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Information Resources for Cassava Research and Breeding

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Abstract

Cassava is a globally important food security and industrial crop produced for food, feed, starch and biofuel. Cassava is drought-tolerant and can grow in poor soils. Roots can be stored in the ground for long periods as part of intact growing plants, allowing flexible harvest times for poor farmers in the tropics. In addition, due to cassava’s inherently high starch content, it is a popular source of carbon for industrial purposes and increasingly biofuel. It is, however, relatively low in nutrients and susceptible to several pests and diseases, including attacks from whitefly, mealybug, green mite, cassava mosaic viruses and cassava brown streak viruses. A number of groups worldwide are working to improve cassava by conventional breeding, by molecular marker-aided breeding, and through the use of transgenic approaches. To facilitate the work of these groups, easy access to up-to-date and integrated information resources are essential to enable knowledge sharing and data mining. Here we review the information resources currently available to breeders and researchers and discuss future directions for the cassava community’s data integration and curation.

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Abbreviations

AATF:

African Agricultural Technology Foundation

AFLP:

Amplified Fragment Length Polymorphism

CABI:

Centre for Agricultural Bioscience International

CAMBIA:

Center for the Application of Molecular Biology to International Agriculture

CATAS:

Chinese Academy of Tropical Agricultural Sciences

CBSD:

Cassava Brown Streak Disease

CBSV:

Cassava Brown Streak Virus

CGIAR:

Consultative Group on International Agricultural Research

CIAT:

Centro Internacional de Agricultura Tropical

DMS:

Data Management System

DOE JGI:

Department of Energy Joint Genome Institute

EMBRAPA:

Empresa Brasileira de Pesquisa Agropecuária

EST:

Expressed Sequence Tag

ESTIMA:

EST Information Management Application

ETH Zurich:

Swiss Federal Institute of Technology Zurich

FTO:

Freedom To Operate

GCP:

Generation Challenge Program

GEOSHARE:

Geospatial Open Source Hosting of Agriculture, Resources and Environmental Data

GIS:

Geographic Information System

GMS:

Geneology Management System

ICIS:

International Crop Information System

IITA:

International Institute of Tropical Agriculture

IP:

Intellectual Property

NARS:

National Agricultural Research Systems

NCBI:

National Center for Biotechnology Information

NRCRI:

National Root Crops Research Institute

PIPRA:

Public Intellectual Property Resource for Agriculture

PlantTFDB:

Plant Transcription Factor Database

PlnTFDB:

Plant Transcription Factor Database

PMN:

Plant Metabolic Network

QTL:

Quantitative Trait Loci

RAPD:

Randomly Amplified Polymorphic DNA

RFLP:

Restriction fragment Length Polymorphism

RIKEN:

Rikagaku Kenkyusho (Institute of Physical and Chemical Research Japan)

SCCB:

Shanghai Center for Cassava Biotechnology Chinese Academy of Sciences

SINGER:

System-wide Information Network for Genetic Resources

SNP:

Single Nucleotide Polymorphism

SRAP:

Sequence-Related Amplified Polymorphism

SSR:

Simple Sequence Repeat

USDA:

United States Department of Agriculture

WHO:

World Health Organization

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Acknowledgements

The authors would like to thank the anonymous reviewers and acknowledge contributions from a number of members of the cassava community for reviewing the white paper draft upon which this review has been based:

Olalekan Akinbo, Luis Augusto Becerra Lopez Lavalle, Luiz Carvalho, Claude Fauquet, Melaku Gedil, Clair Hershey, Glenn Hyman, Andy Jarvis, Joseph Kamau, Pheneas Ntawuruhunga, Motoaki Seki, Peng Zhang

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Authors and Affiliations

  1. The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, UK

    Sarah Ayling

  2. International Institute of Tropical Agriculture (IITA), c/o International Livestock Research Institute (ILRI), P.O. Box 30709, Nairobi, 00100, Kenya

    Morag Ferguson

  3. Dow Agroscience, 9330 Zionsville Rd, Indianapolis, IN, 46268, USA

    Steve Rounsley

  4. International Institute of Tropical Agriculture (IITA), PMB 5320, Ibadan, Nigeria

    Peter Kulakow

  5. IITA, Carolyn House, 26 Dingwall Road, Croydon, CR9 3EE, UK

    Peter Kulakow

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  1. Sarah Ayling
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Correspondence to Peter Kulakow.

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Communicated by: Nigel Taylor

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Ayling, S., Ferguson, M., Rounsley, S. et al. Information Resources for Cassava Research and Breeding. Tropical Plant Biol. 5, 140–151 (2012). https://doi.org/10.1007/s12042-012-9093-x

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