High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.
Identifieur interne : 001E37 ( Main/Corpus ); précédent : 001E36; suivant : 001E38High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.
Auteurs : Wellington Muchero ; Jianjun Guo ; Stephen P. Difazio ; Jin-Gui Chen ; Priya Ranjan ; Gancho T. Slavov ; Lee E. Gunter ; Sara Jawdy ; Anthony C. Bryan ; Robert Sykes ; Angela Ziebell ; Jaroslav Klápšt ; Ilga Porth ; Oleksandr Skyba ; Faride Unda ; Yousry A. El-Kassaby ; Carl J. Douglas ; Shawn D. Mansfield ; Joel Martin ; Wendy Schackwitz ; Luke M. Evans ; Olaf Czarnecki ; Gerald A. TuskanSource :
- BMC genomics [ 1471-2164 ] ; 2015.
English descriptors
- KwdEn :
- Alleles (MeSH), Base Sequence (MeSH), Cell Wall (genetics), Cellulose (metabolism), Chromosome Mapping (MeSH), Genes, Plant (MeSH), Genetic Linkage (MeSH), Genotype (MeSH), Lignin (biosynthesis), Lod Score (MeSH), Phenotype (MeSH), Plant Proteins (chemistry), Plant Proteins (genetics), Polymorphism, Single Nucleotide (MeSH), Populus (genetics), Quantitative Trait Loci (MeSH), Sequence Alignment (MeSH), Transcription Factors (chemistry), Transcription Factors (genetics).
- MESH :
- chemical , biosynthesis : Lignin.
- chemical , chemistry : Plant Proteins, Transcription Factors.
- chemical , genetics : Plant Proteins, Transcription Factors.
- chemical , metabolism : Cellulose.
- genetics : Cell Wall, Populus.
- Alleles, Base Sequence, Chromosome Mapping, Genes, Plant, Genetic Linkage, Genotype, Lod Score, Phenotype, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Sequence Alignment.
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.
CONCLUSION
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.
DOI: 10.1186/s12864-015-1215-z
PubMed: 25613058
PubMed Central: PMC4307895
Links to Exploration step
pubmed:25613058Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.</title>
<author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. mucherow@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Guo, Jianjun" sort="Guo, Jianjun" uniqKey="Guo J" first="Jianjun" last="Guo">Jianjun Guo</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jianjun@stanford.edu.</nlm:affiliation>
</affiliation>
<affiliation><nlm:affiliation>Current address: Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA. jianjun@stanford.edu.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name>
<affiliation><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. stephen.difazio@mail.wvu.edu.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. chenj@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. ranjanp@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Slavov, Gancho T" sort="Slavov, Gancho T" uniqKey="Slavov G" first="Gancho T" last="Slavov">Gancho T. Slavov</name>
<affiliation><nlm:affiliation>Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK. gts@aber.ac.uk.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Gunter, Lee E" sort="Gunter, Lee E" uniqKey="Gunter L" first="Lee E" last="Gunter">Lee E. Gunter</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. gunterle@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Jawdy, Sara" sort="Jawdy, Sara" uniqKey="Jawdy S" first="Sara" last="Jawdy">Sara Jawdy</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jawdys@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Bryan, Anthony C" sort="Bryan, Anthony C" uniqKey="Bryan A" first="Anthony C" last="Bryan">Anthony C. Bryan</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. bryanac@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Sykes, Robert" sort="Sykes, Robert" uniqKey="Sykes R" first="Robert" last="Sykes">Robert Sykes</name>
<affiliation><nlm:affiliation>Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. Robert.Sykes@nrel.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Ziebell, Angela" sort="Ziebell, Angela" uniqKey="Ziebell A" first="Angela" last="Ziebell">Angela Ziebell</name>
<affiliation><nlm:affiliation>Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. angelaziebell@hotmail.com.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Klapst, Jaroslav" sort="Klapst, Jaroslav" uniqKey="Klapst J" first="Jaroslav" last="Klápšt">Jaroslav Klápšt</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
