Nucleotide diversity in lignification genes and QTNs for lignin quality in a multi-parental population of Eucalyptus urophylla View Full Text


Ontology type: schema:ScholarlyArticle      Open Access: True


Article Info

DATE

2014-07-03

AUTHORS

Eric Mandrou, Marie Denis, Christophe Plomion, Franck Salin, Frédéric Mortier, Jean-Marc Gion

ABSTRACT

Lignin is a major chemical compound of wood and one of the most abundant organic biopolymers on earth. It accumulates in the secondary cell wall of xylem cells and is a major target for tree breeders because of its foreseen role in the emerging bioeconomy. In this study, we paved the way toward an accelerated domestication of a widely grown tree species, Eucalyptus urophylla, by molecular breeding. To this end, we first described the pattern of nucleotide variation occurring at seven structural and regulatory genes of the lignin biosynthesis pathway and found high levels of average nucleotide and haplotype diversity per gene (π = 0.0065 and Hd = 0.853). Then, taking advantage of a pre-existing factorial mating design, a candidate-gene-based quantitative trait locus (QTL) detection strategy was used to compare the variation of lignin quality (syringyl by guaiacyl ratio (S/G)) with the nucleotidic variability in these seven genes in 304 genotypes belonging to 33 connected full-sib families. Two genes, encoding cinnamoyl-CoA reductase (CCR) and a Rho-like GTPase (ROP1), were shown to be linked to the variation of S/G through different single and multi-locus single-nucleotide polymorphism (SNP)- and haplotype-based association methods. Providing that relevant candidate genes are selected and their patterns of nucleotide diversity is accurately described, we showed that quantitative trait nucleotides (QTNs) can be detected taking advantage of pre-existing field experiments and trait measurements gathered in the framework of a forest tree breeding program. More... »

PAGES

1281-1290

References to SciGraph publications

  • 2002-01-01. Understanding quantitative genetic variation in NATURE REVIEWS GENETICS
  • 2004-05-06. Identification of quantitative trait loci for wood and fibre properties in two full-sib pedigrees of Eucalyptus globulus in THEORETICAL AND APPLIED GENETICS
  • 2013-08-23. Combined linkage and linkage disequilibrium QTL mapping in multiple families of maize (Zea mays L.) line crosses highlights complementarities between models based on parental haplotype and single locus polymorphism in THEORETICAL AND APPLIED GENETICS
  • 2006-04-23. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture in NATURE GENETICS
  • 2011-06-08. Comprehensive genetic dissection of wood properties in a widely-grown tropical tree: Eucalyptus in BMC GENOMICS
  • 2009-05-31. Patterns of DNA sequence variation at candidate gene loci in black poplar (Populus nigra L.) as revealed by single nucleotide polymorphisms in GENETICA
  • 2009-07-01. QTL influencing growth and wood properties in Eucalyptus globulus in TREE GENETICS & GENOMES
  • 2004-03-15. The efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage in GENETICS SELECTION EVOLUTION
  • 2011-12-03. A candidate gene for lignin composition in Eucalyptus: cinnamoyl-CoA reductase (CCR) in TREE GENETICS & GENOMES
  • 2012-06-17. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations in NATURE GENETICS
  • 2008-06-30. High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome in BMC GENOMICS
  • 2007-01-01. Eucalypts in FOREST TREES
  • 2003-09. Sequence variation in two lignin biosynthesis genes, cinnamoyl CoA reductase (CCR) and cinnamyl alcohol dehydrogenase 2 (CAD2) in MOLECULAR BREEDING
  • 2009-09-24. Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways in BMC GENOMICS
  • 2012-04-15. Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus in TREE GENETICS & GENOMES
  • 2005-12-25. A unified mixed-model method for association mapping that accounts for multiple levels of relatedness in NATURE GENETICS
  • 2010-05-22. Quantitative trait locus (QTL) analysis of growth and vegetative propagation traits in Eucalyptus nitens full-sib families in TREE GENETICS & GENOMES
  • 2009-10-07. Contrasting relationships between the diversity of candidate genes and variation of bud burst in natural and segregating populations of European oaks in HEREDITY
  • 2013-03-09. Genetic variation of wood chemical traits and association with underlying genes in Eucalyptus urophylla in TREE GENETICS & GENOMES
  • 2011-08-26. Association mapping for growth, straightness and wood chemistry traits in the Pinus pinaster Aquitaine breeding population in TREE GENETICS & GENOMES
  • 2008-11-18. Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.) in TREE GENETICS & GENOMES
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s11295-014-0760-y

    DOI

    http://dx.doi.org/10.1007/s11295-014-0760-y

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1016112190


    Indexing Status Check whether this publication has been indexed by Scopus and Web Of Science using the SN Indexing Status Tool
    Incoming Citations Browse incoming citations for this publication using opencitations.net

    JSON-LD is the canonical representation for SciGraph data.

