxford Nanopore Technology full length cDNA, mRNAseq data, protein evidence, and gene finders.

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Genome wide evaluation of off-targets from gene editing reagents in seed vs. vegetatively propagated crop species

The overall objective of this project is to address genome-wide variability/risk assessment of current genome-editing technology involving CRISPR systems, TALENs and base editors.

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Evolutionary Origins of Tubers

Major crop species use tubers to bypass sexual reproduction. This project aims to identify how tubers have evolved multiple times and provide insight into tuber development.

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Effects of Root and Shoot Architecture on Nutrition in Dry Bean

This project aims to identify indirect selection events in dry bean root systems after 100+ years of breeding for shoot architecture traits.

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Accelerated Resistance Gene Discovery in Common Bean

A USDA funded project to enhance durable disease resistance in beans using genomics-enabled plant breeding techniques.

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Circadian Clock in Potato

This project is focused on the role of the circadian clock in potato domestication and development through the use of genetic, genomic, cell/molecular biology, and bioinformatic techniques.

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Single Cell RNA Sequencing in Plants

A pilot project to help develop single cell RNA sequencing in plants.

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Maize Genomics Resource (MGR) Annotation Project

The Maize Genome Resource provides a range of genomic tools for maize B73. A notable feature is the EFP browser for the developmental B73 gene atlas and several B73 abiotic and biotic stress experiments that were published in Hoopes et al (2018). The MGR also features a comprehensive and regularly updated JBrowse instance including a range of annotation tracks from published data sets.

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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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Mint Genomics

A 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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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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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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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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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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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

We are participating in a consortium led by North Carolina State University funded by the Bill & 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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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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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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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 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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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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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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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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