Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions

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 an...

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Autores: Singh, N., Shuangye Wu, Raupp, W.J., Sunish Sehgal, Sanu Arora, Vijay Tiwari, Vikram, P., Singh, S., Chhuneja, P., Gill, B.S., Poland, J.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2019
País:México
Institución:Centro Internacional de Mejoramiento de Maíz y Trigo
Repositorio:Repositorio Institucional de Publicaciones Multimedia del CIMMYT
OAI Identifier:oai:repository.cimmyt.org:10883/20087
Acceso en línea:https://hdl.handle.net/10883/20087
Access Level:acceso abierto
Palabra clave:AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
GENOTYPES
GENE BANKS
DATA ANALYSIS
CROP IMPROVEMENT
GERMPLASM CONSERVATION
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spelling Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessionsSingh, N.Shuangye WuRaupp, W.J.Sunish SehgalSanu AroraVijay TiwariVikram, P.Singh, S.Chhuneja, P.Gill, B.S.Poland, J.AGRICULTURAL SCIENCES AND BIOTECHNOLOGYAGRICULTURAL SCIENCES AND BIOTECHNOLOGYGENOTYPESGENE BANKSDATA ANALYSISCROP IMPROVEMENTGERMPLASM CONSERVATIONGenebanks 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.NLM (Medline)Springer Nature Publishing2019-03-20T01:10:11Z2019-03-20T01:10:11Z2019Published Versioninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articlePDFapplication/pdfESSN: 2045-2322https://hdl.handle.net/10883/2008710.1038/s41598-018-37269-06509Scientific Reportsreponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYTinstname:Centro Internacional de Mejoramiento de Maíz y Trigoinstacron:CIMMYTEnglishhttps://github.com/nsinghs/Code_GenebankCurationUnited KingdomOpen Accessinfo:eu-repo/semantics/openAccessoai:repository.cimmyt.org:10883/200872024-10-11T19:56:34Z
dc.title.none.fl_str_mv Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
title Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
spellingShingle Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
Singh, N.
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
GENOTYPES
GENE BANKS
DATA ANALYSIS
CROP IMPROVEMENT
GERMPLASM CONSERVATION
title_short Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
title_full Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
title_fullStr Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
title_full_unstemmed Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
title_sort Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions
dc.creator.none.fl_str_mv Singh, N.
Shuangye Wu
Raupp, W.J.
Sunish Sehgal
Sanu Arora
Vijay Tiwari
Vikram, P.
Singh, S.
Chhuneja, P.
Gill, B.S.
Poland, J.
author Singh, N.
author_facet Singh, N.
Shuangye Wu
Raupp, W.J.
Sunish Sehgal
Sanu Arora
Vijay Tiwari
Vikram, P.
Singh, S.
Chhuneja, P.
Gill, B.S.
Poland, J.
author_role author
author2 Shuangye Wu
Raupp, W.J.
Sunish Sehgal
Sanu Arora
Vijay Tiwari
Vikram, P.
Singh, S.
Chhuneja, P.
Gill, B.S.
Poland, J.
author2_role author
author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
GENOTYPES
GENE BANKS
DATA ANALYSIS
CROP IMPROVEMENT
GERMPLASM CONSERVATION
topic AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY
GENOTYPES
GENE BANKS
DATA ANALYSIS
CROP IMPROVEMENT
GERMPLASM CONSERVATION
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.
publishDate 2019
dc.date.none.fl_str_mv 2019-03-20T01:10:11Z
2019-03-20T01:10:11Z
2019
dc.type.none.fl_str_mv Published Version
info:eu-repo/semantics/publishedVersion
info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv ESSN: 2045-2322
https://hdl.handle.net/10883/20087
10.1038/s41598-018-37269-0
identifier_str_mv ESSN: 2045-2322
10.1038/s41598-018-37269-0
url https://hdl.handle.net/10883/20087
dc.language.none.fl_str_mv English
language_invalid_str_mv English
dc.relation.none.fl_str_mv https://github.com/nsinghs/Code_GenebankCuration
dc.rights.none.fl_str_mv Open Access
info:eu-repo/semantics/openAccess
rights_invalid_str_mv Open Access
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv PDF
application/pdf
dc.coverage.none.fl_str_mv United Kingdom
dc.publisher.none.fl_str_mv NLM (Medline)
Springer Nature Publishing
publisher.none.fl_str_mv NLM (Medline)
Springer Nature Publishing
dc.source.none.fl_str_mv 650
9
Scientific Reports
reponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYT
instname:Centro Internacional de Mejoramiento de Maíz y Trigo
instacron:CIMMYT
instname_str Centro Internacional de Mejoramiento de Maíz y Trigo
instacron_str CIMMYT
institution CIMMYT
reponame_str Repositorio Institucional de Publicaciones Multimedia del CIMMYT
collection Repositorio Institucional de Publicaciones Multimedia del CIMMYT
repository.name.fl_str_mv
repository.mail.fl_str_mv
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