    TIP: You can open this SciGraph record using an external JSON-LD service: JSON-LD Playground Google SDTT

    [
      {
        "@context": "https://springernature.github.io/scigraph/jsonld/sgcontext.json", 
        "about": [
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/06", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Biological Sciences", 
            "type": "DefinedTerm"
          }, 
          {
            "id": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France", 
              "id": "http://www.grid.ac/institutes/grid.412041.2", 
              "name": [
                "Centre de Recherche Vallourec, CEV, 59620, Aulnoye-Aymeries, France", 
                "CIRAD, UMR AGAP, Equipe G\u00e9n\u00e9tique et Am\u00e9lioration des Esp\u00e8ces P\u00e9rennes: Mod\u00e8les For\u00eat et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France", 
                "INRA, UMR 1202 BIOGECO, 69 route d\u2019Arcachon, 33610, Cestas, France", 
                "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mandrou", 
            "givenName": "Eric", 
            "id": "sg:person.0743150654.55", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0743150654.55"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "CIRAD, UMR AGAP, Equipe G\u00e9n\u00e9tique et Am\u00e9lioration des Esp\u00e8ces P\u00e9rennes: Mod\u00e8les For\u00eat et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France", 
              "id": "http://www.grid.ac/institutes/grid.8183.2", 
              "name": [
                "CIRAD, UMR AGAP, Equipe G\u00e9n\u00e9tique et Am\u00e9lioration des Esp\u00e8ces P\u00e9rennes: Mod\u00e8les For\u00eat et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Denis", 
            "givenName": "Marie", 
            "id": "sg:person.0605571370.10", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0605571370.10"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France", 
              "id": "http://www.grid.ac/institutes/grid.412041.2", 
              "name": [
                "INRA, UMR 1202 BIOGECO, 69 route d\u2019Arcachon, 33610, Cestas, France", 
                "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Plomion", 
            "givenName": "Christophe", 
            "id": "sg:person.0666701026.90", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666701026.90"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France", 
              "id": "http://www.grid.ac/institutes/grid.412041.2", 
              "name": [
                "INRA, UMR 1202 BIOGECO, 69 route d\u2019Arcachon, 33610, Cestas, France", 
                "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Salin", 
            "givenName": "Franck", 
            "id": "sg:person.0627256573.57", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627256573.57"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "CIRAD, UR B&SEF, Biens et Services des Ecosyst\u00e8mes Forestiers et Tropicaux, Campus International de Baillarguet, TA C-105/D, 34398, Montpellier, France", 
              "id": "http://www.grid.ac/institutes/grid.8183.2", 
              "name": [
                "CIRAD, UR B&SEF, Biens et Services des Ecosyst\u00e8mes Forestiers et Tropicaux, Campus International de Baillarguet, TA C-105/D, 34398, Montpellier, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Mortier", 
            "givenName": "Fr\u00e9d\u00e9ric", 
            "id": "sg:person.011005525522.35", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011005525522.35"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France", 
              "id": "http://www.grid.ac/institutes/grid.412041.2", 
              "name": [
                "CIRAD, UMR AGAP, Equipe G\u00e9n\u00e9tique et Am\u00e9lioration des Esp\u00e8ces P\u00e9rennes: Mod\u00e8les For\u00eat et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France", 
                "INRA, UMR 1202 BIOGECO, 69 route d\u2019Arcachon, 33610, Cestas, France", 
                "Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Gion", 
            "givenName": "Jean-Marc", 
            "id": "sg:person.01015124413.32", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015124413.32"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "sg:pub.10.1007/s11295-011-0426-y", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012862469", 
              "https://doi.org/10.1007/s11295-011-0426-y"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-008-0188-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024144974", 
              "https://doi.org/10.1007/s11295-008-0188-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-011-0446-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039097214", 
              "https://doi.org/10.1007/s11295-011-0446-7"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-10-452", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046303245", 
              "https://doi.org/10.1186/1471-2164-10-452"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1297-9686-36-2-145", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1050116004", 
              "https://doi.org/10.1186/1297-9686-36-2-145"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s10709-009-9371-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023077813", 
              "https://doi.org/10.1007/s10709-009-9371-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-9-312", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010043397", 
              "https://doi.org/10.1186/1471-2164-9-312"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nrg700", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040916543", 
              "https://doi.org/10.1038/nrg700"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1023/a:1026006828721", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1012933175", 
              "https://doi.org/10.1023/a:1026006828721"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng1784", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1039398234", 
              "https://doi.org/10.1038/ng1784"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-009-0222-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006308641", 
              "https://doi.org/10.1007/s11295-009-0222-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-004-1699-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003377219", 
              "https://doi.org/10.1007/s00122-004-1699-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/978-3-540-34541-1_4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023669854", 
              "https://doi.org/10.1007/978-3-540-34541-1_4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-013-2167-9", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1019430072", 