<affiliation><nlm:affiliation>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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Porth, Ilga" sort="Porth, Ilga" uniqKey="Porth I" first="Ilga" last="Porth">Ilga Porth</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Skyba, Oleksandr" sort="Skyba, Oleksandr" uniqKey="Skyba O" first="Oleksandr" last="Skyba">Oleksandr Skyba</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Unda, Faride" sort="Unda, Faride" uniqKey="Unda F" first="Faride" last="Unda">Faride Unda</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="El Kassaby, Yousry A" sort="El Kassaby, Yousry A" uniqKey="El Kassaby Y" first="Yousry A" last="El-Kassaby">Yousry A. El-Kassaby</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name>
<affiliation><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. carl.douglas@ubc.ca.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Martin, Joel" sort="Martin, Joel" uniqKey="Martin J" first="Joel" last="Martin">Joel Martin</name>
<affiliation><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. j_martin@lbl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Schackwitz, Wendy" sort="Schackwitz, Wendy" uniqKey="Schackwitz W" first="Wendy" last="Schackwitz">Wendy Schackwitz</name>
<affiliation><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. WSSchackwitz@lbl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Evans, Luke M" sort="Evans, Luke M" uniqKey="Evans L" first="Luke M" last="Evans">Luke M. Evans</name>
<affiliation><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. Luke.Evans@mail.wvu.edu.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Czarnecki, Olaf" sort="Czarnecki, Olaf" uniqKey="Czarnecki O" first="Olaf" last="Czarnecki">Olaf Czarnecki</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. olaf.czarnecki@gmx.de.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. tuskanga@ornl.gov.</nlm:affiliation>
</affiliation>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.</title>
<author><name sortKey="Muchero, Wellington" sort="Muchero, Wellington" uniqKey="Muchero W" first="Wellington" last="Muchero">Wellington Muchero</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. mucherow@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Guo, Jianjun" sort="Guo, Jianjun" uniqKey="Guo J" first="Jianjun" last="Guo">Jianjun Guo</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jianjun@stanford.edu.</nlm:affiliation>
</affiliation>
<affiliation><nlm:affiliation>Current address: Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA. jianjun@stanford.edu.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Difazio, Stephen P" sort="Difazio, Stephen P" uniqKey="Difazio S" first="Stephen P" last="Difazio">Stephen P. Difazio</name>
<affiliation><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. stephen.difazio@mail.wvu.edu.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Chen, Jin Gui" sort="Chen, Jin Gui" uniqKey="Chen J" first="Jin-Gui" last="Chen">Jin-Gui Chen</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. chenj@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Ranjan, Priya" sort="Ranjan, Priya" uniqKey="Ranjan P" first="Priya" last="Ranjan">Priya Ranjan</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. ranjanp@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Slavov, Gancho T" sort="Slavov, Gancho T" uniqKey="Slavov G" first="Gancho T" last="Slavov">Gancho T. Slavov</name>
<affiliation><nlm:affiliation>Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK. gts@aber.ac.uk.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Gunter, Lee E" sort="Gunter, Lee E" uniqKey="Gunter L" first="Lee E" last="Gunter">Lee E. Gunter</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. gunterle@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Jawdy, Sara" sort="Jawdy, Sara" uniqKey="Jawdy S" first="Sara" last="Jawdy">Sara Jawdy</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jawdys@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Bryan, Anthony C" sort="Bryan, Anthony C" uniqKey="Bryan A" first="Anthony C" last="Bryan">Anthony C. Bryan</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. bryanac@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Sykes, Robert" sort="Sykes, Robert" uniqKey="Sykes R" first="Robert" last="Sykes">Robert Sykes</name>
<affiliation><nlm:affiliation>Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. Robert.Sykes@nrel.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Ziebell, Angela" sort="Ziebell, Angela" uniqKey="Ziebell A" first="Angela" last="Ziebell">Angela Ziebell</name>
<affiliation><nlm:affiliation>Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. angelaziebell@hotmail.com.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Klapst, Jaroslav" sort="Klapst, Jaroslav" uniqKey="Klapst J" first="Jaroslav" last="Klápšt">Jaroslav Klápšt</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
