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