Ontology type: schema:ScholarlyArticle Open Access: True
2019-12
AUTHORSNarinder Singh, Shuangye Wu, W. John Raupp, Sunish Sehgal, Sanu Arora, Vijay Tiwari, Prashant Vikram, Sukhwinder Singh, Parveen Chhuneja, Bikram S. Gill, Jesse Poland
ABSTRACTGenebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources. More... »
PAGES650
http://scigraph.springernature.com/pub.10.1038/s41598-018-37269-0
DOIhttp://dx.doi.org/10.1038/s41598-018-37269-0
DIMENSIONShttps://app.dimensions.ai/details/publication/pub.1111643165
PUBMEDhttps://www.ncbi.nlm.nih.gov/pubmed/30679756
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"
}
],
"author": [
{
"affiliation": {
"alternateName": "Kansas State University",
"id": "https://www.grid.ac/institutes/grid.36567.31",
"name": [
"Interdepartmental Genetics Program, Kansas State University, 66506, Manhattan, KS, USA",
"Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA"
],
"type": "Organization"
},
"familyName": "Singh",
"givenName": "Narinder",
"id": "sg:person.01272717171.15",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01272717171.15"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Kansas State University",
"id": "https://www.grid.ac/institutes/grid.36567.31",
"name": [
"Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA"
],
"type": "Organization"
},
"familyName": "Wu",
"givenName": "Shuangye",
"id": "sg:person.0626000351.21",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0626000351.21"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Kansas State University",
"id": "https://www.grid.ac/institutes/grid.36567.31",
"name": [
"Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA"
],
"type": "Organization"
},
"familyName": "Raupp",
"givenName": "W. John",
"id": "sg:person.012536537167.39",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.012536537167.39"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "South Dakota State University",
"id": "https://www.grid.ac/institutes/grid.263791.8",
"name": [
"Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, 57007, Brookings, SD, USA"
],
"type": "Organization"
},
"familyName": "Sehgal",
"givenName": "Sunish",
"id": "sg:person.0635213136.41",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0635213136.41"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "John Innes Centre",
"id": "https://www.grid.ac/institutes/grid.14830.3e",
"name": [
"Crop Genetics, John Innes Center, NR4 7UH, Norwich, United Kingdom"
],
"type": "Organization"
},
"familyName": "Arora",
"givenName": "Sanu",
"id": "sg:person.01013606042.80",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01013606042.80"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "University of Maryland, College Park",
"id": "https://www.grid.ac/institutes/grid.164295.d",
"name": [
"Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA",
"Department of Plant Sciences and Landscape Architecture, University of Maryland, 20742, College Park, MD, USA"
],
"type": "Organization"
},
"familyName": "Tiwari",
"givenName": "Vijay",
"id": "sg:person.01171224710.75",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01171224710.75"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "International Maize and Wheat Improvement Center",
"id": "https://www.grid.ac/institutes/grid.433436.5",
"name": [
"International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera M\u00e9xico-Veracruz, Colonia El Bat\u00e1n, Texcoco, Edo, 56130, De M\u00e9xico, CP, Mexico"
],
"type": "Organization"
},
"familyName": "Vikram",
"givenName": "Prashant",
"id": "sg:person.0714767515.50",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0714767515.50"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "International Maize and Wheat Improvement Center",
"id": "https://www.grid.ac/institutes/grid.433436.5",
"name": [
"International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera M\u00e9xico-Veracruz, Colonia El Bat\u00e1n, Texcoco, Edo, 56130, De M\u00e9xico, CP, Mexico"
],
"type": "Organization"
},
"familyName": "Singh",
"givenName": "Sukhwinder",
"id": "sg:person.01126237306.11",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.01126237306.11"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Punjab Agricultural University",
"id": "https://www.grid.ac/institutes/grid.412577.2",
"name": [
"School of Agricultural Biotechnology, Punjab Agricultural University, 141004, Ludhiana, Punjab, India"
],
"type": "Organization"
},
"familyName": "Chhuneja",
"givenName": "Parveen",
"id": "sg:person.0767131444.18",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.0767131444.18"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Kansas State University",
"id": "https://www.grid.ac/institutes/grid.36567.31",
"name": [
"Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA"
],
"type": "Organization"
},
"familyName": "Gill",
"givenName": "Bikram S.",
"id": "sg:person.011761304667.21",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.011761304667.21"
],
"type": "Person"
},
{
"affiliation": {
"alternateName": "Kansas State University",
"id": "https://www.grid.ac/institutes/grid.36567.31",
"name": [
"Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, 66506, Manhattan, KS, USA"
],
"type": "Organization"
},
"familyName": "Poland",
"givenName": "Jesse",
"id": "sg:person.015631243271.25",
"sameAs": [
"https://app.dimensions.ai/discover/publication?and_facet_researcher=ur.015631243271.25"
],
"type": "Person"
}
],
"citation": [
{
"id": "https://doi.org/10.4324/9780203158043",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1000202129"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/srep23092",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001287744",
"https://doi.org/10.1038/srep23092"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0063107",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1001670628"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2164-11-702",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002065866",
"https://doi.org/10.1186/1471-2164-11-702"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10722-011-9775-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1002159892",
"https://doi.org/10.1007/s10722-011-9775-5"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0132112",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1003883546"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/nph.12164",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1004066570"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0066428",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1005123472"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0102448",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1007228075"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.1116437108",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1010458316"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s10681-007-9624-y",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1011332359",