<affiliation><nlm:affiliation>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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Porth, Ilga" sort="Porth, Ilga" uniqKey="Porth I" first="Ilga" last="Porth">Ilga Porth</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Skyba, Oleksandr" sort="Skyba, Oleksandr" uniqKey="Skyba O" first="Oleksandr" last="Skyba">Oleksandr Skyba</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Unda, Faride" sort="Unda, Faride" uniqKey="Unda F" first="Faride" last="Unda">Faride Unda</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="El Kassaby, Yousry A" sort="El Kassaby, Yousry A" uniqKey="El Kassaby Y" first="Yousry A" last="El-Kassaby">Yousry A. El-Kassaby</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Douglas, Carl J" sort="Douglas, Carl J" uniqKey="Douglas C" first="Carl J" last="Douglas">Carl J. Douglas</name>
<affiliation><nlm:affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. carl.douglas@ubc.ca.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Mansfield, Shawn D" sort="Mansfield, Shawn D" uniqKey="Mansfield S" first="Shawn D" last="Mansfield">Shawn D. Mansfield</name>
<affiliation><nlm: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.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Martin, Joel" sort="Martin, Joel" uniqKey="Martin J" first="Joel" last="Martin">Joel Martin</name>
<affiliation><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. j_martin@lbl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Schackwitz, Wendy" sort="Schackwitz, Wendy" uniqKey="Schackwitz W" first="Wendy" last="Schackwitz">Wendy Schackwitz</name>
<affiliation><nlm:affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. WSSchackwitz@lbl.gov.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Evans, Luke M" sort="Evans, Luke M" uniqKey="Evans L" first="Luke M" last="Evans">Luke M. Evans</name>
<affiliation><nlm:affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. Luke.Evans@mail.wvu.edu.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Czarnecki, Olaf" sort="Czarnecki, Olaf" uniqKey="Czarnecki O" first="Olaf" last="Czarnecki">Olaf Czarnecki</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. olaf.czarnecki@gmx.de.</nlm:affiliation>
</affiliation>
</author>
<author><name sortKey="Tuskan, Gerald A" sort="Tuskan, Gerald A" uniqKey="Tuskan G" first="Gerald A" last="Tuskan">Gerald A. Tuskan</name>
<affiliation><nlm:affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. tuskanga@ornl.gov.</nlm:affiliation>
</affiliation>
</author>
</analytic>
<series><title level="j">BMC genomics</title>
<idno type="eISSN">1471-2164</idno>
<imprint><date when="2015" type="published">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Alleles (MeSH)</term>
<term>Base Sequence (MeSH)</term>
<term>Cell Wall (genetics)</term>
<term>Cellulose (metabolism)</term>
<term>Chromosome Mapping (MeSH)</term>
<term>Genes, Plant (MeSH)</term>
<term>Genetic Linkage (MeSH)</term>
<term>Genotype (MeSH)</term>
<term>Lignin (biosynthesis)</term>
<term>Lod Score (MeSH)</term>
<term>Phenotype (MeSH)</term>
<term>Plant Proteins (chemistry)</term>
<term>Plant Proteins (genetics)</term>
<term>Polymorphism, Single Nucleotide (MeSH)</term>
<term>Populus (genetics)</term>
<term>Quantitative Trait Loci (MeSH)</term>
<term>Sequence Alignment (MeSH)</term>
<term>Transcription Factors (chemistry)</term>
<term>Transcription Factors (genetics)</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="biosynthesis" xml:lang="en"><term>Lignin</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Plant Proteins</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Plant Proteins</term>
<term>Transcription Factors</term>
</keywords>
<keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Cellulose</term>
</keywords>
<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Cell Wall</term>
<term>Populus</term>
</keywords>
<keywords scheme="MESH" xml:lang="en"><term>Alleles</term>
<term>Base Sequence</term>
<term>Chromosome Mapping</term>
<term>Genes, Plant</term>
<term>Genetic Linkage</term>
<term>Genotype</term>
<term>Lod Score</term>
<term>Phenotype</term>
<term>Polymorphism, Single Nucleotide</term>
<term>Quantitative Trait Loci</term>
<term>Sequence Alignment</term>
</keywords>
</textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p><b>BACKGROUND</b>
</p>
<p>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.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>RESULTS</b>
</p>
<p>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.</p>
</div>
<div type="abstract" xml:lang="en"><p><b>CONCLUSION</b>
</p>
<p>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.</p>
