Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world View Full Text


Ontology type: schema:ScholarlyArticle     


Article Info

DATE

2015-09

AUTHORS

Kenji Fujino, Mari Obara, Tomohito Ikegaya, Kenichi Tamura

ABSTRACT

The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions. More... »

PAGES

1739-1746

References to SciGraph publications

  • 2005-07. Mapping of QTLs conferring extremely early heading in rice (Oryza sativa L.) in THEORETICAL AND APPLIED GENETICS
  • 2005-08. The map-based sequence of the rice genome in NATURE
  • 2005-01. Assessing temporal changes in genetic diversity of maize varieties using microsatellite markers in THEORETICAL AND APPLIED GENETICS
  • 2014-04. Historical changes in population structure during rice breeding programs in the northern limits of rice cultivation in THEORETICAL AND APPLIED GENETICS
  • 2004-03. Mapping of quantitative trait loci controlling low-temperature germinability in rice (Oryza sativa L.) in THEORETICAL AND APPLIED GENETICS
  • 2011-11. Selection for low-temperature germinability on the short arm of chromosome 3 in rice cultivars adapted to Hokkaido, Japan in THEORETICAL AND APPLIED GENETICS
  • 2005-06. SSR allelic diversity changes in 480 European bread wheat varieties released from 1840 to 2000 in THEORETICAL AND APPLIED GENETICS
  • 2010-06. Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice in THEORETICAL AND APPLIED GENETICS
  • 2005-04. Identification of an active transposon in intact rice plants in MOLECULAR GENETICS AND GENOMICS
  • 2010-12. Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms in BMC GENOMICS
  • 2008-03. Detection of quantitative trait loci controlling extremely early heading in rice in THEORETICAL AND APPLIED GENETICS
  • 2008-02. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza in GENOME BIOLOGY
  • 2009-09. BreakDancer: an algorithm for high-resolution mapping of genomic structural variation in NATURE METHODS
  • 2012-10-03. A map of rice genome variation reveals the origin of cultivated rice in NATURE
  • 2013-03. Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation in THEORETICAL AND APPLIED GENETICS
  • 2011-01. Origins of functional nucleotide polymorphisms in a major quantitative trait locus, qLTG3-1, controlling low-temperature germinability in rice in PLANT MOLECULAR BIOLOGY
  • Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/s00122-015-2543-8

