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Toward Better Data Sharing Methods for Genebanks

Evangelia Papoutsoglou, Rajaram Kaliyaperumal, Theo van Hintum, Richard G. F. Visser, Ioannis N. Athanasiadis, Richard Finkers
2017 International Semantic Web Conference  
For this, common means of data exchange and effective methods to profit from the collected information need to be established.  ...  PGR users can select among predefined questions, for example for specific crops, accessions or phenotypes..  ...  This work was supported by Luiz Bonino and Kees Burger (Dutch Techcenter for Life Sciences), as well as Marco Roos (Leiden University Medical Center) and Patrick Hendrickx (Wageningen University and Research  ... 
dblp:conf/semweb/PapoutsoglouKHV17 fatcat:vyljfajvpfaj5nmrucnhvwtzei

Genebanks and genomics: how to interconnect data from both communities?

Richard Finkers, Pierre-Yves Chibon, Rob van Treuren, Richard Visser, Theo van Hintum
2014 Plant genetic resources  
Genebanks are important suppliers of genetic resources to the genomics research community, and access to the resulting information will allow traditional genebank users to better select genetic material  ...  for their breeding and scientific programmes.  ...  For more complex data types, development of an application programming interface is the preferred method (W3C, 2008).  ... 
doi:10.1017/s1479262114000689 fatcat:k5lyooelbbbpdkokmtzdxmijlu

Advanced Strategic Research to Promote the Use of Rice Genetic Resources

Jae-Sung Lee, Dmytro Chebotarov, John Damien Platten, Kenneth McNally, Ajay Kohli
2020 Agronomy  
Such data, when combined with that from the digital rice genebank consisting of genome sequencing data, will significantly increase the efficiency in breeding efforts.  ...  Recent genome sequencing data of the rice wild species will also add to the resources available for pre-breeding efforts such as the introgression of useful genes into modern rice varieties.  ...  Acknowledgments: We thank Steve Klassen and Stephen Timple at IRRI for technical support. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/agronomy10111629 fatcat:kgj4t4fovjettazpjp5gdkc3di

Securing Diversity for Food Security: The Case of Conservation and Use of Rice Genetic Resources [chapter]

Roel C. Rabara, Marilyn C. Ferrer, Jennifer Jara-Rabara, Rachel C. Sotto
2018 New Visions in Plant Science  
Information generated from innovative approaches must be documented and processed as germplasm characterization data and must remain accessible at genebanks that exist centrally to conserve biodiversity  ...  As knowledge builds up with these biotechniques, more rice genetic resources can be characterized at the molecular and systems levels for further utility in breeding better cultivars.  ...  Seeds and information generated from stages 1 to 3 generation and submission of information to genebank for the provision of better passport and characterization data of accessions or germplasm for future  ... 
doi:10.5772/intechopen.77216 fatcat:yvtv5f6cvbfohbindqdadij5ry

A Performance Management System for Long-Term Germplasm Conservation in CGIAR Genebanks: Aiming for Quality, Efficiency and Improvement

Charlotte Lusty, Janny van Beem, Fiona R. Hay
2021 Plants  
To manage these factors efficiently and effectively, genebanks require sound data and quality management systems.  ...  These mechanisms do not conform to the usual monitoring systems put in place for research programs and have only been possible thanks to the flexibility of CGIAR in recognising that the genebanks were  ...  Acknowledgments: We thank the guest editors of this special issue, Jan Engels and Andreas Ebert for inviting us to write this article and providing valuable suggestions on the content and writing.  ... 
doi:10.3390/plants10122627 pmid:34961098 pmcid:PMC8709014 fatcat:zoetoagbafbg3ozbjjhx5hxjte

The Vulnerability of Plant Genetic Resources Conserved Ex Situ

Yong-Bi Fu
2017 Crop science  
We would also like to thank two anonymous journal reviewers for their helpful comments to improve the paper.  ...  Acknowledgments We would like to thank many colleagues for their helpful comments on the earlier versions of manuscript.  ...  better genebank systems.  ... 
doi:10.2135/cropsci2017.01.0014 fatcat:cte7a7i6wfcq7ct77pn2lrmj6m

Germplasm Acquisition and Distribution by CGIAR Genebanks

Michael Halewood, Nelissa Jamora, Isabel Lopez Noriega, Noelle L. Anglin, Peter Wenzl, Thomas Payne, Marie-Noelle Ndjiondjop, Luigi Guarino, P. Lava Kumar, Mariana Yazbek, Alice Muchugi, Vania Azevedo (+6 others)
2020 Plants  
The genebanks' rates of both acquisition and distribution increased over the last decade.  ...  The international collections of plant genetic resources for food and agriculture (PGRFA) hosted by 11 CGIAR Centers are important components of the United Nations Food and Agriculture Organization's global  ...  a long-term view towards helping this process and linking publications and data back to accessions.  ... 
doi:10.3390/plants9101296 pmid:33019539 pmcid:PMC7601315 fatcat:7xsnnwm6zrd3fixsyte32yflb4

The Darwin Core extension for genebanks opens up new opportunities for sharing genebank datasets

Dag Terje Filip Endresen, Helmut Knüpffer
2012 Biodiversity Informatics  
The new Darwin Core extension for genebanks declares the additional terms required for describing genebank data sets, and is based on established standards from the plant genetic resources community.  ...  for data exchange.  ...  The new Darwin Core extension for genebanks is required to enable the GBIF IPT to share a standard set of minimum terms for germplasm data sets.  ... 
doi:10.17161/bi.v8i1.4095 fatcat:e7m3gktvqzfgdo45ift5ujphna