</div>
</front>
</TEI>
<pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25613058</PMID>
<DateCompleted><Year>2016</Year>
<Month>01</Month>
<Day>19</Day>
</DateCompleted>
<DateRevised><Year>2018</Year>
<Month>11</Month>
<Day>13</Day>
</DateRevised>
<Article PubModel="Electronic"><Journal><ISSN IssnType="Electronic">1471-2164</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>16</Volume>
<PubDate><Year>2015</Year>
<Month>Jan</Month>
<Day>23</Day>
</PubDate>
</JournalIssue>
<Title>BMC genomics</Title>
<ISOAbbreviation>BMC Genomics</ISOAbbreviation>
</Journal>
<ArticleTitle>High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus.</ArticleTitle>
<Pagination><MedlinePgn>24</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1186/s12864-015-1215-z</ELocationID>
<Abstract><AbstractText Label="BACKGROUND" NlmCategory="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.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="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.</AbstractText>
<AbstractText Label="CONCLUSION" NlmCategory="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.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Muchero</LastName>
<ForeName>Wellington</ForeName>
<Initials>W</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. mucherow@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Guo</LastName>
<ForeName>Jianjun</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jianjun@stanford.edu.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Current address: Department of Plant Biology, Carnegie Institute for Science, Stanford, CA, 94305, USA. jianjun@stanford.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>DiFazio</LastName>
<ForeName>Stephen P</ForeName>
<Initials>SP</Initials>
<AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. stephen.difazio@mail.wvu.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Chen</LastName>
<ForeName>Jin-Gui</ForeName>
<Initials>JG</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. chenj@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ranjan</LastName>
<ForeName>Priya</ForeName>
<Initials>P</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. ranjanp@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Slavov</LastName>
<ForeName>Gancho T</ForeName>
<Initials>GT</Initials>
<AffiliationInfo><Affiliation>Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, SY23 3EB, UK. gts@aber.ac.uk.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Gunter</LastName>
<ForeName>Lee E</ForeName>
<Initials>LE</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. gunterle@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Jawdy</LastName>
<ForeName>Sara</ForeName>
<Initials>S</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. jawdys@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Bryan</LastName>
<ForeName>Anthony C</ForeName>
<Initials>AC</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. bryanac@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Sykes</LastName>
<ForeName>Robert</ForeName>
<Initials>R</Initials>
<AffiliationInfo><Affiliation>Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. Robert.Sykes@nrel.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Ziebell</LastName>
<ForeName>Angela</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Bioscience Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, CO 80401, USA. angelaziebell@hotmail.com.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Klápště</LastName>
<ForeName>Jaroslav</ForeName>
<Initials>J</Initials>
<AffiliationInfo><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.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>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.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Porth</LastName>
<ForeName>Ilga</ForeName>
<Initials>I</Initials>
<AffiliationInfo><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.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Skyba</LastName>
<ForeName>Oleksandr</ForeName>
<Initials>O</Initials>
<AffiliationInfo><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.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Unda</LastName>
<ForeName>Faride</ForeName>
<Initials>F</Initials>
<AffiliationInfo><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.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>El-Kassaby</LastName>
<ForeName>Yousry A</ForeName>
<Initials>YA</Initials>
<AffiliationInfo><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.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Douglas</LastName>