    DOI

    http://dx.doi.org/10.1007/s00122-015-2543-8

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1032329183

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/26021294


    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/2008/0604", 
            "inDefinedTermSet": "http://purl.org/au-research/vocabulary/anzsrc-for/2008/", 
            "name": "Genetics", 
            "type": "DefinedTerm"
          }, 
          {
            "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"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA Transposable Elements", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "DNA, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Duplication", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Gene Frequency", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetic Variation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genetics, Population", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Genome, Plant", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "INDEL Mutation", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Japan", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Oryza", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Phenotype", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Plant Breeding", 
            "type": "DefinedTerm"
          }, 
          {
            "inDefinedTermSet": "https://www.nlm.nih.gov/mesh/", 
            "name": "Sequence Analysis, DNA", 
            "type": "DefinedTerm"
          }
        ], 
        "author": [
          {
            "affiliation": {
              "alternateName": "National Agricultural Research Center for Hokkaido Region", 
              "id": "https://www.grid.ac/institutes/grid.419106.b", 
              "name": [
                "NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization, 062-8555, Sapporo, Hokkaido, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Fujino", 
            "givenName": "Kenji", 
            "id": "sg:person.01155315454.01", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01155315454.01"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Agricultural Research Center for Hokkaido Region", 
              "id": "https://www.grid.ac/institutes/grid.419106.b", 
              "name": [
                "NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization, 062-8555, Sapporo, Hokkaido, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Obara", 
            "givenName": "Mari", 
            "id": "sg:person.01110350306.33", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110350306.33"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Agricultural Research Center for Hokkaido Region", 
              "id": "https://www.grid.ac/institutes/grid.419106.b", 
              "name": [
                "NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization, 062-8555, Sapporo, Hokkaido, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Ikegaya", 
            "givenName": "Tomohito", 
            "id": "sg:person.01003110637.80", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003110637.80"
            ], 
            "type": "Person"
          }, 
          {
            "affiliation": {
              "alternateName": "National Agricultural Research Center for Hokkaido Region", 
              "id": "https://www.grid.ac/institutes/grid.419106.b", 
              "name": [
                "NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization, 062-8555, Sapporo, Hokkaido, Japan"
              ], 
              "type": "Organization"
            }, 
            "familyName": "Tamura", 
            "givenName": "Kenichi", 
            "id": "sg:person.0776111324.45", 
            "sameAs": [
              "https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776111324.45"
            ], 
            "type": "Person"
          }
        ], 
        "citation": [
          {
            "id": "https://doi.org/10.1371/journal.pone.0086312", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002225985"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.76.10.5269", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1002874048"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-010-1299-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003201856", 
              "https://doi.org/10.1007/s00122-010-1299-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-010-1299-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1003201856", 
              "https://doi.org/10.1007/s00122-010-1299-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.55.141", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006632091"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.55.141", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1006632091"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-011-1650-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014095283", 
              "https://doi.org/10.1007/s00122-011-1650-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.60.648", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1014612256"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.55.431", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015183223"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.55.431", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015183223"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-004-1834-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1015768870", 
              "https://doi.org/10.1007/s00122-004-1834-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/bioinformatics/btp336", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1016441007"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-003-1509-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018190931", 
              "https://doi.org/10.1007/s00122-003-1509-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-003-1509-4", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018190931", 
              "https://doi.org/10.1007/s00122-003-1509-4"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/nar/8.19.4321", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1018245215"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature11532", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020113305", 
              "https://doi.org/10.1038/nature11532"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1363", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020581697", 
              "https://doi.org/10.1038/nmeth.1363"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nmeth.1363", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020581697", 
              "https://doi.org/10.1038/nmeth.1363"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s11103-010-9697-1", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1020937342", 
              "https://doi.org/10.1007/s11103-010-9697-1"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.3766306", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1021450511"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/pcp/pcr003", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1023752314"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pbio.0030196", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024152647"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1371/journal.pbio.0030196", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024152647"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1093/jxb/ert226", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024221259"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-012-2005-5", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1024523607", 
