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Biotechnologies for the Management of Genetic Resources for Food and Agriculture

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Biotechnologies for the Management of Genetic Resources for Food and Agriculture BACKGROUND STUDY PAPER NO. 52 May 2011 E COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE BIOTECHNOLOGIES FOR THE MANAGEMENT OF GENETIC RESOURCES FOR FOOD AND AGRICULTURE by Preetmoninder Lidder and Andrea Sonnino This document has been prepared at the request of the Secretariat of the Commission on Genetic Resources for Food and Agriculture by Preetmoninder Lidder and Andrea Sonnino, from the FAO Working Group on Biotechnology as a contribution to the cross-sectoral theme, Application and integration of biotechnologies in the conservation and utilization of genetic resources. The content of this document is entirely the responsibility of the authors, and does not necessarily represent the views of the FAO or its Members. The document was finalized in May 2011. For resaons of economy, this document is produced in a limited number of copies. Delegates and observers are kindly requested to bring their copies to meetings and to refrain from asking for additional copies, unless strictly necessary. The documents for this meeting are available on Internet at: http://www.fao.org ii BACKGROUND STUDY PAPER NO. 52 TABLE OF CONTENTS Page List of Abbreviations and acronyms 1 Executive summary 6 I. Introduction 7 II. Biotechnologies applied to the characterization, conservation and utilization of genetic resources for food and agriculture 8 2.1 Characterization of GRFA 9 2.1.1 Molecular Markers (Cross-sectoral) 9 2.1.2 ―Omic‖ technologies (Cross-sectoral) 12 2.1.3 Bioinformatics (Cross-sectoral) 13 2.2 Conservation of GRFA 14 2.2.1 Cryopreservation (Cross-sectoral) 15 2.2.2 In vitro slow growth storage (Crops and forest trees) 15 2.2.3 Reproductive biotechnologies (Livestock and fisheries/aquaculture) 15 2.3 Utilization of GRFA 17 2.3.1 Reproductive biotechnologies (Livestock and fisheries/aquaculture) 17 2.3.2 Biotechnologies for disease diagnostics (Cross-sectoral) 17 2.3.3 Biotechnologies for disease control (Livestock and fisheries/aquaculture) 18 2.3.4 Chromosome set manipulation (Crops, forest trees and fisheries/aquaculture) 19 2.3.5 Tissue culture-based techniques (Crops and forest trees) 19 2.3.6 Molecular marker-assisted selection (Cross-sectoral) 20 2.3.7 Fermentation (Microbial) 20 2.3.8 Biofertilizers (Microbial) 21 2.3.9 Biopesticides (Microbial) 21 2.3.10 Bioremediation (Microbial) 21 2.3.11 Probiotics (Microbial) 21 2.3.12 Mutagenesis (Cross-sectoral) 22 2.3.13 Transgenesis (cross-sectoral) 22 III. Current status of biotechnolgoies for the management of crop genetic resources 22 3.1 Molecular markers 22 3.2 ―Omics‖ 26 3.3 Bioinformatics 27 3.4 Cryopreservation 27 3.5 In vitro slow growth storage 29 3.6 Wide crossing 30 3.7 Somatic hybridization 30 3.8 Micropropagation 31 3.9 Chromosome set manipulation 31 BACKGROUND STUDY PAPER NO. 52 iii 3.10 Biotechnologies for disease diagnosis 32 3.11 Molecular marker-assisted selection 33 3.12 Mutagenesis 35 3.13 Transgenesis 36 IV. Current status of biotechnologies for the management of forest genetic resources 37 4.1. Molecular markers 37 4.2 ―Omics‖ 39 4.3 Bioinformatics 40 4.4 Cryopreservation 40 4.5 In vitro slow growth storage 41 4.6 Micropropagation 42 4.7 Chromosome set manipulation 43 4.8 Molecular marker-assisted selection 43 4.9 Mutagenesis 44 4.10 Transgenesis 44 V. Current status of biotechnologies for the management of animal genetic resources 44 5.1 Molecular markers 45 5.2 ―Omics‖ 46 5.3 Bioinformatics 47 5.4 Cryopreservation 48 5.5 Reproductive biotechnologies 49 5.6 Biotechnologies for disease diagnosis and prevention 52 5.7 Molecular marker-assisted selection 54 5.8 Mutagenesis 55 5.9 Transgenesis 56 VI. Current status of biotechnologies for the management of aquatic genetic resources 56 6.1 Molecular markers 56 6.2 ―Omics‖ 59 6.3 Bioinformatics 60 6.4 Cryopreservation 60 6.5 Reproductive biotechnologies 61 6.6 Chromosome set manipulation 63 6.7 Biotechnologies for disease diagnosis and prevention 65 6.8 Molecular marker-assisted selection 67 6.9 Transgenesis 67 VII. Current status of biotechnologies for the management of microbial genetic resources 67 7.1 Molecular markers 68 7.2 ―Omics‖ 69 7.3 Bioinformatics 70 7.4 Cryopreservation 71 iv BACKGROUND STUDY PAPER NO. 52 7.5 Pathogen detection in food 71 7.6 Food preservation and production of food and feed ingredients 72 7.7 Biofertilizers 73 7.8 Biopesticides 75 7.9 Bioremediation 76 7.10 Probiotics 77 7.11 Mutagenesis 78 7.12 Transgenesis 78 VIII. Conclusions and Outlook 79 Acknowledgements 80 References 80 BACKGROUND STUDY PAPER NO. 52 1 LIST OF ABBREVIATIONS AND ACRONYMS ABDC-10 FAO international technical conference on Agricultural Biotechnologies in Developing Countries AbHV Abalone