DRAFT NOT FOR CITATION THE STATE OF THE WORLD’s AQUATIC GENETIC RESOURCES FOR FOOD AND AGRICULTURE COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS Rome, 2018 i This page intentionally left blank ii CONTENTS Abbreviations and acronyms iv Acknowledgements vi Introduction 1 Chapter 1 The state of world aquaculture and fisheries 8 Chapter 2 The use and exchange of aquatic genetic resources of farmed aquatic species and their wild 32 relatives within national jurisdiction Chapter 3 Drivers and trends in aquaculture: consequences for aquatic genetic resources within 80 national jurisdiction Chapter 4 In situ conservation of farmed aquatic species and their wild relatives within national 120 jurisdiction Chapter 5 Ex situ conservation of aquatic genetic resources of farmed aquatic species and their wild 132 relatives within national jurisdiction Chapter 6 Stakeholders with interests in aquatic genetic resources of farmed aquatic species and their 151 wild relatives within national jurisdictions Chapter 7 National policies and legislation for aquatic genetic resources of farmed aquatic species 165 and their wild relatives within national jurisdiction Chapter 8 Research, education, training and extension on aquatic genetic resources within national 176 jurisdiction: coordination, networking and information Chapter 9 International collaboration on aquatic genetic resources of farmed aquatic species and their 200 wild relatives Chapter 10 Synthesis of key findings and conclusions 218 iii ABBREVIATIONS AND ACRONYMS ABS access and benefit sharing AqGR aquatic genetic resources ASFIS Aquatic Sciences and Fisheries Information System BAC bacterial artificial chromosome CBD Convention on Biological Diversity CCRF Code of Conduct for Responsible Fisheries CGRFA Commission on Genetic Resources for Food and Agriculture CITES Convention on International Trade in Endangered Species of Wild Fauna and Flora CMS Convention on the Conservation of Migratory Species of Wild Animals COFI FAO Committee on Fisheries COFI AWG AqGR/T COFI Advisory Working Group on Aquatic Genetic Resources and Technologies CRISPR clustered regulatory interspaced short palindromic repeats CRISPR/Cas clustered regularly interspaced short palindromic repeats-CRISPR associated ddRADseq DNA sequencing DIAS Database on Introductions of Aquatic Species DNA deoxyribonucleic acid DPS distinct population segment EAF Ecosystem Approach to Fisheries ESA Endangered Species Act EST expressed sequence tag ESU evolutionarily significant unit EU European Union EUSDR EU Strategy for the Danube Region FAM freshwater aquatic macrophyte FAO Food and Agriculture Organization of the United Nations FAO/FI FAO Fisheries and Aquaculture Department FPA freshwater protected area GIFT genetically improved farmed tilapia GMAD Global Marine Aquarium Database GMO genetically modified organism GSI genetic stock identification ICES International Council for the Exploration of the Sea ICPR International Commission for the Protection of the Rhine IGO intergovernmental organization or international governmental organization INGA International Network on Genetics in Aquaculture ISSCAAP International Standard Statistical Classification of Aquatic Animals and Plants ITWG AqGR Intergovernmental Technical Working Group on Aquatic Genetic Resources IUCN International Union for Conservation of Nature MAS marker-assisted selection MPA marine protected area MTA Material Transfer Agreement mtDNA mitochondrial DNA nei not elsewhere included NGO non-governmental organization NFPA National Framework for Priority Action OIE World Organisation for Animal Health PPP public-private partnership iv QTL Quantitative Trait Loci RAPD random amplified polymorphic DNA RFLP restriction fragment length polymorphism RNA ribonucleic acid RNA-seq ribonucleic acid sequencing SADC Southern African Development Community SMS single molecule sequences SNP single nucleotide polymorphism SOFIA State of World Fisheries and Aquaculture SoW AqGR State of the World’s Aquatic Genetic Resources for Food and Agriculture TALEN transcription activator-like effector nuclease UNCLOS United Nations Convention on the Law of the Sea UNFCCC United Nations Framework Convention on Climate Change USGS United States Geological Service ZFN zinc finger nuclease v Acknowledgements The Report of The State of the World’s Aquatic Genetic Resources for Food and Agriculture represents the culmination of a tremendous amount of work undertaken in FAO Member Countries, including capacity building workshops and expert meetings, and in the offices and workstations of FAO. FAO gratefully acknowledges the contributions of the many colleagues who contributed their time and expertise to this endeavor. The Report was prepared and