              "https://doi.org/10.1007/s00122-012-2005-5"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1469-8137.2005.01406.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026779337"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1111/j.1469-8137.2005.01406.x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1026779337"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.96.8.4710", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1027009396"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/gb-2008-9-2-r45", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1028172505", 
              "https://doi.org/10.1186/gb-2008-9-2-r45"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1073/pnas.0805303105", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1032990281"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature03895", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034843726", 
              "https://doi.org/10.1038/nature03895"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature03895", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034843726", 
              "https://doi.org/10.1038/nature03895"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1038/nature03895", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1034843726", 
              "https://doi.org/10.1038/nature03895"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1105/tpc.108.063727", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1036582234"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-014-2274-2", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1037576364", 
              "https://doi.org/10.1007/s00122-014-2274-2"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-007-0704-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038194319", 
              "https://doi.org/10.1007/s00122-007-0704-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-007-0704-0", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1038194319", 
              "https://doi.org/10.1007/s00122-007-0704-0"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1016/0300-9084(96)84768-7", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040440349"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-2035-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040694121", 
              "https://doi.org/10.1007/s00122-005-2035-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-2035-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040694121", 
              "https://doi.org/10.1007/s00122-005-2035-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-2035-3", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1040694121", 
              "https://doi.org/10.1007/s00122-005-2035-3"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.58.281", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1042978765"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1101/gr.728603", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1043651112"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.1270/jsbbs.58.367", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1044784553"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1186/1471-2164-11-267", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1045868449", 
              "https://doi.org/10.1186/1471-2164-11-267"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.4161/fly.19695", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1046734556"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00438-005-1131-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048693912", 
              "https://doi.org/10.1007/s00438-005-1131-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00438-005-1131-z", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1048693912", 
              "https://doi.org/10.1007/s00438-005-1131-z"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-2014-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051200603", 
              "https://doi.org/10.1007/s00122-005-2014-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-2014-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051200603", 
              "https://doi.org/10.1007/s00122-005-2014-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "sg:pub.10.1007/s00122-005-2014-8", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1051200603", 
              "https://doi.org/10.1007/s00122-005-2014-8"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2135/cropsci1990.0011183x003000040030x", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1069022524"
            ], 
            "type": "CreativeWork"
          }, 
          {
            "id": "https://doi.org/10.2135/cropsci2003.1989", 
            "sameAs": [
              "https://app.dimensions.ai/details/publication/pub.1069028191"
            ], 
            "type": "CreativeWork"
          }
        ], 
        "datePublished": "2015-09", 
        "datePublishedReg": "2015-09-01", 
        "description": "The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions.", 
        "genre": "research_article", 
        "id": "sg:pub.10.1007/s00122-015-2543-8", 
        "inLanguage": [
          "en"
        ], 
        "isAccessibleForFree": false, 
        "isPartOf": [
          {
            "id": "sg:journal.1135804", 
            "issn": [
              "0040-5752", 
              "1432-2242"
            ], 
            "name": "Theoretical and Applied Genetics", 
            "type": "Periodical"
          }, 
          {
            "issueNumber": "9", 
            "type": "PublicationIssue"
          }, 
          {
            "type": "PublicationVolume", 
            "volumeNumber": "128"
          }
        ], 
        "name": "Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world", 
        "pagination": "1739-1746", 
        "productId": [
          {
            "name": "readcube_id", 
            "type": "PropertyValue", 
            "value": [
              "9a026fc90e7d2fe5915e6bdcab3bff2e7f22702fc26e994b2ac700c3f7887112"
            ]
          }, 
          {
            "name": "pubmed_id", 
            "type": "PropertyValue", 
            "value": [
              "26021294"
            ]
          }, 
          {
            "name": "nlm_unique_id", 
            "type": "PropertyValue", 
            "value": [
              "0145600"
            ]
          }, 
          {
            "name": "doi", 
            "type": "PropertyValue", 
            "value": [
              "10.1007/s00122-015-2543-8"
            ]
          }, 
          {
            "name": "dimensions_id", 
            "type": "PropertyValue", 
            "value": [
              "pub.1032329183"
            ]
          }
        ], 
        "sameAs": [
          "https://doi.org/10.1007/s00122-015-2543-8", 
          "https://app.dimensions.ai/details/publication/pub.1032329183"
        ], 
        "sdDataset": "articles", 
        "sdDatePublished": "2019-04-10T15:50", 
        "sdLicense": "https://scigraph.springernature.com/explorer/license/", 
        "sdPublisher": {
          "name": "Springer Nature - SN SciGraph project", 
          "type": "Organization"
        }, 
        "sdSource": "s3://com-uberresearch-data-dimensions-target-20181106-alternative/cleanup/v134/2549eaecd7973599484d7c17b260dba0a4ecb94b/merge/v9/a6c9fde33151104705d4d7ff012ea9563521a3ce/jats-lookup/v90/0000000001_0000000264/records_8664_00000506.jsonl", 
        "type": "ScholarlyArticle", 
        "url": "http://link.springer.com/10.1007%2Fs00122-015-2543-8"
      }
    ]
     