              "https://doi.org/10.1007/s00122-013-2167-9"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng.2314", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1007536029", 
              "https://doi.org/10.1038/ng.2314"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-013-0606-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037803135", 
              "https://doi.org/10.1007/s11295-013-0606-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/ng1702", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1035781360", 
              "https://doi.org/10.1038/ng1702"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-010-0298-6", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021730629", 
              "https://doi.org/10.1007/s11295-010-0298-6"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/hdy.2009.134", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1008985819", 
              "https://doi.org/10.1038/hdy.2009.134"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-12-301", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023586428", 
              "https://doi.org/10.1186/1471-2164-12-301"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11295-012-0491-x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1010153501", 
              "https://doi.org/10.1007/s11295-012-0491-x"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2014-07-03", 
        "datePublishedReg": "2014-07-03", 
        "description": "Lignin is a major chemical compound of wood and one of the most abundant organic biopolymers on earth. It accumulates in the secondary cell wall of xylem cells and is a major target for tree breeders because of its foreseen role in the emerging bioeconomy. In this study, we paved the way toward an accelerated domestication of a widely grown tree species, Eucalyptus urophylla, by molecular breeding. To this end, we first described the pattern of nucleotide variation occurring at seven structural and regulatory genes of the lignin biosynthesis pathway and found high levels of average nucleotide and haplotype diversity per gene (\u03c0\u2009=\u20090.0065 and Hd\u2009=\u20090.853). Then, taking advantage of a pre-existing factorial mating design, a candidate-gene-based quantitative trait locus (QTL) detection strategy was used to compare the variation of lignin quality (syringyl by guaiacyl ratio (S/G)) with the nucleotidic variability in these seven genes in 304 genotypes belonging to 33 connected full-sib families. Two genes, encoding cinnamoyl-CoA reductase (CCR) and a Rho-like GTPase (ROP1), were shown to be linked to the variation of S/G through different single and multi-locus single-nucleotide polymorphism (SNP)- and haplotype-based association methods. Providing that relevant candidate genes are selected and their patterns of nucleotide diversity is accurately described, we showed that quantitative trait nucleotides (QTNs) can be detected taking advantage of pre-existing field experiments and trait measurements gathered in the framework of a forest tree breeding program.", 
        "genre": "article", 
        "id": "sg:pub.10.1007/s11295-014-0760-y", 
        "inLanguage": "en", 
        "isAccessibleForFree": true, 
        "isPartOf": [
          {
            "id": "sg:journal.1036007", 
            "issn": [
              "1614-2942", 
              "1614-2950"
            ], 
            "name": "Tree Genetics & Genomes", 
            "publisher": "Springer Nature", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "5", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "10"
          }
        ], 
        "keywords": [
          "quantitative trait nucleotides", 
          "cinnamoyl-CoA reductase", 
          "Eucalyptus urophylla", 
          "forest tree breeding programs", 
          "nucleotide diversity", 
          "lignin quality", 
          "tree breeding programs", 
          "multi-parental populations", 
          "factorial mating design", 
          "haplotype-based association methods", 
          "full-sib families", 
          "Rho-like GTPase", 
          "lignin biosynthesis pathway", 
          "secondary cell walls", 
          "accelerated domestication", 
          "tree breeders", 
          "breeding programs", 
          "molecular breeding", 
          "mating design", 
          "relevant candidate genes", 
          "tree species", 
          "field experiment", 
          "lignification genes", 
          "haplotype diversity", 
          "average nucleotide", 
          "biosynthesis pathway", 
          "regulatory genes", 
          "single nucleotide polymorphisms", 
          "xylem cells", 
          "nucleotide variations", 
          "candidate genes", 
          "cell wall", 
          "urophylla", 
          "major chemical compounds", 
          "genes", 
          "diversity", 
          "major target", 
          "nucleotides", 
          "breeding", 
          "breeders", 
          "domestication", 
          "chemical compounds", 
          "genotypes", 
          "GTPase", 
          "association method", 
          "bioeconomy", 
          "wood", 
          "species", 
          "SNPs", 
          "reductase", 
          "variation", 
          "high levels", 
          "organic biopolymers", 
          "pathway", 
          "quality", 
          "polymorphism", 
          "cells", 
          "lignin", 
          "family", 
          "patterns", 
          "variability", 
          "target", 
          "population", 
          "role", 
          "experiments", 
          "program", 
          "strategies", 
          "levels", 
          "compounds", 
          "wall", 
          "biopolymers", 
          "advantages", 
          "study", 
          "detection strategy", 
          "end", 
          "Earth", 
          "design", 
          "way", 
          "method", 
          "measurements", 
          "framework"
        ], 
        "name": "Nucleotide diversity in lignification genes and QTNs for lignin quality in a multi-parental population of Eucalyptus urophylla", 
        "pagination": "1281-1290", 
        "productId": [
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1016112190"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s11295-014-0760-y"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s11295-014-0760-y", 
          "https://app.dimensions.ai/details/publication/pub.1016112190"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2022-06-01T22:14", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-springernature-scigraph/baseset/20220601/entities/gbq_results/article/article_643.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "https://doi.org/10.1007/s11295-014-0760-y"
      }
    ]
     

