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.
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References
Abraham P, Adams R, Giannone R, Kalluri U, Ranjan P, Erickson B, Shah M, Tuskan G, Hettich R (2012) Defining the boundaries and characterizing the landscape of functional genome expression in vascular tissues of Populus using shotgun proteomics. J Proteome Res 11(1):449–460
Cao J, Schneeberger K, Ossowski S, Günther T, Bender S et al (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43:956–963
Geraldes A, DiFazio S, Slavov GT, Priya R, Muchero W et al (2013) A 34K SNP genotyping array for Populus trichocarpa (black cottonwood): design, application to the study of natural populations and transferability to other Populus. Molecular Ecology Resources 13(2):306–323
Induri BR, Ellis DR, Slavov GT, Yin T, Zhang X, Muchero W, Tuskan GA, DiFazio SP (2012) Identification of Quantitative Trait Loci (QTL) and candidate genes for cadmium tolerance in Populus. Tree Physiol 32(5):626–638
Iwano M, Takayama S (2012) Self/non-self discrimination in angiosperm self-incompatibility. Curr Opin Plant Biol 15:78–83
Kereszt A, Kondorosi E (2011) Unlocking the door to invasion. Science 331:865–866
Labbé J, Jorge V, Kohler A, Vion P, Marçais B, Bastien C, Tuskan GA, Martin F, Le Tacon F (2011) Identification of quantitative trait loci affecting ectomycorrhizal symbiosis in an interspecific F1 poplar cross and differential expression of genes in ectomycorrhizas of the two parents: Populus deltoides and Populus trichocarpa. Tree Genet Genom 7:617–627
Muchero W, Sewell MM, Ranjan P, Gunter LE, Tschaplinski TJ, Yin T, Tuskan GA (2013) Genome anchored QTLs for biomass productivity in Hybrid Populus grown under contrasting environments. PLoS ONE 8(1):e54468
Rodgers-Melnick E, Mane SP, Dharmawardhana P, Slavov GT, Crasta OR, Strauss SH, Brunner AM, DiFazio SP (2012) Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus. Genome Res 22:95–105
Schwessinger B, Ronald PC (2012) Plant innate immunity: perception of conserved microbial signatures. Annu Rev Plant Biol 63:451–482
Slavov GT, DiFazio SP, Martin J, Schackwitz W, Muchero W et al (2012) Genome resequencing reveals multiscale geographic structure and extensive linkage disequilibrium in the forest tree Populus trichocarpa. New Phytologist 196(3):713–725. doi:10.1111/j.1469-8137.2012.04258.x
Tagu D, Rampant PF, Lapeyrie F, Frey-Klett P, Vion P, Villar M (2001) Variation in the ability to form ectomycorrhizas in the F1 of an interspecific poplar (Populus spp.) cross. Mycorrhiza 10:237–240
Tuskan GA (1998) Short-rotation forestry: what we know and what we need to know. Biomass Bioenergy 14(4):307–315
Tuskan GA, Walsh M (2001) Short-rotation woody crop systems, atmospheric carbon dioxide and carbon management. For Chron 77:259–264
Tuskan GA et al (2006) The genome of black cottonwood, Populus trichocarpa (Torr & Gray). Science 313:1596–1604
Yang X, Kalluri UC, DiFazio SP, Wullschleger SD, Tschaplinski TJ, Cheng Z-M, Tuskan GA (2009) Poplar genomics: state of the science. Crit Rev Plant Sci 28:285–308
Acknowledgements
This work was supported, in part, by the BioEnergy Science Center and by the Office of Science, Biological and Environmental Research (BER), as part of the Plant Microbe Interfaces Scientific Focus Area at Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Dept. of Energy under contract DE-AC05-00OR22725. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. No additional external funding received for this study.
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Muchero, W., Labbé, J., Ranjan, P., DiFazio, S., Tuskan, G.A. (2014). Genome Resequencing in Populus: Revealing Large-Scale Genome Variation and Implications on Specialized-Trait Genomics. In: Fenning, T. (eds) Challenges and Opportunities for the World's Forests in the 21st Century. Forestry Sciences, vol 81. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-7076-8_25
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