    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/s00122-015-2543-8'

    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/s00122-015-2543-8'

    Turtle is a human-readable linked data format.

    curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/s00122-015-2543-8'

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

    curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/s00122-015-2543-8'


     

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

    272 TRIPLES      21 PREDICATES      80 URIs      34 LITERALS      22 BLANK NODES

    Subject Predicate Object
    1 sg:pub.10.1007/s00122-015-2543-8 schema:about N0f8cc96958c4473db95d20f977c65c20
    2 N1aca62a80e664ddfa4f48f0838f9c9b5
    3 N28ef21e9eaf04e85a98a379c3f9eeee4
    4 N2d5c40fc06274a1e907ec8ad218ba52b
    5 N62a3a7716ae749bd9e5046bd19fdeb8f
    6 N75615c06680f4757948b76e6ff4f7464
    7 N8940bf470b06479691f607dee62cd7d6
    8 N96fd9b882c78489c8ec0b8b8331ec94e
    9 N9a5b2eee90b54656abc89eb82b82c492
    10 Nad926a296dab4b7997c2a669495b01de
    11 Nb2ae02d4e2ef44408295cf72f3a30e13
    12 Ncb9f33bc35124a20bb04025050fc5f26
    13 Nfeb90ae7f4e44310b788bbe33f848c52
    14 anzsrc-for:06
    15 anzsrc-for:0604
    16 schema:author N9bc85ff05c2a4ca8a18a75ad8280882b
    17 schema:citation sg:pub.10.1007/s00122-003-1509-4
    18 sg:pub.10.1007/s00122-004-1834-2
    19 sg:pub.10.1007/s00122-005-2014-8
    20 sg:pub.10.1007/s00122-005-2035-3
    21 sg:pub.10.1007/s00122-007-0704-0
    22 sg:pub.10.1007/s00122-010-1299-4
    23 sg:pub.10.1007/s00122-011-1650-4
    24 sg:pub.10.1007/s00122-012-2005-5
    25 sg:pub.10.1007/s00122-014-2274-2
    26 sg:pub.10.1007/s00438-005-1131-z
    27 sg:pub.10.1007/s11103-010-9697-1
    28 sg:pub.10.1038/nature03895
    29 sg:pub.10.1038/nature11532
    30 sg:pub.10.1038/nmeth.1363
    31 sg:pub.10.1186/1471-2164-11-267
    32 sg:pub.10.1186/gb-2008-9-2-r45
    33 https://doi.org/10.1016/0300-9084(96)84768-7
    34 https://doi.org/10.1073/pnas.0805303105
    35 https://doi.org/10.1073/pnas.76.10.5269
    36 https://doi.org/10.1073/pnas.96.8.4710
    37 https://doi.org/10.1093/bioinformatics/btp336
    38 https://doi.org/10.1093/jxb/ert226
    39 https://doi.org/10.1093/nar/8.19.4321
    40 https://doi.org/10.1093/pcp/pcr003
    41 https://doi.org/10.1101/gr.3766306
    42 https://doi.org/10.1101/gr.728603
    43 https://doi.org/10.1105/tpc.108.063727
    44 https://doi.org/10.1111/j.1469-8137.2005.01406.x
    45 https://doi.org/10.1270/jsbbs.55.141
    46 https://doi.org/10.1270/jsbbs.55.431
    47 https://doi.org/10.1270/jsbbs.58.281
    48 https://doi.org/10.1270/jsbbs.58.367
    49 https://doi.org/10.1270/jsbbs.60.648
    50 https://doi.org/10.1371/journal.pbio.0030196
    51 https://doi.org/10.1371/journal.pone.0086312
    52 https://doi.org/10.2135/cropsci1990.0011183x003000040030x
    53 https://doi.org/10.2135/cropsci2003.1989
    54 https://doi.org/10.4161/fly.19695
    55 schema:datePublished 2015-09
    56 schema:datePublishedReg 2015-09-01
    57 schema:description The rapid accumulation of pre-existing mutations may play major roles in the establishment and shaping of adaptability for local regions in current rice breeding programs. The cultivated rice, Oryza sativa L., which originated from tropical regions, is now grown worldwide due to the concerted efforts of breeding programs. However, the process of establishing local populations and their origins remain unclear. In the present study, we characterized DNA polymorphisms in the rice variety KITAAKE from Hokkaido, one