    Download the RDF metadata as:  json-ld nt turtle xml License info

    HOW TO GET THIS DATA PROGRAMMATICALLY:

    JSON-LD is a popular format for linked data which is fully compatible with JSON.

    curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/s11295-014-0760-y'

    N-Triples is a line-based linked data format ideal for batch operations.

    curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/s11295-014-0760-y'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s11295-014-0760-y'

    RDF/XML is a standard XML format for linked data.

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s11295-014-0760-y'


     

    This table displays all metadata directly associated to this object as RDF triples.

    266 TRIPLES      22 PREDICATES      127 URIs      98 LITERALS      6 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s11295-014-0760-y schema:about anzsrc-for:06
    2 anzsrc-for:0604
    3 schema:author N895d1c15ebd549bca4d378c239763818
    4 schema:citation sg:pub.10.1007/978-3-540-34541-1_4
    5 sg:pub.10.1007/s00122-004-1699-4
    6 sg:pub.10.1007/s00122-013-2167-9
    7 sg:pub.10.1007/s10709-009-9371-1
    8 sg:pub.10.1007/s11295-008-0188-3
    9 sg:pub.10.1007/s11295-009-0222-0
    10 sg:pub.10.1007/s11295-010-0298-6
    11 sg:pub.10.1007/s11295-011-0426-y
    12 sg:pub.10.1007/s11295-011-0446-7
    13 sg:pub.10.1007/s11295-012-0491-x
    14 sg:pub.10.1007/s11295-013-0606-z
    15 sg:pub.10.1023/a:1026006828721
    16 sg:pub.10.1038/hdy.2009.134
    17 sg:pub.10.1038/ng.2314
    18 sg:pub.10.1038/ng1702
    19 sg:pub.10.1038/ng1784
    20 sg:pub.10.1038/nrg700
    21 sg:pub.10.1186/1297-9686-36-2-145
    22 sg:pub.10.1186/1471-2164-10-452
    23 sg:pub.10.1186/1471-2164-12-301
    24 sg:pub.10.1186/1471-2164-9-312
    25 schema:datePublished 2014-07-03
    26 schema:datePublishedReg 2014-07-03
    27 schema:description Lignin is a major chemical compound of wood and one of the most abundant organic biopolymers on earth. It accumulates in the secondary cell wall of xylem cells and is a major target for tree breeders because of its foreseen role in the emerging bioeconomy. In this study, we paved the way toward an accelerated domestication of a widely grown tree species, Eucalyptus urophylla, by molecular breeding. To this end, we first described the pattern of nucleotide variation occurring at seven structural and regulatory genes of the lignin biosynthesis pathway and found high levels of average nucleotide and haplotype diversity per gene (π = 0.0065 and Hd = 0.853). Then, taking advantage of a pre-existing factorial mating design, a candidate-gene-based quantitative trait locus (QTL) detection strategy was used to compare the variation of lignin quality (syringyl by guaiacyl ratio (S/G)) with the nucleotidic variability in these seven genes in 304 genotypes belonging to 33 connected full-sib families. Two genes, encoding cinnamoyl-CoA reductase (CCR) and a Rho-like GTPase (ROP1), were shown to be linked to the variation of S/G through different single and multi-locus single-nucleotide polymorphism (SNP)- and haplotype-based association methods. Providing that relevant candidate genes are selected and their patterns of nucleotide diversity is accurately described, we showed that quantitative trait nucleotides (QTNs) can be detected taking advantage of pre-existing field experiments and trait measurements gathered in the framework of a forest tree breeding program.
    28 schema:genre article
    29 schema:inLanguage en
    30 schema:isAccessibleForFree true
    31 schema:isPartOf N650b332e751f4e1295a665dca764159d
    32 N8c784f8d5e7d46a39dba112b7c557e65
    33 sg:journal.1036007
    34 schema:keywords Earth
