Page Banner

United States Department of Agriculture

Agricultural Research Service

Research Project: Enhanced Alfalfa Germplasm and Genomic Resources for Yield, Quality, and Environmental Protection

Location: Plant Science Research

Title: Assembly and annotation of the wildrice transcriptome challenged by Cochliobolus miyabeanus, the fungal brown spot pathogen

Authors
item Castell-Miller, Claudia -
item Gutierrez, Juan
item Figueroa, Melania -
item Garvin, David
item Samac, Deborah

Submitted to: American Phytopathological Society Annual Meeting
Publication Type: Abstract Only
Publication Acceptance Date: May 12, 2014
Publication Date: N/A

Technical Abstract: American wildrice (Zizania palustris) is an aquatic cereal that is harvested from natural stands and commercial paddies for its gourmet grain. Fungal brown spot (FBS), caused by Cochliobolus miyabeanus, is the most important disease that inflicts annual yield losses in this crop. The development of resistant wildrice cultivars against FBS has been hampered by the lack of characterization of defense responses in this pathosystem. To alleviate this gap in knowledge we conducted RNA-seq analysis to obtain the transcriptional profile of mock- and C. miyabeanus-inoculated plants (cultivar Itasca C-12) at 48 hours after inoculation. Single-end cDNA sequencing of multiplexed, 50 bp reads was conducted with an Illumina HiSeq2000. A total of 350 million reads were used as input for the transcriptome-specialized Trinity de-novo assembler, which yielded over 78,000 transcript isoforms with an average length of 681 bp. Transcripts were annotated based on a Blast search against the GenBank non-redundant protein database. Transcripts associated with PAMP-triggered and effector-triggered immunity were identified and analyses to compare gene expression are underway. This assembly constitutes the first comprehensive transcriptome study in wildrice and provides a valuable resource for enhancing disease resistance and other important traits. Transcripts involved in preventing disease progression may be useful in marker development for parent selection in wildrice breeding programs.

Last Modified: 9/23/2014
Footer Content Back to Top of Page