finalized by a core team in the FAO Fisheries and Aquaculture Department under the overall coordination of Matthias Halwart. The Report is based on a questionnaire that was initially developed by Roger S.V. Pullin and Devin M. Bartley. Enrico Anello turned the questionnaire into a user friendly dynamic PDF that was distributed to all FAO Member Countries and key partners. This questionnaire formed the basis of the countries’ reporting to FAO. Capacity building workshops were organized mainly in collaboration with regional fishery bodies and aquaculture networks including Lake Victoria Fisheries Organization, African Union – Interafrican Bureau for Animal Resources, Network of Aquaculture Centres in Asia and the Pacific, Central America Fisheries and Aquaculture Organization, and partner institutions in the People’s Republic of China. These workshops were essential in helping countries understand the type of information requested by the questionnaire. The Government of Germany was a key partner in this process providing both financial and technical support to the workshops. The main body of information synthesized in the Report came from the Country Reports submitted by 92 governments. These governments, their national focal points and the numerous individuals who provided information to the country reports are especially acknowledged for their important contributions. Once the Country Reports were received by FAO, Enrico Anello and Anthony Jarret incorporated the information into a database and developed a system to query the data. Ruth Garcia-Gomez and Zhiyi Zhang extracted and organized information from the database for use by the authors of the various chapters in the Report. The Report was prepared by the Fisheries and Aquaculture Department of FAO and especially the Aquaculture Branch and the Statistics and Information Branch. The assistance of the aquaculture statistician, Xiaowei Zhou, was especially important throughout the process. The logistical support of Elena Irde, Daniela Lucente and Chiara Sirani is much appreciated. Editing and layout were expertly done by Maria Giannini and Joanne Morgante. FAO further thanks the members of the COFI Advisory Working Group on Aquatic Genetic Resources and Technologies and Kuldeep K. Lal for their review, comments and information provided on early drafts of the Report. The guidance provided through two sessions of the Ad Hoc Intergovernmental Technical Working Group on Aquatic Genetic Resources is greatly appreciated and was essential to producing a balanced and complete Report. The authors of the Thematic Background Studies and those individuals who provided editorial improvements were essential in adding substantial information to the Report that may not have been well-covered in the Country Reports. The support of the secretariat of the Commission on Genetic Resources for Food and Agriculture throughout the process was essential and provided helpful guidance based on its past experience in producing several excellent State of the World Reports for other sectors. Details of the authors of the individual chapters and the thematic background studies are provided in the table below. The technical editorial team of Matthias Halwart, Devin M. Bartley, Graham Mair and Austin Stankus is gratefully acknowledged for improving each chapter and the overall Report. vi Section Title Author(s) Introduction Introduction Matthias Halwart Graham C. Mair, Xiaowei Zhou, Chapter 1 The state of world aquaculture and fisheries Simon Funge-Smith The use and exchange of aquatic genetic resources of Chapter 2 farmed aquatic species and their wild relatives within Devin M. Bartley national jurisdiction Drivers and trends in aquaculture: consequences for Chapter 3 Simon Funge-Smith aquatic genetic resources within national jurisdiction In situ conservation of farmed aquatic species and Chapter 4 Devin M. Bartley their wild relatives within national jurisdiction Ex situ conservation of aquatic genetic resources of Chapter 5 farmed aquatic species and their wild relatives within Ruth Garcia-Gomez national jurisdiction Stakeholders with interests in aquatic genetic Chapter 6 resources of farmed aquatic species and their wild Malcolm Beveridge relatives within national jurisdictions National policies and legislation for aquatic genetic Chapter 7 resources of farmed aquatic species and their wild Devin M. Bartley relatives within national jurisdiction Research, education, training and extension on aquatic Chapter 8 genetic resources within national jurisdiction: Ruth Garcia-Gomez coordination, networking and information International collaboration on aquatic genetic Chapter 9 resources of farmed aquatic species and their wild Matthias Halwart relatives Matthias Halwart,