herpes-like virus AFLP Amplified fragment length polymorphism AFOCEL Association Forêt-Cellulose AGeS Annotation of Microbial Genome Sequences AI Artificial insemination AMF Arbuscular mycorrhizal fungi AW-IPM Area-wide integrated pest management BecA Biosciences eastern and central Africa BiMFG Bioinformatics tools for Marine and Freshwater Genomics BOLD Barcode of Life Data Systems BWB Breeding without breeding CATIE Centro Agronómico Tropical de Investigación y Enseñanza CBD Convention on Biological Diversity CBOL Consortium for the Barcode of Life CBPP Contagious bovine pleuropneumonia cDNA Complementary DNA C-ELISA Competitive ELISA CGIAR Consultative Group on International Agricultural Research CGRFA Commission on Genetic Resources for Food and Agriculture CIAT International Centre for Tropical Agriculture CIBEX Center for Information Biology Gene Expression Database CIP International Potato Center CIRAD Centre de Coopération Internationale en Recherche Agronomique pour le Développement COSAVE Comité de Sanidad Vegetal del Cono Sur CSV Classical swine fever CWR Crop wild relatives DArT Diversity arrays technology 2 BACKGROUND STUDY PAPER NO. 52 DDBJ DNA Databank of Japan DGGE Denaturing gradient gel electrophoresis DH Doubled haploid DIVA vaccine Vaccine capable of differentiating infected and vaccinated animals DPTF Database of Poplar Transcription Factors ECBOL European Consortium for the Barcode of Life EHNV Epizootic haematopoietic necrosis virus ELISA Enzyme-linked immunosorbent assay EMBL European Molecular Biology Laboratory EMBnet European Molecular Biology Network EMS Ethylmethane sulfonate EPPO European and Mediterranean Plant Protection Organization EST Expressed sequence tag ET Embryo transfer EU European Union EUCAGEN International Eucalyptus Genome Network FAO Food and Agriculture Organization of the United Nations FGI Fungal Genome Initiative of The Broad Institute FMD Foot and mouth disease FPPI Fusarium graminearum Protein-Protein Interaction Database GCP Generation Challenge Program GENOLYPTUS Brazilian Network of Eucalyptus Genome Research GEO Gene Expression Omnibus GLEWS Global Early Warning and Response System GM(O) Genetically modified (organism) GnRH Gonadotropin-releasing hormone GOLD Genomes OnLine Database GPMDB Global Proteome Machine Database GREP Global Rinderpest Eradication Programme GRFA Genetic resources for food and agriculture GRIN Germplasm Resource Information System BACKGROUND STUDY PAPER NO. 52 3 GS Genomic selection GWAS Genome-wide association studies HACCP Hazard Analysis and Critical Control Point hCG Human chorionic gonadotropin IAEA International Atomic Energy Agency iBOL International Barcode of Life project ICRAF World Agroforestry Centre IFAD International Fund for Agricultural Development IHHNV Infectious hypodermic and haematopoeitic necrosis virus IHN Infectious haematopoietic necrosis IHNV Infectious haematopoietic necrosis virus IITA International Institute of Tropical Agriculture ILRI International Livestock Research Institute IMEx International Molecular Exchange Consortium IMTA Integrated multi-trophic aquaculture INIBAP International Network for the Improvement of Banana and Plantain INSDC International Nucleotide Sequence Database Collaboration IPM Integrated pest management IPNV Infectious pancreatic necrosis virus IPPC International Plant Protection Convention IPR Intellectual property rights ISAG International Society of Animal Genetics ISPM International Standards for Phytosanitary Measure IUCN International Union for Conservation of Nature IVF In vitro fertilization KHV Koi herpesvirus LAMP PCR Loop-mediated isothermal amplification PCR MAS Marker-assisted selection MEGAN MEtaGenome ANalyzer MNU N-methyl-N-nitrosourea MOET Multiple ovulation and embryo transfer 4 BACKGROUND STUDY PAPER NO. 52 MPID Magnaporthe grisea Protein-Protein Interaction Database MrNV Macrobrachium rosenbergii nodavirus NACA Network of Aquaculture Centres in Asia-Pacific NAPPO North American Plant Protection Organization NBPGR National Bureau of Plant Genetic Resources NCBI National Centre for Biotechnology Information Ne Effective population size NERICA New Rice for Africa NGS Next generation sequencing OIE World Organisation for Animal Health PATTEC Pan African Tsetse Eradication Campaign PCR Polymerase chain reaction PDB Protein Data Bank PopGenIE Populus Genome Integrative Explorer PPR Peste des petits ruminants PPRV Peste des petits ruminants virus PRIDE PRoteomics IDEntifications database PSB P-solubilizing bacteria PSF P-solubilizing fungi QBOL Quarantine Barcoding of Life QPM Quality protein maize QTL Quantitative trait locus RAPD Random amplified polymorphic DNA RFLP Restriction fragment length polymorphism RIA Radioimmunoassay RP Rinderpest rRNA Ribosomal RNA rRT-PCR Real-time RT-PCR RT-PCR Reverse transcriptase PCR SE Somatic embryogenesis SGD Saccharomyces Genome
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