title: High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.
abstract: BACKGROUND
  QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping has been proposed as a cloning tool, and recent advances in high-throughput genotyping and whole-genome resequencing enable marker saturation to levels sufficient for association mapping with no a priori candidate gene selection. Here, multiyear and multienvironment evaluation of cell wall phenotypes was conducted in an interspecific P. trichocarpa x P. deltoides pseudo-backcross mapping pedigree and two partially overlapping populations of unrelated P. trichocarpa genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. QTL mapping was conducted using a high-density genetic map with 3,568 SNP markers. As a fine-mapping approach, chromosome-wide association mapping targeting a QTL hot-spot on linkage group XIV was performed in the two P. trichocarpa populations. Both populations were genotyped using the 34 K Populus Infinium SNP array and whole-genome resequencing of one of the populations facilitated marker-saturation of candidate intervals for gene identification.
  
  
  RESULTS
  Five QTLs ranging in size from 0.6 to 1.8 Mb were mapped on linkage group XIV for lignin content, syringyl to guaiacyl (S/G) ratio, 5- and 6-carbon sugars using the mapping pedigree. Six candidate loci exhibiting significant associations with phenotypes were identified within QTL intervals. These associations were reproducible across multiple environments, two independent genotyping platforms, and different plant growth stages. cDNA sequencing for allelic variants of three of the six loci identified polymorphisms leading to variable length poly glutamine (PolyQ) stretch in a transcription factor annotated as an ANGUSTIFOLIA C-terminus Binding Protein (CtBP) and premature stop codons in a KANADI transcription factor as well as a protein kinase. Results from protoplast transient expression assays suggested that each of the polymorphisms conferred allelic differences in the activation of cellulose, hemicelluloses, and lignin pathway marker genes.
  
  
  CONCLUSIONS
  This study illustrates the utility of complementary QTL and association mapping as tools for gene discovery with no a priori candidate gene selection. This proof of concept in a perennial organism opens up opportunities for discovery of novel genetic determinants of economically important but complex traits in plants.
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. mucherow@ornl.gov.
authors.forename: Wellington
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authors.lastname: Muchero
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jianjun@stanford.edu.|Current address: Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA. jianjun@stanford.edu.
authors.forename: Jianjun
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authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. stephen.difazio@mail.wvu.edu.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: DiFazio
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. chenj@ornl.gov.
authors.forename: Jin-Gui
authors.initials: JG
authors.lastname: Chen
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. ranjanp@ornl.gov.
authors.forename: Priya
authors.initials: P
authors.lastname: Ranjan
authors.affiliation: Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK. gts@aber.ac.uk.
authors.forename: Gancho T
authors.initials: GT
authors.lastname: Slavov
authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. gunterle@ornl.gov.
authors.forename: Lee E
authors.initials: LE
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authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jawdys@ornl.gov.
authors.forename: Sara
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authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. bryanac@ornl.gov.
authors.forename: Anthony C
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authors.affiliation: Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. Robert.Sykes@nrel.gov.
authors.forename: Robert
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authors.affiliation: Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. angelaziebell@hotmail.com.
authors.forename: Angela
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authors.lastname: Ziebell
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. jklapste@mail.ubc.ca.|Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences in Prague, Kamýcká 129, 165 21, Praha 6, Czech Republic. jklapste@mail.ubc.ca.
authors.forename: Jaroslav
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authors.lastname: Klápště
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. porth@mail.ubc.ca.
authors.forename: Ilga
authors.initials: I
authors.lastname: Porth
authors.affiliation: Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. askyba@gmail.com.
authors.forename: Oleksandr
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authors.lastname: Skyba
authors.affiliation: Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. farideu@interchange.ubc.ca.
authors.forename: Faride
authors.initials: F
authors.lastname: Unda
authors.affiliation: Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. y.el-kassaby@ubc.ca.
authors.forename: Yousry A
authors.initials: YA
authors.lastname: El-Kassaby
authors.affiliation: Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. carl.douglas@ubc.ca.
authors.forename: Carl J
authors.initials: CJ
authors.lastname: Douglas
authors.affiliation: Department of Wood Science, Faculty of Forestry, University of British Columbia, Forest Sciences Centre, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada. shawn.mansfield@ubc.ca.
authors.forename: Shawn D
authors.initials: SD
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authors.affiliation: U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. j_martin@lbl.gov.
authors.forename: Joel
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authors.affiliation: U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. WSSchackwitz@lbl.gov.
authors.forename: Wendy
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authors.affiliation: Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. Luke.Evans@mail.wvu.edu.
authors.forename: Luke M
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authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. olaf.czarnecki@gmx.de.
authors.forename: Olaf
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authors.affiliation: BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. tuskanga@ornl.gov.
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mesh_terms: D000483:Alleles; D001483:Base Sequence; D002473:Cell Wall / Q000235:genetics*; D002482:Cellulose / Q000378:metabolism; D002874:Chromosome Mapping; D017343:Genes, Plant; D008040:Genetic Linkage; D005838:Genotype; D008031:Lignin / Q000096:biosynthesis; D008126:Lod Score; D010641:Phenotype; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D032107:Populus / Q000235:genetics*; D040641:Quantitative Trait Loci; D016415:Sequence Alignment; D014157:Transcription Factors / Q000737:chemistry / Q000235:genetics
chemical_list: D010940:Plant Proteins; D014157:Transcription Factors; D002482:Cellulose; D008031:Lignin