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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 principales: Singh, Narinder, Wu, Shuangye, Raupp, W. John, Sehgal, Sunish, Arora, Sanu, Tiwari, Vijay, Vikram, Prashant, Singh, Sukhwinder, Chhuneja, Parveen, Gill, Bikram S., Poland, Jesse
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346010/
https://www.ncbi.nlm.nih.gov/pubmed/30679756
http://dx.doi.org/10.1038/s41598-018-37269-0
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author Singh, Narinder
Wu, Shuangye
Raupp, W. John
Sehgal, Sunish
Arora, Sanu
Tiwari, Vijay
Vikram, Prashant
Singh, Sukhwinder
Chhuneja, Parveen
Gill, Bikram S.
Poland, Jesse
author_facet Singh, Narinder
Wu, Shuangye
Raupp, W. John
Sehgal, Sunish
Arora, Sanu
Tiwari, Vijay
Vikram, Prashant
Singh, Sukhwinder
Chhuneja, Parveen
Gill, Bikram S.
Poland, Jesse
author_sort Singh, Narinder
collection PubMed
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.
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spelling pubmed-63460102019-01-29 Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions Singh, Narinder Wu, Shuangye Raupp, W. John Sehgal, Sunish Arora, Sanu Tiwari, Vijay Vikram, Prashant Singh, Sukhwinder Chhuneja, Parveen Gill, Bikram S. Poland, Jesse Sci Rep Article 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. Nature Publishing Group UK 2019-01-24 /pmc/articles/PMC6346010/ /pubmed/30679756 http://dx.doi.org/10.1038/s41598-018-37269-0 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Singh, Narinder
Wu, Shuangye
Raupp, W. John
Sehgal, Sunish
Arora, Sanu
Tiwari, Vijay
Vikram, Prashant
Singh, Sukhwinder
Chhuneja, Parveen
Gill, Bikram S.
Poland, Jesse
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
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_short 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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6346010/
https://www.ncbi.nlm.nih.gov/pubmed/30679756
http://dx.doi.org/10.1038/s41598-018-37269-0
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