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 01/01/16 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.