Source: UNIVERSITY OF ILLINOIS submitted to NRP
GENETIC MAPPING OF EVOLVED HERBICIDE-RESISTANCE TRAITS.
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
COMPLETE
Funding Source
AFRI COMPETITIVE GRANT
Reporting Frequency
Annual
Accession No.
1022602
Grant No.
2020-67013-31854
Cumulative Award Amt.
$454,987.00
Proposal No.
2019-05216
Multistate No.
(N/A)
Project Start Date
Jun 15, 2020
Project End Date
Jun 14, 2024
Grant Year
2020
Program Code
[A1112]- Pests and Beneficial Species in Agricultural Production Systems
Recipient Organization
UNIVERSITY OF ILLINOIS
2001 S. Lincoln Ave.
URBANA,IL 61801
Performing Department
Crop Sciences
Non Technical Summary
The evolution of weed populations resistant to herbicides is analogous to the evolution of human pathogens that are resistant to antibiotics. Weed populations that possess multiple herbicide resistance mechanisms, and resistance mechanisms that confer unpredictable cross resistance to a broad array of herbicides, are a significant threat to contemporary weed management systems. To date, we have a very limited understanding of resistance mechanisms that confer cross resistance because of the challenges in identifying the responsible genes. Recent advances in genomics, however, are providing new opportunities to identify herbicide-resistance genes. This research will take advantage of a recently obtained genome of waterhemp (Amaranthus tuberculatus) to identify herbicide-resistance genes in this species, one of the most economically important weeds in the U.S.
Animal Health Component
10%
Research Effort Categories
Basic
90%
Applied
10%
Developmental
(N/A)
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
21323001140100%
Knowledge Area
213 - Weeds Affecting Plants;

Subject Of Investigation
2300 - Weeds;

Field Of Science
1140 - Weed science;
Goals / Objectives
The long-term goal of this research is to sustain the efficacy of current and future herbicides through a better understanding of herbicide-resistance mechanisms. Towards this goal, the objective of this proposal is to pioneer the use of genetic mapping to identify herbicide-resistance genes. The resources and procedures that we will develop and demonstrate will alter the existing paradigm for elucidating herbicide-resistance mechanismsand pave the way for identifying causative genes for other traits of interest in weeds for which a genome is available. Our objective will be achieved by the following three specific aims:1) Identify quantitative trait loci (QTL) and their effect sizesfor resistance to 2,4-D, dicamba, and S-metolachlor, and fine map to identify causative genes.2) Identify gene-expression changes that contribute to S-metolachlor resistance.3) Contribute a genotyped universal sensitive waterhemp population for the research community.
Project Methods
Molecular markers will be used to identify QTL associated with herbicide-resistance traits in an F2 mapping population. Subpopulations will be created to fine-map individual QTL for each of the resistance traits. A transcriptomics approach will be used to identify gene expression changes that contribute to S-metolachor resistance. A similar approach has already been initiated for the other herbicide resistance traits in our target population. Consequently, upon the completion of this research, we will have a robust dataset for making comparisons across the different herbicide-resistance traits. Such cross comparisons from both the genetic mapping and the transcriptomic approaches will enable us to parse the relative contributions of "generalist" and "specialist" herbicide-resistance mechanisms. In the process of creating the population for genetic mapping, we will also create from an initial pair-wise cross a waterhemp population that is uniformly sensitive to herbicides. Whole-genome sequencing will be performed on the parental plants of this population. This sequenced and herbicide-sensitive population will be deposited with a USDA germplasm collection, ensuring its availability to the research community.

Progress 06/15/20 to 06/14/24

Outputs
Target Audience:The target audience for this project is the weed science research community. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?Over the course of this project four graduate students received training ingeneration of germplasm for genetic and genomic analysis and in computational anlysis of large bioinformatic data sets. These students also developed their professional skills inwriting and presenting scientific research. Multiple undergraduate students received training in conducting routine greenhouse and laboratory weed science research. How have the results been disseminated to communities of interest?Two peer-reviewed papers have been published and two more will be submitted soon. Preliminary findings have been disseminated annually via presentations at scientific meetings of the weed science community. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Essentially all the major goals of this project were completed. Two manuscripts, each describing research towards goals 1 and 2, arecurrently being finalized for submission. We additionally published in 2024 a manuscript desribing gene expression changes associated with resistanceto dicamba. The universal sensitive waterhemp population was deposited with USDA GRIN, where it is now publicly available. Overall, this project substantially increased our understanding of non-target-site herbicide resistance, which is one of the greatest challenges to our contemporary weed management systems. In particular, research findings informed our review article that was published in 2024. This article provides strategies for better predicting herbicide cross resistance; such strategies are critical for better management and mitigation of herbicide-resistant weed populations.

