Source: UNIV OF MINNESOTA submitted to
UNDERSTANDING THE ROLE OF TRANSPOSABLE ELEMENTS IN MAIZE ABIOTIC STRESS RESPONSE
Sponsoring Institution
National Institute of Food and Agriculture
Project Status
NEW
Funding Source
Reporting Frequency
Annual
Accession No.
1008666
Grant No.
2016-67013-24747
Project No.
MIN-71-G13
Proposal No.
2015-06818
Multistate No.
(N/A)
Program Code
A1101
Project Start Date
Jan 1, 2016
Project End Date
Dec 31, 2018
Grant Year
2016
Project Director
Springer, N.
Recipient Organization
UNIV OF MINNESOTA
(N/A)
ST PAUL,MN 55108
Performing Department
Department of Plant Biology
Non Technical Summary
Abiotic stress, such as extreme temperatures or drought, severely limit agricultural productivity. Many plant species exhibit natural variation for phenotypic and molecular responses to abiotic stress. This project would test the idea that transposable elements contribute to plants ability to respond to abiotic stress. We have evidence that certain families of transposons can confer stress-responsive expression patterns to nearby genes in maize. The first specific aim of this proposal is to define the role of transposons in gene expression responses to abiotic stress in several different tissues and genotypes. This aim will generate a detailed understanding of which transposons might contribute to plant responses to cold, heat or salt stress, and will also provide evidence for the role of these transposons in generating allelic variation. The second aim will focus on determining the mechanism by which transposons influence the stress-responsive expression of nearby genes. A combination of bioinformatic analyses and transient expression assays will be used to define the mechanisms of transposon influence. The third aim will document natural variation for insertion sites of the transposons that confer stress-responsive gene expression and will attempt to identify protocols to mobilize these elements to generate novel allelic diversity in maize. Some of these novel insertions may generate alleles that would provide increased stress tolerance. The proposed research would provide novel understanding of the molecular processes that underlie gene expression responses to abiotic stress.
Animal Health Component
20%
Research Effort Categories
Basic
70%
Applied
20%
Developmental
10%
Classification

Knowledge Area (KA)Subject of Investigation (SOI)Field of Science (FOS)Percent
20115101080100%
Knowledge Area
201 - Plant Genome, Genetics, and Genetic Mechanisms;

Subject Of Investigation
1510 - Corn;

Field Of Science
1080 - Genetics;
Goals / Objectives
Abiotic stress, such as extreme temperatures or drought, severely limit agricultural productivity. Many plant species exhibit natural variation for phenotypic and molecular responses to abiotic stress. This project would test the idea that transposable elements contribute to plants ability to respond to abiotic stress. We have evidence that certain families of transposons can confer stress-responsive expression patterns to nearby genes in maize.The first goal of this proposal is to define the role of transposons in gene expression responses to abiotic stress in several different tissues and genotypes. This aim will generate a detailed understanding of which transposons might contribute to plant responses to cold, heat or salt stress, and will also provide evidence for the role of these transposons in generating allelic variation.The second goalwill focus on determining the mechanism by which transposons influence the stress-responsive expression of nearby genes. A combination of bioinformatic analyses and transient expression assays will be used to define the mechanisms of transposon influence.The third goal is todocument natural variation for insertion sites of the transposons that confer stress-responsive gene expression and will attempt to identify protocols to mobilize these elements to generate novel allelic diversity in maize. Some of these novel insertions may generate alleles that would provide increased stress tolerance.
Project Methods
The methods for this project will involve growth of plants in growth chamber conditions including control and heat/cold stress treatments. RNAseq will be used to profile the transcriptome of these plants and novel methods for allele-specific expression analysis will be used to document allelic variation for stress response. Bioinfomatic analyses will be used to better understand the mechanisms of stress response.

Progress 01/01/17 to 12/31/17

Outputs
Target Audience:The primary target audiences reached by our efforts are plant scientists and plant breeders. Our efforts have provided knowledge about the sources of variation that could provide important traits in crops such as maize. We are developing tools to induce, and track, these types of variation. This information will be of interest for plant biotechnology and plant breeding audiences. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided?A post-doctoral researcher, Sarah Anderson, has worked full-time on this project during the past year. She has had several opportunities to present her work at conferences in the past year and has been a lead author and a co-author on publications. We have provided active mentoring to Sarah and worked with her to develop skills necessary for obtaining, and succeeding in, an academic position. In addition, two undergraduate students have worked on this project and have developed basic molecular biology and computational biology skills. How have the results been disseminated to communities of interest?Two publications have resulted from this work in the past year. We are currently preparing additional manuscripts as well. In addition, we have made presentations at Plant and Animal Genome conference, Maize Genetics conference, a Gordon research conference and a Plant Genome workshop at New York University on the research associated with this project. What do you plan to do during the next reporting period to accomplish the goals?We plan to finalize the analyses associated with the first and second goal in the coming year. This should provide a comprehensive analysis of changes in transposon expression associated with nearby changes in gene expression. We will also perform a more in-depth analysis of transposon polymorphisms in order to document potential roles of transposons in the observed expression responses.