of the northern limits of rice cultivation in the world. Indel polymorphisms were attributed to transposable element-like insertions, tandem duplications, and non-TE deletions as the original mutation events in the NIPPONBARE and KITAAKE genomes. The allele frequencies of the KITAAKE alleles markedly shifted to the current variety types among the local population from Hokkaido in the last two decades. The KITAAKE alleles widely distributed throughout wild rice and cultivated rice over the world. These have accumulated in the local population from Hokkaido via Japanese landraces as the ancestral population of Hokkaido. These results strongly suggested that combinations of pre-existing mutations played a role in the establishment of adaptability. This approach using the re-sequencing of local varieties in unique environmental conditions will be useful as a genetic resource in plant breeding programs in local regions.
    58 schema:genre research_article
    59 schema:inLanguage en
    60 schema:isAccessibleForFree false
    61 schema:isPartOf N154f5a87b9e84e0fa513868ee8c712ba
    62 N903f351039d64af38de84041c42cdf3d
    63 sg:journal.1135804
    64 schema:name Genetic shift in local rice populations during rice breeding programs in the northern limit of rice cultivation in the world
    65 schema:pagination 1739-1746
    66 schema:productId N11a2bd96b5aa4f4b9554e179fdb0940e
    67 N323712ad08f149308aab3a4119ad888a
    68 N3d0d51e991c847248fa47edc4aeeff1c
    69 N6ad6acdd804f4d0faa0c97626365397a
    70 Nd8eda3c9096e4f57a5c2be4e2fdfa768
    71 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032329183
    72 https://doi.org/10.1007/s00122-015-2543-8
    73 schema:sdDatePublished 2019-04-10T15:50
    74 schema:sdLicense https://scigraph.springernature.com/explorer/license/
    75 schema:sdPublisher N554e70c92b604a338d78357b7ea45b5d
    76 schema:url http://link.springer.com/10.1007%2Fs00122-015-2543-8
    77 sgo:license sg:explorer/license/
    78 sgo:sdDataset articles
    79 rdf:type schema:ScholarlyArticle
    80 N0f8cc96958c4473db95d20f977c65c20 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    81 schema:name Japan
    82 rdf:type schema:DefinedTerm
    83 N11a2bd96b5aa4f4b9554e179fdb0940e schema:name nlm_unique_id
    84 schema:value 0145600
    85 rdf:type schema:PropertyValue
    86 N154f5a87b9e84e0fa513868ee8c712ba schema:issueNumber 9
    87 rdf:type schema:PublicationIssue
    88 N1aca62a80e664ddfa4f48f0838f9c9b5 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    89 schema:name Gene Duplication
    90 rdf:type schema:DefinedTerm
    91 N28ef21e9eaf04e85a98a379c3f9eeee4 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    92 schema:name Genetics, Population
    93 rdf:type schema:DefinedTerm
    94 N2d5c40fc06274a1e907ec8ad218ba52b schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    95 schema:name DNA, Plant
    96 rdf:type schema:DefinedTerm
    97 N323712ad08f149308aab3a4119ad888a schema:name readcube_id
    98 schema:value 9a026fc90e7d2fe5915e6bdcab3bff2e7f22702fc26e994b2ac700c3f7887112
    99 rdf:type schema:PropertyValue
    100 N3d0d51e991c847248fa47edc4aeeff1c schema:name dimensions_id
    101 schema:value pub.1032329183
    102 rdf:type schema:PropertyValue
    103 N4e7e490f767f4897ba41820013c55bdc rdf:first sg:person.0776111324.45
    104 rdf:rest rdf:nil
    105 N554e70c92b604a338d78357b7ea45b5d schema:name Springer Nature - SN SciGraph project
    106 rdf:type schema:Organization
    107 N61567ab826614b0abb9e392773368440 rdf:first sg:person.01110350306.33
