Genome-wide Impact of mPing Transposition on Rice Phenotypic Diversity

01 Mar 2011 28 Feb 2018

Susan Wessler (PI) , Thomas P Brutnell (CoPI), Qi Sun (CoPI), Jason E Stajich (CoPI)


PI: Susan R. Wessler (University of California - Riverside)

CoPIs: Thomas Brutnell (Boyce Thompson Institute), Jason Stajich (University of California - Riverside) and Qi Sun (Cornell University)

Senior Personnel: Joyce Van Eck (Boyce Thompson Institute), James Burnette (University of California - Riverside), Wen-Gui Yan (USDA-ARS Dale Bumpers National Rice Research Center) and Yutaka Okumoto (Kyoto University)

The overall goal of this project is to understand the impact of a rapidly amplifying high copy number transposable element (TE) called mPing on generating diversity in rice. This goal has both applied and basic aspects. The applied goal is to develop and make freely available novel collections of reverse genetic resources that will be characterized from genome to transcriptome to phenome. The basic goal is to analyze for the first time how a high copy TE rapidly diversifies the genome of an organism and, in doing so, alters its ability to respond to a changing environment. It is paradoxical that rice, with the most stable genome among characterized crop plants, is host to the most active TE characterized in any eukaryote. This fortunate set of circumstances will facilitate the application of next generation sequencing methodologies to sequence related rice cultivars and survey global changes in gene expression associated with abiotic stress responses. To this end the project will resequence five closely related rice strains where mPing has amplified to over 1000 copies during the past century and where it is still actively transposing. Comparison with the closely related reference genome Nipponbare will document for the first time the global impact of independent TE bursts in any organism. To assess the consequences of mPing insertion(s) on quantitative traits, the project will exploit recombinant inbred (RI) populations where the parents vary widely in their copy number of mPing insertions and where significant phenotypic variation exists for many traits. The contribution of candidate genes with mPing insertions to phenotypic variation will be assayed in transgenic rice. To exploit the full range of mPing amplification, from very low to very high, the project will activate mPing in US cultivars and create up to 1500 lines carrying novel mPing insertions through a non-transgenic approach. Finally, the project will use expression profiling (RNA-seq) to examine the role of mPing in reshaping the leaf transcriptome in response to abiotic stress.

The expected broader impact of the project includes the development of novel collections of non-transgenic mPing-mutagenized rice strains that will be characterized from genome to transcriptome to phenome. All genomics data generated will be deposited at GenBank. Visualization of the datasets will be supported using in-house servers and at Gramene. All biological materials generated during the course of this project will be propagated at the Dale Bumpers National Rice Research Center in Stuttgart (AR) and seed stocks of non-transgenic materials will be freely distributed through USDA-ARS Genetic Stocks - Oryza (GSOR) Collection.

All outreach activities will be channeled through the PI's "The Dynamic Genome" courses, which will be taught in a newly constructed Science Learning Facility at the University of California - Riverside. These courses, which are designed to replicate the PI's research laboratory, will serve as a conduit that integrates the research output of this project with the development of classroom modules for colleges and high schools focused on next generation sequencing methodologies. As such, these courses will bring the excitement of next-generation technologies to undergraduates and high school students and teachers. Finally, project involvement in the iPlant Collaborative's Education Outreach Team will facilitate the broader dissemination of successful modules.