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United States Department of Agriculture

Agricultural Research Service

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Research Project: Screening Transcriptomes of Leafy Spurge to Identify Key Molecular Targets Regulating Developmental Processes

Location: Sunflower Research

Project Number: 5442-21220-026-07
Project Type: Specific Cooperative Agreement

Start Date: Jul 01, 2013
End Date: Jun 30, 2018

Objective:
1) Implement next-generation, high throughput sequencing technology to assemble and quantify mRNA transcript abundance in various experimental tissues of leafy spurge. 2) Analyze transcriptome data using sophisticated bioinformatics programs to identify key molecular targets and gene products involved in regulating development processes, which might hold promise for future manipulation of invasive perennial weeds.

Approach:
Understanding how gene expression and molecular mechanism respond to plant growth regulators and ecological factors in invasiveness perennial weeds of the Northern plains is critical to making recommendations for next-generation weed management. Advances in next generation sequence technologies and bioinformatics now make it reasonably affordable to conduct high-throughput sequencing of libraries developed using mRNA isolated from underground adventitious bud tissue and/or aerial shoots of leafy spurge. To gain a better understanding of molecular networks involved in glyphosate-induced “witches brooming” and other cellular process regulating development processes, mRNA extracted from experimental tissues collected in Fargo, ND will be sent to the Univ. of Illinois, Keck Center for construction of strand-specific barcoded RNASeq libraries. These libraries will then undergo one paired-end lane sequencing on a HiSeq2500 sequencer. Sophisticated bioinformatics programs will be used to assemble and quantify the abundance of transcript present in each tissue, at specific time points, and in response to growth regulating treatments. The transcript data will further be analyzed using Sub-network enrichment analysis to identify key molecular mechanism and gene products involved in regulating plant growth and development.

Last Modified: 7/22/2014
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