<ForeName>Carl J</ForeName>
<Initials>CJ</Initials>
<AffiliationInfo><Affiliation>Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada. carl.douglas@ubc.ca.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Mansfield</LastName>
<ForeName>Shawn D</ForeName>
<Initials>SD</Initials>
<AffiliationInfo><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.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Martin</LastName>
<ForeName>Joel</ForeName>
<Initials>J</Initials>
<AffiliationInfo><Affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. j_martin@lbl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Schackwitz</LastName>
<ForeName>Wendy</ForeName>
<Initials>W</Initials>
<AffiliationInfo><Affiliation>U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA. WSSchackwitz@lbl.gov.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Evans</LastName>
<ForeName>Luke M</ForeName>
<Initials>LM</Initials>
<AffiliationInfo><Affiliation>Department of Biology, West Virginia University, Morgantown, WV, 26506, USA. Luke.Evans@mail.wvu.edu.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Czarnecki</LastName>
<ForeName>Olaf</ForeName>
<Initials>O</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. olaf.czarnecki@gmx.de.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Tuskan</LastName>
<ForeName>Gerald A</ForeName>
<Initials>GA</Initials>
<AffiliationInfo><Affiliation>BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. tuskanga@ornl.gov.</Affiliation>
</AffiliationInfo>
</Author>
</AuthorList>
<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
<PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType>
<PublicationType UI="D013486">Research Support, U.S. Gov't, Non-P.H.S.</PublicationType>
</PublicationTypeList>
<ArticleDate DateType="Electronic"><Year>2015</Year>
<Month>01</Month>
<Day>23</Day>
</ArticleDate>
</Article>
<MedlineJournalInfo><Country>England</Country>
<MedlineTA>BMC Genomics</MedlineTA>
<NlmUniqueID>100965258</NlmUniqueID>
<ISSNLinking>1471-2164</ISSNLinking>
</MedlineJournalInfo>
<ChemicalList><Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D010940">Plant Proteins</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>0</RegistryNumber>
<NameOfSubstance UI="D014157">Transcription Factors</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>9004-34-6</RegistryNumber>
<NameOfSubstance UI="D002482">Cellulose</NameOfSubstance>
</Chemical>
<Chemical><RegistryNumber>9005-53-2</RegistryNumber>
<NameOfSubstance UI="D008031">Lignin</NameOfSubstance>
</Chemical>
</ChemicalList>
<CitationSubset>IM</CitationSubset>
<MeshHeadingList><MeshHeading><DescriptorName UI="D000483" MajorTopicYN="N">Alleles</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D001483" MajorTopicYN="N">Base Sequence</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002473" MajorTopicYN="N">Cell Wall</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002482" MajorTopicYN="N">Cellulose</DescriptorName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D002874" MajorTopicYN="N">Chromosome Mapping</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D017343" MajorTopicYN="Y">Genes, Plant</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008040" MajorTopicYN="N">Genetic Linkage</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D005838" MajorTopicYN="N">Genotype</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008031" MajorTopicYN="N">Lignin</DescriptorName>
<QualifierName UI="Q000096" MajorTopicYN="N">biosynthesis</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D008126" MajorTopicYN="N">Lod Score</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010641" MajorTopicYN="N">Phenotype</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D010940" MajorTopicYN="N">Plant Proteins</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D020641" MajorTopicYN="N">Polymorphism, Single Nucleotide</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D032107" MajorTopicYN="N">Populus</DescriptorName>
<QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D040641" MajorTopicYN="N">Quantitative Trait Loci</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D016415" MajorTopicYN="N">Sequence Alignment</DescriptorName>
</MeshHeading>
<MeshHeading><DescriptorName UI="D014157" MajorTopicYN="N">Transcription Factors</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
</MeshHeading>
</MeshHeadingList>
</MedlineCitation>
<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2014</Year>
<Month>04</Month>
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<Month>01</Month>
<Day>02</Day>
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