Genome Resequencing in Populus: Revealing Large-Scale Genome Variation and Implications on Specialized-Trait Genomics
To date, Populus ranks among a few plant species with complete genome sequences and other highly developed genomic resources. With the first reference genome among all tree species, Populus has been adopted as a suitable model organism for genomic studies
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Abstract To date, Populus ranks among a few plant species with complete genome sequences and other highly developed genomic resources. With the first reference genome among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel and fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in biological processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized traits.
W. Muchero (*) • J. Labbé • G.A. Tuskan Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, TN 37831, USA e-mail: [email protected] P. Ranjan University of Tennessee, Knoxville, TN 37916, USA S. DiFazio West Virginia University, Morgantown, VA 26506, USA 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_25, © Springer Science+Business Media Dordrecht 2014
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Introduction
The genus Populus is an economically important tree crop widely grown as feedstock for lignocellulosic biofuels and pulp and paper products, in part, for its rapid growth (Tuskan 1998; Yang et al. 2009) and ability to thrive on economically marginal lands that are not suitable for food crop production (Tuskan and Walsh 2001). Aside from its key importance as an industrial feedstock, Populus is also a biological model system for perennial tree crops due to its relatively compact genome, high level of interspecies diversity and ease of experimental manipulation compared to other tree genera (Tuskan et al. 2006). Given its central role in both economic and scientific realms, substantial investment has been made in developing genomic and genetic resources to facilitate experimental enquiry into the biology of adaptive traits in Populus. These resources include (1) the first reference genome of any tree species (Tuskan et al. 2006), over 900 resequenced P. trichocarpa, a repository of more than 48 million high-quality single nucleotide polymorphism (SNPs), Illumina Infinium SNP arrays with 34,131 and 5,390 SNP probes (Slavov et al. 2012; Geraldes et al. 2013), over 2,200 SSR mar
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