    108 rdf:rest Ndcfdeecc07a44c9d87619285310974b2
    109 N62a3a7716ae749bd9e5046bd19fdeb8f schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    110 schema:name Oryza
    111 rdf:type schema:DefinedTerm
    112 N6ad6acdd804f4d0faa0c97626365397a schema:name pubmed_id
    113 schema:value 26021294
    114 rdf:type schema:PropertyValue
    115 N75615c06680f4757948b76e6ff4f7464 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    116 schema:name Genome, Plant
    117 rdf:type schema:DefinedTerm
    118 N8940bf470b06479691f607dee62cd7d6 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    119 schema:name Gene Frequency
    120 rdf:type schema:DefinedTerm
    121 N903f351039d64af38de84041c42cdf3d schema:volumeNumber 128
    122 rdf:type schema:PublicationVolume
    123 N96fd9b882c78489c8ec0b8b8331ec94e schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    124 schema:name DNA Transposable Elements
    125 rdf:type schema:DefinedTerm
    126 N9a5b2eee90b54656abc89eb82b82c492 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    127 schema:name Genetic Variation
    128 rdf:type schema:DefinedTerm
    129 N9bc85ff05c2a4ca8a18a75ad8280882b rdf:first sg:person.01155315454.01
    130 rdf:rest N61567ab826614b0abb9e392773368440
    131 Nad926a296dab4b7997c2a669495b01de schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    132 schema:name INDEL Mutation
    133 rdf:type schema:DefinedTerm
    134 Nb2ae02d4e2ef44408295cf72f3a30e13 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    135 schema:name Sequence Analysis, DNA
    136 rdf:type schema:DefinedTerm
    137 Ncb9f33bc35124a20bb04025050fc5f26 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    138 schema:name Phenotype
    139 rdf:type schema:DefinedTerm
    140 Nd8eda3c9096e4f57a5c2be4e2fdfa768 schema:name doi
    141 schema:value 10.1007/s00122-015-2543-8
    142 rdf:type schema:PropertyValue
    143 Ndcfdeecc07a44c9d87619285310974b2 rdf:first sg:person.01003110637.80
    144 rdf:rest N4e7e490f767f4897ba41820013c55bdc
    145 Nfeb90ae7f4e44310b788bbe33f848c52 schema:inDefinedTermSet https://www.nlm.nih.gov/mesh/
    146 schema:name Plant Breeding
    147 rdf:type schema:DefinedTerm
    148 anzsrc-for:06 schema:inDefinedTermSet anzsrc-for:
    149 schema:name Biological Sciences
    150 rdf:type schema:DefinedTerm
    151 anzsrc-for:0604 schema:inDefinedTermSet anzsrc-for:
    152 schema:name Genetics
    153 rdf:type schema:DefinedTerm
    154 sg:journal.1135804 schema:issn 0040-5752
    155 1432-2242
    156 schema:name Theoretical and Applied Genetics
    157 rdf:type schema:Periodical
    158 sg:person.01003110637.80 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
    159 schema:familyName Ikegaya
    160 schema:givenName Tomohito
    161 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01003110637.80
    162 rdf:type schema:Person
    163 sg:person.01110350306.33 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
    164 schema:familyName Obara
    165 schema:givenName Mari
    166 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01110350306.33
    167 rdf:type schema:Person
    168 sg:person.01155315454.01 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
    169 schema:familyName Fujino
    170 schema:givenName Kenji
    171 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01155315454.01
    172 rdf:type schema:Person
    173 sg:person.0776111324.45 schema:affiliation https://www.grid.ac/institutes/grid.419106.b
    174 schema:familyName Tamura
    175 schema:givenName Kenichi