"https://doi.org/10.1007/s10681-007-9624-y"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s12374-012-0901-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1013168462",
"https://doi.org/10.1007/s12374-012-0901-5"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0090346",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021321243"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1111/tpj.13036",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1021595766"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1073/pnas.0401076101",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023456458"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12864-015-1424-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023984878",
"https://doi.org/10.1186/s12864-015-1424-5"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s12864-015-1424-5",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1023984878",
"https://doi.org/10.1186/s12864-015-1424-5"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/499023a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1024217602",
"https://doi.org/10.1038/499023a"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s001220050942",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028120323",
"https://doi.org/10.1007/s001220050942"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s001220050942",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1028120323",
"https://doi.org/10.1007/s001220050942"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/nar/29.4.e25",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1031417617"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1007/s40003-012-0029-3",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1038422444",
"https://doi.org/10.1007/s40003-012-0029-3"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1371/journal.pone.0032253",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041572486"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1139/g91-059",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1041976660"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/nplants.2015.99",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1042707581",
"https://doi.org/10.1038/nplants.2015.99"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-015-0606-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044620070",
"https://doi.org/10.1186/s13059-015-0606-4"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/s13059-015-0606-4",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1044620070",
"https://doi.org/10.1186/s13059-015-0606-4"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3732/ajb.1100385",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1048292238"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1038/538016a",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1049234238",
"https://doi.org/10.1038/538016a"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.1250092",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1050370786"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/bioinformatics/btg412",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1051607942"
],
"type": "CreativeWork"
},
{
"id": "sg:pub.10.1186/1471-2229-13-39",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1052013437",
"https://doi.org/10.1186/1471-2229-13-39"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1126/science.277.5329.1063",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1062557746"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.2135/cropsci2015.06.0356",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1069032732"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3835/plantgenome2012.05.0005",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1071447816"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3835/plantgenome2012.06.0006",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1071447819"
],
"type": "CreativeWork"
},
{
"id": "https://app.dimensions.ai/details/publication/pub.1074647594",
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.1093/oxfordjournals.jhered.a105590",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1083618190"
],
"type": "CreativeWork"
},
{
"id": "https://doi.org/10.3389/fpls.2017.00886",
"sameAs": [
"https://app.dimensions.ai/details/publication/pub.1085716171"
],
"type": "CreativeWork"
}
],
"datePublished": "2019-12",
"datePublishedReg": "2019-12-01",
"description": "Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.",
"genre": "research_article",
"id": "sg:pub.10.1038/s41598-018-37269-0",
"inLanguage": [
"en"
],
"isAccessibleForFree": true,
"isFundedItemOf": [
{
"id": "sg:grant.3488930",
"type": "MonetaryGrant"
}
],
"isPartOf": [
{
"id": "sg:journal.1045337",
"issn": [
"2045-2322"
],
"name": "Scientific Reports",
"type": "Periodical"
},
{
"issueNumber": "1",
"type": "PublicationIssue"
},
{
"type": "PublicationVolume",
"volumeNumber": "9"
}
],
"name": "Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions",
"pagination": "650",
"productId": [
{
"name": "readcube_id",
"type": "PropertyValue",
"value": [
"6c55d038abe756b4426fba7cf07fdbd8db2d93c7123edce2cf67b7a5a1e09a78"
]
},
{
"name": "pubmed_id",
"type": "PropertyValue",
"value": [
"30679756"
]
},
{
"name": "nlm_unique_id",
"type": "PropertyValue",
"value": [
"101563288"
]
},
{
"name": "doi",
"type": "PropertyValue",
"value": [
"10.1038/s41598-018-37269-0"
]
},
{
"name": "dimensions_id",
"type": "PropertyValue",
"value": [
"pub.1111643165"
]
}
],
"sameAs": [
"https://doi.org/10.1038/s41598-018-37269-0",
"https://app.dimensions.ai/details/publication/pub.1111643165"
],
"sdDataset": "articles",
"sdDatePublished": "2019-04-11T08:58",
"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/v90/0000000326_0000000326/records_68460_00000000.jsonl",
"type": "ScholarlyArticle",
"url": "https://www.nature.com/articles/s41598-018-37269-0"
}
]
Download the RDF metadata as: json-ld nt turtle xml License info
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.10.1038/s41598-018-37269-0'
N-Triples is a line-based linked data format ideal for batch operations.
curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37269-0'
Turtle is a human-readable linked data format.
curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37269-0'
RDF/XML is a standard XML format for linked data.
curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1038/s41598-018-37269-0'
This table displays all metadata directly associated to this object as RDF triples.
277 TRIPLES
21 PREDICATES
65 URIs
21 LITERALS
9 BLANK NODES