    35 Eucalyptus urophylla
    36 GTPase
    37 Rho-like GTPase
    38 SNPs
    39 accelerated domestication
    40 advantages
    41 association method
    42 average nucleotide
    43 bioeconomy
    44 biopolymers
    45 biosynthesis pathway
    46 breeders
    47 breeding
    48 breeding programs
    49 candidate genes
    50 cell wall
    51 cells
    52 chemical compounds
    53 cinnamoyl-CoA reductase
    54 compounds
    55 design
    56 detection strategy
    57 diversity
    58 domestication
    59 end
    60 experiments
    61 factorial mating design
    62 family
    63 field experiment
    64 forest tree breeding programs
    65 framework
    66 full-sib families
    67 genes
    68 genotypes
    69 haplotype diversity
    70 haplotype-based association methods
    71 high levels
    72 levels
    73 lignification genes
    74 lignin
    75 lignin biosynthesis pathway
    76 lignin quality
    77 major chemical compounds
    78 major target
    79 mating design
    80 measurements
    81 method
    82 molecular breeding
    83 multi-parental populations
    84 nucleotide diversity
    85 nucleotide variations
    86 nucleotides
    87 organic biopolymers
    88 pathway
    89 patterns
    90 polymorphism
    91 population
    92 program
    93 quality
    94 quantitative trait nucleotides
    95 reductase
    96 regulatory genes
    97 relevant candidate genes
    98 role
    99 secondary cell walls
    100 single nucleotide polymorphisms
    101 species
    102 strategies
    103 study
    104 target
    105 tree breeders
    106 tree breeding programs
    107 tree species
    108 urophylla
    109 variability
    110 variation
    111 wall
    112 way
    113 wood
    114 xylem cells
    115 schema:name Nucleotide diversity in lignification genes and QTNs for lignin quality in a multi-parental population of Eucalyptus urophylla
    116 schema:pagination 1281-1290
    117 schema:productId Nac479beb4628417ebd20e37b717d2956
    118 Nb9f4135bc53c4020a215786767dd81e4
    119 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016112190
    120 https://doi.org/10.1007/s11295-014-0760-y
    121 schema:sdDatePublished 2022-06-01T22:14
    122 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    123 schema:sdPublisher N2fd108cea4f346fa898a28408043b569
    124 schema:url https://doi.org/10.1007/s11295-014-0760-y
    125 sgo:license sg:explorer/license/
    126 sgo:sdDataset articles
    127 rdf:type schema:ScholarlyArticle
    128 N2fd108cea4f346fa898a28408043b569 schema:name Springer Nature - SN SciGraph project
    129 rdf:type schema:Organization
    130 N3c713a39af524660a92359182438dd72 rdf:first sg:person.0666701026.90
    131 rdf:rest N7ab813bc5a57462d9d11c3d10afa5b5f
    132 N650b332e751f4e1295a665dca764159d schema:volumeNumber 10
    133 rdf:type schema:PublicationVolume
    134 N7ab813bc5a57462d9d11c3d10afa5b5f rdf:first sg:person.0627256573.57
    135 rdf:rest N918d58aa48224e9fa12a30e6cead0413
    136 N883746db88f94ed29f8ce4c18d867e83 rdf:first sg:person.0605571370.10
    137 rdf:rest N3c713a39af524660a92359182438dd72
    138 N895d1c15ebd549bca4d378c239763818 rdf:first sg:person.0743150654.55
    139 rdf:rest N883746db88f94ed29f8ce4c18d867e83
    140 N8c784f8d5e7d46a39dba112b7c557e65 schema:issueNumber 5
    141 rdf:type schema:PublicationIssue
    142 N918d58aa48224e9fa12a30e6cead0413 rdf:first sg:person.011005525522.35
    143 rdf:rest Ne8280dd8b6f74af9aabdbdb5514dbd9d
    144 Nac479beb4628417ebd20e37b717d2956 schema:name dimensions_id
    145 schema:value pub.1016112190
    146 rdf:type schema:PropertyValue
    147 Nb9f4135bc53c4020a215786767dd81e4 schema:name doi
    148 schema:value 10.1007/s11295-014-0760-y
    149 rdf:type schema:PropertyValue