    176 schema:sameAs https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0776111324.45
    177 rdf:type schema:Person
    178 sg:pub.10.1007/s00122-003-1509-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018190931
    179 https://doi.org/10.1007/s00122-003-1509-4
    180 rdf:type schema:CreativeWork
    181 sg:pub.10.1007/s00122-004-1834-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015768870
    182 https://doi.org/10.1007/s00122-004-1834-2
    183 rdf:type schema:CreativeWork
    184 sg:pub.10.1007/s00122-005-2014-8 schema:sameAs https://app.dimensions.ai/details/publication/pub.1051200603
    185 https://doi.org/10.1007/s00122-005-2014-8
    186 rdf:type schema:CreativeWork
    187 sg:pub.10.1007/s00122-005-2035-3 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040694121
    188 https://doi.org/10.1007/s00122-005-2035-3
    189 rdf:type schema:CreativeWork
    190 sg:pub.10.1007/s00122-007-0704-0 schema:sameAs https://app.dimensions.ai/details/publication/pub.1038194319
    191 https://doi.org/10.1007/s00122-007-0704-0
    192 rdf:type schema:CreativeWork
    193 sg:pub.10.1007/s00122-010-1299-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1003201856
    194 https://doi.org/10.1007/s00122-010-1299-4
    195 rdf:type schema:CreativeWork
    196 sg:pub.10.1007/s00122-011-1650-4 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014095283
    197 https://doi.org/10.1007/s00122-011-1650-4
    198 rdf:type schema:CreativeWork
    199 sg:pub.10.1007/s00122-012-2005-5 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024523607
    200 https://doi.org/10.1007/s00122-012-2005-5
    201 rdf:type schema:CreativeWork
    202 sg:pub.10.1007/s00122-014-2274-2 schema:sameAs https://app.dimensions.ai/details/publication/pub.1037576364
    203 https://doi.org/10.1007/s00122-014-2274-2
    204 rdf:type schema:CreativeWork
    205 sg:pub.10.1007/s00438-005-1131-z schema:sameAs https://app.dimensions.ai/details/publication/pub.1048693912
    206 https://doi.org/10.1007/s00438-005-1131-z
    207 rdf:type schema:CreativeWork
    208 sg:pub.10.1007/s11103-010-9697-1 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020937342
    209 https://doi.org/10.1007/s11103-010-9697-1
    210 rdf:type schema:CreativeWork
    211 sg:pub.10.1038/nature03895 schema:sameAs https://app.dimensions.ai/details/publication/pub.1034843726
    212 https://doi.org/10.1038/nature03895
    213 rdf:type schema:CreativeWork
    214 sg:pub.10.1038/nature11532 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020113305
    215 https://doi.org/10.1038/nature11532
    216 rdf:type schema:CreativeWork
    217 sg:pub.10.1038/nmeth.1363 schema:sameAs https://app.dimensions.ai/details/publication/pub.1020581697
    218 https://doi.org/10.1038/nmeth.1363
    219 rdf:type schema:CreativeWork
    220 sg:pub.10.1186/1471-2164-11-267 schema:sameAs https://app.dimensions.ai/details/publication/pub.1045868449
    221 https://doi.org/10.1186/1471-2164-11-267
    222 rdf:type schema:CreativeWork
    223 sg:pub.10.1186/gb-2008-9-2-r45 schema:sameAs https://app.dimensions.ai/details/publication/pub.1028172505
    224 https://doi.org/10.1186/gb-2008-9-2-r45
    225 rdf:type schema:CreativeWork
    226 https://doi.org/10.1016/0300-9084(96)84768-7 schema:sameAs https://app.dimensions.ai/details/publication/pub.1040440349
    227 rdf:type schema:CreativeWork
    228 https://doi.org/10.1073/pnas.0805303105 schema:sameAs https://app.dimensions.ai/details/publication/pub.1032990281
    229 rdf:type schema:CreativeWork
