Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus
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Bioinformatics-Based Identification of Candidate Genes from QTLs Associated with Cell Wall Traits in Populus Priya Ranjan & Tongming Yin & Xinye Zhang & Udaya C. Kalluri & Xiaohan Yang & Sara Jawdy & Gerald A. Tuskan Published online: 6 November 2009 # Springer Science + Business Media, LLC. 2009
Abstract Quantitative trait locus (QTL) studies are an integral part of plant research and are used to characterize the genetic basis of phenotypic variation observed in structured populations and inform marker-assisted breeding efforts. These QTL intervals can span large physical regions on a chromosome comprising hundreds of genes, thereby hampering candidate gene identification. Genome history, evolution, and expression evidence can be used to narrow the genes in the interval to a smaller list that is manageable for detailed downstream functional genomics characterization. Our primary motivation for the present study was to address the need for a research methodology that identifies candidate genes within a broad QTL interval. Here we present a bioinformatics-based approach for subdividing candidate genes within QTL intervals into alternate groups of high probability candidates. Application of this approach in the context of studying cell wall traits, specifically lignin content and S/G ratios of stem and root in Populus plants, resulted in manageable sets of genes of both known and putative cell wall biosynthetic function. These results provide a roadmap for future experimental work leading to identification of new genes controlling cell wall recalcitrance and, ultimately, in the utility of plant biomass as an energy feedstock. Electronic supplementary material The online version of this article (doi:10.1007/s12155-009-9060-z) contains supplementary material, which is available to authorized users. P. Ranjan (*) : T. Yin : X. Zhang : U. C. Kalluri : X. Yang : S. Jawdy : G. A. Tuskan Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA e-mail: [email protected] P. Ranjan : T. Yin : X. Zhang : U. C. Kalluri : X. Yang : S. Jawdy : G. A. Tuskan The Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
Keywords Populus . Whole-genome duplication . Quantitative trait loci . Wood chemistry . Syringyl lignin . Guaiacyl lignin . Biofuels Abbreviations QTL Quantitative trait loci S/G Syringyl and guaiacyl ratio RL Root lignin content RSG Root S/G ratio SL Stem lignin content SSG Stem S/G ratio SSR Simple sequence repeats
Introduction Plant biomass has recently been promoted as a source of renewable feedstock for the conversion to liquid transportation fuels [13, 15, 22, 29]. Plant cell walls can be biochemically or thermochemically deconstructed into the primary subcomponents (cellulose, hemicellulose, and lignin) necessary for this conversion [14, 19, 20, 26]. The carbohydrate fractions are used as feedstocks for sugar and ultimately ethanol production, and lignins are typically separated and used in combustion processes to fuel the reactions. The resistance of lig
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