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ARS Home » Midwest Area » East Lansing, Michigan » Sugarbeet and Bean Research » Research » Publications at this Location » Publication #306153

Research Project: Genetic Dissection of Traits for Sugar Beet Improvement

Location: Sugarbeet and Bean Research

Title: Transcriptome of the developing ‘C869’ root

item Galewski, Paul - Michigan State University
item Mcgrath, J Mitchell - Mitch

Submitted to: Annual Beet Sugar Development Foundation Research Report
Publication Type: Research Notes
Publication Acceptance Date: 5/1/2014
Publication Date: 6/1/2014
Citation: Galewski, P., McGrath, J.M. 2014. Transcriptome of the developing 'C869' root. [CD-ROM]. 2013 Annual Beet Sugar Development Foundation Research Report. Denver, Colorado: Beet Sugar Development Foundation.

Interpretive Summary:

Technical Abstract: Transcriptomes were obtained via RNA-seq using Illumina 100 bp paired-end reads from 'C869' at six stages of early season growth; 3-, 4-, 5-, 6- 7-, and 10-weeks after emergence (WAE). Paired-end sequences were aligned and assembled to the 'C869UK_0.1' draft genome sequence and the Tuxedo suite of software tools (Bowtie, TopHat, and Cufflinks), which counts assembled transcripts (expressed as fragments per kilobase of exon per million reads mapped, FPKM). Expression topologies were examined with multi-linear principal components on the entire expression dataset of FPKM expression values. Each WAE was well separated on the first two components, with WAE 3 and WAE 10 very well discriminated, and a general clustering of the intermediate WAE. A Weighted Gene Co-expression Network Analysis analysis suggested 21 gene expression modules implicated in early development of the sugar beet root.