    230 https://doi.org/10.1073/pnas.76.10.5269 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002874048
    231 rdf:type schema:CreativeWork
    232 https://doi.org/10.1073/pnas.96.8.4710 schema:sameAs https://app.dimensions.ai/details/publication/pub.1027009396
    233 rdf:type schema:CreativeWork
    234 https://doi.org/10.1093/bioinformatics/btp336 schema:sameAs https://app.dimensions.ai/details/publication/pub.1016441007
    235 rdf:type schema:CreativeWork
    236 https://doi.org/10.1093/jxb/ert226 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024221259
    237 rdf:type schema:CreativeWork
    238 https://doi.org/10.1093/nar/8.19.4321 schema:sameAs https://app.dimensions.ai/details/publication/pub.1018245215
    239 rdf:type schema:CreativeWork
    240 https://doi.org/10.1093/pcp/pcr003 schema:sameAs https://app.dimensions.ai/details/publication/pub.1023752314
    241 rdf:type schema:CreativeWork
    242 https://doi.org/10.1101/gr.3766306 schema:sameAs https://app.dimensions.ai/details/publication/pub.1021450511
    243 rdf:type schema:CreativeWork
    244 https://doi.org/10.1101/gr.728603 schema:sameAs https://app.dimensions.ai/details/publication/pub.1043651112
    245 rdf:type schema:CreativeWork
    246 https://doi.org/10.1105/tpc.108.063727 schema:sameAs https://app.dimensions.ai/details/publication/pub.1036582234
    247 rdf:type schema:CreativeWork
    248 https://doi.org/10.1111/j.1469-8137.2005.01406.x schema:sameAs https://app.dimensions.ai/details/publication/pub.1026779337
    249 rdf:type schema:CreativeWork
    250 https://doi.org/10.1270/jsbbs.55.141 schema:sameAs https://app.dimensions.ai/details/publication/pub.1006632091
    251 rdf:type schema:CreativeWork
    252 https://doi.org/10.1270/jsbbs.55.431 schema:sameAs https://app.dimensions.ai/details/publication/pub.1015183223
    253 rdf:type schema:CreativeWork
    254 https://doi.org/10.1270/jsbbs.58.281 schema:sameAs https://app.dimensions.ai/details/publication/pub.1042978765
    255 rdf:type schema:CreativeWork
    256 https://doi.org/10.1270/jsbbs.58.367 schema:sameAs https://app.dimensions.ai/details/publication/pub.1044784553
    257 rdf:type schema:CreativeWork
    258 https://doi.org/10.1270/jsbbs.60.648 schema:sameAs https://app.dimensions.ai/details/publication/pub.1014612256
    259 rdf:type schema:CreativeWork
    260 https://doi.org/10.1371/journal.pbio.0030196 schema:sameAs https://app.dimensions.ai/details/publication/pub.1024152647
    261 rdf:type schema:CreativeWork
    262 https://doi.org/10.1371/journal.pone.0086312 schema:sameAs https://app.dimensions.ai/details/publication/pub.1002225985
    263 rdf:type schema:CreativeWork
    264 https://doi.org/10.2135/cropsci1990.0011183x003000040030x schema:sameAs https://app.dimensions.ai/details/publication/pub.1069022524
    265 rdf:type schema:CreativeWork
    266 https://doi.org/10.2135/cropsci2003.1989 schema:sameAs https://app.dimensions.ai/details/publication/pub.1069028191
    267 rdf:type schema:CreativeWork
    268 https://doi.org/10.4161/fly.19695 schema:sameAs https://app.dimensions.ai/details/publication/pub.1046734556
    269 rdf:type schema:CreativeWork
    270 https://www.grid.ac/institutes/grid.419106.b schema:alternateName National Agricultural Research Center for Hokkaido Region
    271 schema:name NARO Hokkaido Agricultural Research Center, National Agricultural Research Organization, 062-8555, Sapporo, Hokkaido, Japan
    272 rdf:type schema:Organization
     




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


    ...