Publications

  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Bobadilla LK and Tranel PJ (2024) Identification of candidate genes involved with dicamba resistance in waterhemp (Amaranthus tuberculatus) via transcriptomics analyses. Weed Sci. 72:125136. doi: 10.1017/wsc.2023.73.
  • Type: Journal Articles Status: Published Year Published: 2024 Citation: Bobadilla LK and Tranel PJ (2024) Predicting the unpredictable: the regulatory nature and promiscuity of herbicide cross resistance. Pest Manag Sci. 80:235244. doi:10.1002/ps.7728.
  • Type: Conference Papers and Presentations Status: Published Year Published: 2024 Citation: Werle I, Bobadilla L, Machado F, Hager A and Tranel P (2024) Inheritance and segregation of non-target-site resistance to S-metolachlor in waterhemp (Amaranthus tuberculatus). Weed Sci Soc Amer. Abstracts 64:47.


Progress 06/15/22 to 06/14/23

Outputs
Target Audience:The target audience for this project is the weed science research community. Changes/Problems:Because of an initial delay in hiring a post-doc for this project (in part due to COVID 19) a no-cost extension for this project was requested and granted. What opportunities for training and professional development has the project provided?Two graduate students received training in phenotyping plants for herbicide sensitivity and in developing genomicsequencing data. Two undergraduate students received training and experience in day-to-day greenhouse and laboratory research activities in a weed science research program. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?Genomic sequence data obtained will be used for QTL mapping. F2 backcross progeny will be selected based on S-metolachlor sensitivity and used for transcriptomic analysis.

Impacts
What was accomplished under these goals? Individual waterhemp plants from a segregating F2 population were selected based on their sensitivities to each of the twoherbicides, 2,4-D, and dicamba. Backcross progenies from each F2 individual were screened for sensitivity to S-metolachlor. The selected individuals were subjected to genomic sequencing.

Publications


    Progress 06/15/21 to 06/14/22

    Outputs
    Target Audience:The target audience for this reporting period is the weed science research community. Changes/Problems:The ongoing pandemic created challenges in hiring a post-doc for this project. After finally hiring one (over a year into the project), that individual stayed with me for only two months (she moved on to a faculty position). As a result, two graduate students have been working on thisproject. What opportunities for training and professional development has the project provided?Two graduate students working on this project have gained experience conducting plant crosses to generate germplasm for further research. They have also gained experience in phenotyping plants for herbicide sensitivity. Two undergraduate students have gained hands-on experience with greenhouse and laboratory research activities, including isolationof DNA from plant samples. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?We will conduct sequencing of DNA from phenotyped F2 plants, and then use the sequence information for bioinformatics analyses to identify QTLassociated with the herbicide-response phenotypes. Backcross families will be phenotyped for response to metolachlor. Selected familes with either high or low sensitivity to metolachlor will then be used in an RNA-Seq study to identify differentially expressed genes.

    Impacts
    What was accomplished under these goals? We completed the creation of germplasm needed to achieve Objectives 1 and 2 of this project. F2 individuals were phenotyped for resistance/sensitivity to dicamba and 2,4-D. DNA was obtained from phenotyped individuals, and will be used for the QTL mapping (Objective 1). The same individuals were backcrossed to individuals from the herbicide-sensitive parental population; these backcross populations will be used for Objective 2. Objective 3 was completed during the previous reporting period.

    Publications


      Progress 06/15/20 to 06/14/21

      Outputs
      Target Audience:The target audience for this reporting period has been the weed science research community. Changes/Problems:The ongoing COVID-19 pandemic created signifcant challenges and delays with hiringa post-doc to perform the research. As a result, two graduate students were instead assigned to the project. What opportunities for training and professional development has the project provided?Two graduate students working on this project have gained experience with designing and executing plant crosses for obtaining germplasm appropriate for genetic and genomic analyses. One of the graduate students also has gained experience in conducting routine herbicide dose-response assays to characterize herbicide sensitivity. An undergraduate student has gained hands-on experience with generallaboratory and greenhouse research activities. How have the results been disseminated to communities of interest? Nothing Reported What do you plan to do during the next reporting period to accomplish the goals?Germplasm development should be completed during the next reporting period, and the genomic and transcriptomic studies will then be initiatied with this germplasm. Characterization of the standard, herbicide-sensitive population will be completed, and a paper describing this research will be prepared and submitted for publication.

      Impacts
      What was accomplished under these goals? During the current reporting period, activities focused on performing crosses to develop the germplasm that will be used for the QTL mapping study (Objective 1) and for the gene-expression analysis (Objective 2). Development of the germplasm is essentially on schedulewith the proposed timeline. We are ahead of schedule with Objective 3, and have already deposited the population to USDA-GRIN. During the reporting period, the population was characterized for responses to several representative herbicides.

      Publications