Comparative and Evolutionary Genomics of Forest Trees
Comparative and evolutionary genomic approaches can identify genes regulating biological processes, and describe how those genes have been modified through speciation to produce phenotypic variation. These approaches have the potential to address fundamen
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Abstract Comparative and evolutionary genomic approaches can identify genes regulating biological processes, and describe how those genes have been modified through speciation to produce phenotypic variation. These approaches have the potential to address fundamental issues of forest biology, including the regulation of biological traits important to industry and conservation, but have not been widely applied because of technical limitations. Here, we argue that powerful “next generation” DNA sequencing technologies now make comparative and evolutionary genomic approaches not only tractable for basic biological research in trees, but also have the potential to be more informative and cost effective than traditional, one-species-at-a-time approaches. However, designing effective comparative studies for forest trees requires careful consideration of the evolutionary relationships of tree species and biological traits important to forest biology. This chapter first provides an introduction to comparative and evolutionary genomics, followed by a brief review of some of the general features of the evolution and diversification of forest tree species. Next, two biological processes are discussed that are fundamental to forest trees: wood formation and perennial growth. We examine the varied evolutionary histories of these biological processes, and how these histories relate to the comparative genomic approaches used to research the genes and mechanisms underlying these processes. The chapter is concluded with discussion of practical issues that must be addressed to fully enable this new and powerful direction in forest genomics research, as well as how comparative genomics could support future research and applications for forest management.
A. Groover (*) USDA, Davis, CA 95618, USA e-mail: [email protected] S. Jansson Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, 901 87, Umeå, Sweden e-mail: [email protected] T. Fenning (ed.), Challenges and Opportunities for the World’s Forests in the 21st Century, Forestry Sciences 81, DOI 10.1007/978-94-007-7076-8_26, © US Government 2014
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A. Groover and S. Jansson
Introduction
Forest trees are defined by practical attributes, typically as woody perennial plants with a primary stem of some minimum height. The majority of forest trees share additional attributes. Forest trees typically go through a period of juvenility before undergoing phase change and becoming sexually mature. Forest trees tend to be highly out crossing, genetically heterozygous, and suffer from inbreeding depression. And forest trees are largely undomesticated. Forest trees do not represent a monophyletic group of plants, however. Tree-like growth has been gained and lost in different seed plant lineages, and extant forest trees can be found among various gymnosperm and angiosperm taxa (Groover 2005; Spicer and Groover 2010). This situation raises important considerations for research aimed at understanding growth and development of the large number of taxonomical
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