South Dakota State University, USA
Posters-Accepted Abstracts: J Fundam Renewable Energy Appl
Substantial efforts have been invested in the past two decades into identification of plant cell-wall (PCW) related genes in several genomes such as Arabidopsis thaliana, Oryza sativa (rice) and Zea mays (maize) having led to large pools of predicted PCW genes in these organisms. However, no such gene list has been identified in the bioenergy crop switchgrass (Panicum virgatum). Here we present a computational study for prediction of PCW genes in switchgrass using a two-step procedure: Homology mapping of all annotated PCW genes in these three organisms to switchgrass, giving rise to the initial list of 991 genes and candidate selection from the 991 mapped genes based on co-expression analyses of transcriptomic which leads to the identification of 104 large groups of co-expressed genes each under a sufficiently large number of conditions referred to as co-expression modules (CEMs) which cover 830 genes and represent our initial PCW genes in switchgrass. We then extended this co-expression analysis to include all the switchgrass genes and found additional 847 genes that are strongly co-expressed with some of the 104 CEMs, hence also predicted as PCW genes, 123 of the predicted genes are homologous to predicted PCW genes in Arabidopsis.
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