Impacts
What was accomplished under these goals? We have made strong progress towards the first and second goal of the project and are developing materials and approaches for the third primary goal. The release of an improved assembly of the B73v4 along with a structural annotation of transposable elements provided valuable resources for this project. In order to address the first goal of documenting the role of transposons in responses of gene expression to abiotic stress we developed an imformatics approach to document the level of expression for each transposon family in the maize genome that incorporates both unique and multiple-matching sequence reads. In the past year we have used these resources to re-analyze >150 RNAseq datasets to assess transposon expression. These include samples that had been subjected to abiotic stress as well as numerous developmental stages or tissues. We also have assessed gene expression in each of these samples. In addition, we have generated additional samples that have been subjected to abiotic stress and have collected multiple tissues that are being used for expression profiling. These datasets will allow for the identification of genes that have expression changes associated with similar expression changes for nearby transposons. To address the second goal of documenting the mechanism we have been looking at specific isoforms produced in different environmental conditions and looking more closely at the transcripts produced by transposons. We have also been documenting potential regulatory sites and TF binding sites within transposons. We collaborated with Maike Stam's group to assess the putative enhancer regions found within maize transposons resulting in a shared publication in Genome Biology. The recent release of de novo genome assemblies for PH207 and W22 provide opportunities that relate to the third goal. We are documenting shared and polymorphic transposon insertions among these genomes. In addition, we will be able to assess the similarities or differences in gene expression responses in these lines to associate variability of transposon insertions with altered expression responses. We have also completed an analysis of transposon expression in several mutant backgrounds. This has highlighted transposons with the potential for expression and movement in these genotypes and this information was included in a recently submitted manuscript.

Publications

  • Type: Journal Articles Status: Published Year Published: 2017 Citation: Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 2017 Jul 21;18(1):137. doi: 10.1186/s13059-017-1273-4
  • Type: Journal Articles Status: Submitted Year Published: 2017 Citation: Anderson S, Zynda G, Song J, Han Z, Vaughn M, Li Q, Springer NM. Subtle perturbations of the maize methylome reveal genes and transposons silenced by DNA methylation. BioRxiv. doi: https://doi.org/10.1101/221580


Progress 01/01/16 to 12/31/16

Outputs
Target Audience:The target audiance of the proposed research include scientists studying basic aspects of gene regulation in plants as well as plant breeders. To date, our efforts have centered around development of tools for simoultaneously monitoring transposon and gene expression. We have been working to develop new resources for these studies and are preparing to share these with the community. Changes/Problems:There has not really been a major change in the approach. However, new resources have slightly shifted our approach to the first aim. The release of an improved genome assembly for maize along with a radically improved transposon annotation has allowed for new analyses of transposon and gene expression. In addition, the release of a de novo assembly for another maize genotype (PH207) will improve the analyses we can perform in the third aim. We are utilizing these new resources to improve the outputs in our described experiments. What opportunities for training and professional development has the project provided?A post-doctoral researcher, Sarah Anderson, began full time work on the project in August. She has developed skills for performing bioinformatic analyses. She has spent substantial time working on making critical files for a new maize genome assembly and new TE annotation. These files, combined with a new informatics pipeline she has developed, have now given us the ability to coordinately analyze TE and gene expression using existing RNAseq datasets. In addition, she is mentoring two undergraduates that are working to grow plants and perform abiotic stress treatment. How have the results been disseminated to communities of interest?To date we have published one review article. Sarah is currently working to develop a publication that will describe the methods for analyzing transposon expression. This will be coordinated with a publication on the new TE annotation and will provide tools for studying transposon expression. What do you plan to do during the next reporting period to accomplish the goals?We anticipate the completion of the first goal within the next 6 months. Our efforts will then shift to the experiments described in the second and third goals of the project. Once the transposon families that regulate expression of nearby genes have been identified we will initiate the molecular studies to document the exact mechanisms of this interaction. In addition, we have began several experiments that will seek to activate transposons and will be planting these populations in the summer of 2017 to generate materials for the third goal.

Impacts
What was accomplished under these goals? One significant change in the past year has been the release of a new version of the maize genome (version 4) along with a vastly improved annotation of transposons. This has provided new resources for studying transposon expression and the relationship with the expression of nearby genes. However, it has also introduced some additional technical difficulties as the improved annotation now allows re-assembly of transposons that have been interrupted by other transposon insertions. We have found solutions to these issues and have now developed robust methods for determining transposon and gene expression. We are currently using these new resources and approaches to analyze RNAseq data from control plants and plants subjected to abiotic stress to complete the analyses for the first goal of the proposal. We have also initiatied activities that will provide resources and datasets for the second and third goals.

Publications

  • Type: Journal Articles Status: Published Year Published: 2016 Citation: Hirsch CD, Springer NM. 2016. Transposable element influences on gene expression in plants. Biochim Biophys Acta. 2016 May 25. pii: S1874-9399(16)30100-6.