Research

RESEARCH OVERVIEW

The Patterson Lab in housed in the Plant, Soil and Microbial Sciences Department at Michigan State University. The labs mission is to explore and understand the molecular and genetic basis of traits that make certain plant species weedy and attempt to answer the question "what makes a weed, a weed?" Within the labs mission we have three major research areas: 1) assembling, annotating, and comparing the genomes of weedy species, 2) molecular characterization of specific genes through traditional molecular techniques, and 3) the development of diagnostic tests to support decision making of growers and agronomists. The lab is highly collaborative both inside and outside of weed science and works with scientists within Michigan, the United States, and internationally.

ONGOING PROJECTS

International Weed Genomics Consortium

Our lab is a key member of the International Weed Genomics Consortium (IWGC). The IWGC is a community of researchers from private and public spheres that have come together to develop genomic tools and resources and to stimulate global research in weed biology and management. The IWGCs major objectives are to 1) obtain quality reference genomes for the most important weed species worldwide, 2) provide user-friendly genome analytical tools and training through web-based databases and resources, and 3) facilitate inter-disciplinary collaboration and workforce development within this emerging field. The Patterson lab specifically is responsible for annotating all genomes and preparing them for distribution. This project combines bioinformatics and genomics techniques with practical understandings of weeds and weed physiology. For more information go to www.weedgenomics.org

Molecular and Physiological Resistance Diagnostics

Early detection and diagnosis of resistant weed species early in the season can create a big effect on potential yield of crop. Our lab is currently developing a diagnostic pipeline that will use advance molecular techniques to detect weed species that are resistant to particular Mode of Action, early in the season. As of now, the conventional method takes around a complete season (8 to 9 months) to detect any resistant weed species. This process is cumbersome, time-consuming and its results can be used only in next season. We are using Q- PCR technique and then sequencing the bands to get the results within a week. This will help farmers to detect resistance early in the current season, and help them adapt accordingly by using herbicide with different MOA.

Indaziflam Site of Action and Resistance Mechanisms

Indaziflam is a pre-emergence contact herbicide, that is primarily used in turf grasses to control weeds. It is one of latest herbicides that is discovered and thus, a little is known about it. The interesting thing about it is that it works at very small quantities(50g/ha). Our lab is focused on studying this herbicide to find its site of action. This will be very useful in understanding its effectiveness across a wide range of species. Also, it will help in understanding complex plant cell processes, like endocytosis, cellulose bio-synthesis and vesicle trafficking. This will also pave the way for developing new and better herbicides, for future research and application.

Genomic and Epigenomic Responses to Sublethal Doses of Glyphosate

Glyphosate is a non-selective, systemic herbicide for which resistance has become widespread. Increased copy number of EPSPS is the mechanism of resistance in over 9 species, and our lab is interested in detecting how genomic rearrangements like this evolve and are utilized as novel sources of genetic variation for weed adaptation to abiotic stresses. This project aims to study the effects of sublethal doses of glyphosate on the genome and epigenome of kochia by employing both bisulfite sequencing and RNA sequencing before and after herbicide application. There is particular interest in how herbicides influence transposable element activation, copy number variation, and the interplay between the epigenome and stress-related gene expression. Determining how herbicides affect weeds on a genomic and epigenomic level will help us understand resistance evolution in the field and inform future management strategies. This work is supported in part by the National Science Foundation Research Traineeship Program (DGE-1828149).

Clopyralid Resistance in Common Ragweed

Clopyralid is a synthetic auxin herbicide that is used to control troublesome weed species in the Asteraceae family, such as Ambrosia artemisiifolia (Common Ragweed). The first population of A. artemisiifolia with confirmed resistance to clopyralid was discovered in 2018 in Michigan, USA in a Christmas tree farm. The resistant biotype has been found to survive application rates up to 32x the standard rate! We are using physiological, greenhouse, and molecular techniques to find gene(s) of interest that may be the cause of this extreme resistance phenotype.

Structural Genomics

Structural variation (i.e. EPSPS copy number variation) has been shown to be a resistance mechanism for the herbicide glyphosate in at least nine phylogenetically distinct weed species. However, each species has a unique EPSPS duplication mechanism. Our lab is currently investigating the structure and evolutionary origin of two of these species, Kochia scoparia and Eluesine indica. Ultimately we wish to understand how structural variation and copy number variation form and how they can contribute to novel genetic variation. We hypothesize the these novel variants are an important source of genetic material and help weeds adapt to their environment quickly.

FUNDING SOURCES

Industry Partners
Bayer
BASF
Syngenta
Corteva
Academic
International Weed Genomics Consortium
MSU-Project GREEEN
Commodity Partners
Michigan Soybean Committee
Michigan Corn Marketing Committee
North Central Integrated Pest Management Center
Government
United States Department of Agriculture
Foundation for Food & Agriculture Research