Global range expansion history of pepper (Capsicum spp.) revealed by over 10,000 genebank accessions

Pasquale Tripodi, Mark Timothy Rabanus-Wallace, Lorenzo Barchi, Sandip Kale, Salvatore Esposito, Alberto Acquadro, Roland Schafleitner, Maarten van Zonneveld, Jaime Prohens, Maria José Diez, Andreas Börner, Jérémy Salinier (+13 others)
2021 Proceedings of the National Academy of Sciences of the United States of America  
The method ReMIXTURE—using genetic data to quantify the similarity between the complement of peppers from a focal region and those from other regions—was developed to supplement traditional population  ...  Genebanks collect and preserve vast collections of plants and detailed passport information, with the aim of preserving genetic diversity for conservation and breeding.  ...  We gratefully acknowledge Annette Marlow, Beate Kamm, Jacqueline Pohl, Susanne König, Ines Walde, Mary Ziems, and Anne Massire for technical assistance.  ... 
doi:10.1073/pnas.2104315118 pmid:34400501 pmcid:PMC8403938 fatcat:f7yvrzjcsvcgdp7d5buo2ajl2m

Role of genomics in promoting the utilization of plant genetic resources in genebanks

Peterson W Wambugu, Marie-Noelle Ndjiondjop, Robert J Henry
2018 Briefings in Functional Genomics  
We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded.  ...  Increased collaboration between genebank managers and the user community is also recommended  ...  Owing to the large number of unstructured natural populations in genebanks, association mapping studies render themselves better suited for characterizing natural variation of genebank samples as opposed  ... 
doi:10.1093/bfgp/ely014 pmid:29688255 pmcid:PMC5967547 fatcat:pe2xm6tuiff4nb452n5nuufzu4

Envisaging an Effective Global Long-Term Agrobiodiversity Conservation System That Promotes and Facilitates Use

Charlotte Lusty, Ruaraidh Sackville Hamilton, Luigi Guarino, Chris Richards, Nelissa Jamora, Geoffrey Hawtin
2021 Plants  
genetic resources and associated data.  ...  Ultimately, future challenges and opportunities are likely to drive more demand for genetic diversity and provide an important basis for genebanks to gear up.  ...  .; Scope and roles of the CGIAR genebanks: 2030 Vision, available at www.genebanks.org/wp-content/uploads/2020/09/Session-2_CGIAR-genebanks-2030-vision.pdf last accessed on 26 November 2021.  ... 
doi:10.3390/plants10122764 pmid:34961233 pmcid:PMC8706931 fatcat:pkuwfod5xzefxn7mkc6fjtxnra

Genetic diversity and relationship between domesticated rye and its wild relatives as revealed through genotyping-by-sequencing

Mona Schreiber, Axel Himmelbach, Andreas Börner, Martin Mascher
2018 Evolutionary Applications  
We collected genotyping-by-sequencing data for 603 individuals from 101 genebank accessions of domesticated rye and its wild progenitor S. cereale subsp. vavilovii and related species in the genus Secale  ...  Our study highlights the necessity of gauging the representativeness of ex situ germplasm collections for domestication studies and motivates a more in-depth analysis of the interplay between sequence  ...  | RE SULTS | Genotyping-by-sequencing in Secale species We obtained genotyping-by-sequencing data for 101 genebank accessions of domesticated rye and wild Secale forms.  ... 
doi:10.1111/eva.12624 pmid:30622636 pmcid:PMC6304746 fatcat:3h5skq2kznf5fmi2armj3adwdu

Global Ex-Situ Crop Diversity Conservation and the Svalbard Global Seed Vault: Assessing the Current Status

Ola T. Westengen, Simon Jeppson, Luigi Guarino, Wengui Yan
2013 PLoS ONE  
Currently, 774,601 samples are deposited at Svalbard by 53 genebanks.  ...  We assess the completeness of the safety duplication collection in the Svalbard Global Seed Vault with respect to data on the world's ex-situ collections as reported by the Food and Agriculture Organization  ...  Acknowledgments We thank the genebank managers of the institutions with safety duplicates in the Seed Vault for providing accession-level data as well as information about legal and institutional arrangements  ... 
doi:10.1371/journal.pone.0064146 pmid:23671707 pmcid:PMC3650076 fatcat:gcyd6blzmvezjphvmabzi7vktq

Valuing genebanks

Melinda Smale, Nelissa Jamora
2020 Food Security  
We summarize the main messages of the studies included in this special issue of Food Security and explain how they contribute to a better understanding of the role, function, and value of genebanks, particularly  ...  Finally, we draw implications for further applied research and policy.  ...  Acknowledgements Funding for this research was provided by the CGIAR Genebank Platform and the Crop Trust.  ... 
doi:10.1007/s12571-020-01034-x fatcat:g7kn34jvrfhrlpr2t7qcn5b7te

Emerging Avenues for Utilization of Exotic Germplasm

Cuiling Wang, Songlin Hu, Candice Gardner, Thomas Lübberstedt
2017 Trends in Plant Science  
This review will summarize potential challenges for utilization of exotic germplasm and provide solutions. Disciplines Agronomy and Crop Sciences Comments  ...  Exotic germplasm possesses high levels of genetic diversity for valuable traits. However, only a small fraction of naturally occurring genetic diversity is utilized.  ...  It will be necessary to develop a user-friendly germplasm cooperation platform to organize, analyze, integrate different types of data, share information among genebanks, and meet the needs of researchers  ... 
doi:10.1016/j.tplants.2017.04.002 pmid:28476651 fatcat:js2f3uusbvhevccw75rfd5inwe
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