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Bioinformatics Techniques for Understanding and Analyzing Tree Gene Expression Data

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Genomics of Tree Crops

Abstract

There is great interest in enhancing our understanding of the molecular bases of tree biological processes using genomic techniques. One such technique is transcriptional profiling that assays the transcript abundance of thousands of genes. The ­analyses of these inventories of gene expression help explain the genetic diversity of trees and trees’ responses to different developmental stages and environmental conditions. In this chapter, we describe key approaches for collecting transcriptome data and the tree genomic resources available for this data’s use and interpretation. We define the factors that cause gene transcript abundances to vary and elucidate how to quantify these factors’ effects. We also describe approaches to identify co-regulated genes and to assign functions to genes and groups of genes. Finally, we suggest future directions for tree transcriptome analyses.

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Authors and Affiliations

  1. Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON, Canada, N1G2W1

    Lewis Lukens Ph.D. & Gregory Downs B.Sc.

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  1. Lewis Lukens Ph.D.
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  2. Gregory Downs B.Sc.
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Correspondence to Lewis Lukens Ph.D. .

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  1. USDA - ARS, 13601 Old Cutler Road, Miami, 33158, Florida, USA

    R.J. Schnell

  2. of India, Central Experiment Station, Rubber Research Institute, Thompikandom, P.O., Ranni, 689676, Kerala, India

    P.M. Priyadarshan

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Lukens, L., Downs, G. (2012). Bioinformatics Techniques for Understanding and Analyzing Tree Gene Expression Data. In: Schnell, R., Priyadarshan, P. (eds) Genomics of Tree Crops. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-0920-5_2

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