    150 Ne8280dd8b6f74af9aabdbdb5514dbd9d rdf:first sg:person.01015124413.32
    151 rdf:rest rdf:nil
    152 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    153 schema:name Biological Sciences
    154 rdf:type schema:DefinedTerm
    155 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    156 schema:name Genetics
    157 rdf:type schema:DefinedTerm
    158 sg:journal.1036007 schema:issn 1614-2942
    159 1614-2950
    160 schema:name Tree Genetics & Genomes
    161 schema:publisher Springer Nature
    162 rdf:type schema:Periodical
    163 sg:person.01015124413.32 schema:affiliation grid-institutes:grid.412041.2
    164 schema:familyName Gion
    165 schema:givenName Jean-Marc
    166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01015124413.32
    167 rdf:type schema:Person
    168 sg:person.011005525522.35 schema:affiliation grid-institutes:grid.8183.2
    169 schema:familyName Mortier
    170 schema:givenName Frédéric
    171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011005525522.35
    172 rdf:type schema:Person
    173 sg:person.0605571370.10 schema:affiliation grid-institutes:grid.8183.2
    174 schema:familyName Denis
    175 schema:givenName Marie
    176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0605571370.10
    177 rdf:type schema:Person
    178 sg:person.0627256573.57 schema:affiliation grid-institutes:grid.412041.2
    179 schema:familyName Salin
    180 schema:givenName Franck
    181 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0627256573.57
    182 rdf:type schema:Person
    183 sg:person.0666701026.90 schema:affiliation grid-institutes:grid.412041.2
    184 schema:familyName Plomion
    185 schema:givenName Christophe
    186 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0666701026.90
    187 rdf:type schema:Person
    188 sg:person.0743150654.55 schema:affiliation grid-institutes:grid.412041.2
    189 schema:familyName Mandrou
    190 schema:givenName Eric
    191 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0743150654.55
    192 rdf:type schema:Person
    193 sg:pub.10.1007/978-3-540-34541-1_4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023669854
    194 https://doi.org/10.1007/978-3-540-34541-1_4
    195 rdf:type schema:CreativeWork
    196 sg:pub.10.1007/s00122-004-1699-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003377219
    197 https://doi.org/10.1007/s00122-004-1699-4
    198 rdf:type schema:CreativeWork
    199 sg:pub.10.1007/s00122-013-2167-9 schema:sameAs https://app.dimensions.ai/details/publication/pub.1019430072
    200 https://doi.org/10.1007/s00122-013-2167-9
    201 rdf:type schema:CreativeWork
    202 sg:pub.10.1007/s10709-009-9371-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023077813
    203 https://doi.org/10.1007/s10709-009-9371-1
    204 rdf:type schema:CreativeWork
    205 sg:pub.10.1007/s11295-008-0188-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024144974
    206 https://doi.org/10.1007/s11295-008-0188-3
    207 rdf:type schema:CreativeWork
    208 sg:pub.10.1007/s11295-009-0222-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006308641
    209 https://doi.org/10.1007/s11295-009-0222-0
    210 rdf:type schema:CreativeWork
    211 sg:pub.10.1007/s11295-010-0298-6 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021730629
    212 https://doi.org/10.1007/s11295-010-0298-6
    213 rdf:type schema:CreativeWork
    214 sg:pub.10.1007/s11295-011-0426-y schema:sameAs https://app.dimensions.ai/details/publication/pub.1012862469
    215 https://doi.org/10.1007/s11295-011-0426-y
    216 rdf:type schema:CreativeWork
    217 sg:pub.10.1007/s11295-011-0446-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039097214
