The goal of this project is to re-engineer poplar, one of the fastest growing trees in the United States, as a multipurpose crop that can be used for bioenergy, biomaterial, and bioproduct production as the need for sustainable sources of bioproducts and plant-based materials continues to rise.

In this project, we will develop a gene editing platform at scale that will be used to generate novel plant genotypes with reduced gene content and redundancy, which can serve as chassis (i.e., a platform) to rapidly engineer plants with new phenotypes and test heterologous genes relevant to biological processes of interest.

The goal of this project is to eliminate the factors required for making native triterpenes and carotenoids in fruit to allow expression of biosynthetic pathways from other organisms for sustainable production of high value terpenes.

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.

Phaseolus vulgaris, common or dry bean, diverged from its sister species, tepary bean (Phaseolus acutifolius) 2.1 MYA. We will transform common and tepary bean breeding by exploiting their close evolutionary relationship with the development of a computational genomics framework that permits rapid interspecific trait discovery and subsequent introgression using bridging genotypes.

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.

Plants produce a plethora of medicinally important natural products that have significant potential to improve human health yet are often produced in low amounts, in complex mixtures, and/or cannot be produced in a sustainable or economic manner. Omics technologies enable the discovery of the biosynthetic genes of plant natural products which can then be employed in commercial production of medically relevant compounds. In this project, we will use state-of-the-art omics technologies to efficiently discover genes responsible for the biosynthesis of pharmacologically relevant compounds and utilize this knowledge to revitalize an old technology, plant cell culture, to enable robust, sustainable production of these products.

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

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.

Wheat is a major crop providing ~20% of dietary calories and proteins worldwide, and a major concern for global food security. Development of the initial International Wheat Genome Sequencing Consortium Chinese Spring RefSeq served as a springboard for genetics, evolution, breeding and biotechnology advancements in wheat. In this project, we will update the Chinese Spring genome assembly and provide new landrace genomes to enable further advancements in genome-enable research in wheat.

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.

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.

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.

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-21^st century.

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.

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.

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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

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

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.