    218 https://doi.org/10.1007/s11295-011-0446-7
    219 rdf:type schema:CreativeWork
    220 sg:pub.10.1007/s11295-012-0491-x schema:sameAs https://app.dimensions.ai/details/publication/pub.1010153501
    221 https://doi.org/10.1007/s11295-012-0491-x
    222 rdf:type schema:CreativeWork
    223 sg:pub.10.1007/s11295-013-0606-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1037803135
    224 https://doi.org/10.1007/s11295-013-0606-z
    225 rdf:type schema:CreativeWork
    226 sg:pub.10.1023/a:1026006828721 schema:sameAs https://app.dimensions.ai/details/publication/pub.1012933175
    227 https://doi.org/10.1023/a:1026006828721
    228 rdf:type schema:CreativeWork
    229 sg:pub.10.1038/hdy.2009.134 schema:sameAs https://app.dimensions.ai/details/publication/pub.1008985819
    230 https://doi.org/10.1038/hdy.2009.134
    231 rdf:type schema:CreativeWork
    232 sg:pub.10.1038/ng.2314 schema:sameAs https://app.dimensions.ai/details/publication/pub.1007536029
    233 https://doi.org/10.1038/ng.2314
    234 rdf:type schema:CreativeWork
    235 sg:pub.10.1038/ng1702 schema:sameAs https://app.dimensions.ai/details/publication/pub.1035781360
    236 https://doi.org/10.1038/ng1702
    237 rdf:type schema:CreativeWork
    238 sg:pub.10.1038/ng1784 schema:sameAs https://app.dimensions.ai/details/publication/pub.1039398234
    239 https://doi.org/10.1038/ng1784
    240 rdf:type schema:CreativeWork
    241 sg:pub.10.1038/nrg700 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040916543
    242 https://doi.org/10.1038/nrg700
    243 rdf:type schema:CreativeWork
    244 sg:pub.10.1186/1297-9686-36-2-145 schema:sameAs https://app.dimensions.ai/details/publication/pub.1050116004
    245 https://doi.org/10.1186/1297-9686-36-2-145
    246 rdf:type schema:CreativeWork
    247 sg:pub.10.1186/1471-2164-10-452 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046303245
    248 https://doi.org/10.1186/1471-2164-10-452
    249 rdf:type schema:CreativeWork
    250 sg:pub.10.1186/1471-2164-12-301 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023586428
    251 https://doi.org/10.1186/1471-2164-12-301
    252 rdf:type schema:CreativeWork
    253 sg:pub.10.1186/1471-2164-9-312 schema:sameAs https://app.dimensions.ai/details/publication/pub.1010043397
    254 https://doi.org/10.1186/1471-2164-9-312
    255 rdf:type schema:CreativeWork
    256 grid-institutes:grid.412041.2 schema:alternateName Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France
    257 schema:name CIRAD, UMR AGAP, Equipe Génétique et Amélioration des Espèces Pérennes: Modèles Forêt et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France
    258 Centre de Recherche Vallourec, CEV, 59620, Aulnoye-Aymeries, France
    259 INRA, UMR 1202 BIOGECO, 69 route d’Arcachon, 33610, Cestas, France
    260 Univ. Bordeaux, UMR 1202 BIOGECO, 33400, Talence, France
    261 rdf:type schema:Organization
    262 grid-institutes:grid.8183.2 schema:alternateName CIRAD, UMR AGAP, Equipe Génétique et Amélioration des Espèces Pérennes: Modèles Forêt et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France
    263 CIRAD, UR B&SEF, Biens et Services des Ecosystèmes Forestiers et Tropicaux, Campus International de Baillarguet, TA C-105/D, 34398, Montpellier, France
    264 schema:name CIRAD, UMR AGAP, Equipe Génétique et Amélioration des Espèces Pérennes: Modèles Forêt et Palmier, Campus International de Baillarguet, TA A-39/C, Montpellier CEDEX 5, France
    265 CIRAD, UR B&SEF, Biens et Services des Ecosystèmes Forestiers et Tropicaux, Campus International de Baillarguet, TA C-105/D, 34398, Montpellier, France
    266 rdf:type schema:Organization
     




    Preview window. Press ESC to close (or click here)


    ...