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Plant Genetic Resources and Genomics: Mainstreaming Agricultural Research Through Genomics

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Plant Genetic Resources and Genomics: Mainstreaming Agricultural Research Through Genomics Background Study 5 PLANT GENETIC RESOURCES AND GENOMICS: MAINSTREAMING AGRICULTURAL RESEARCH THROUGH GENOMICS Norman Warthmann This document has been produced by the request of the Secretariat of the International Treaty and in the context of the first expert consultation on the Global Information System on Plant Genetic Resources for Food and Agriculture to stimulate the discussion on genomics and to facilitate the consideration of appropriate technical and organizational linkages during the development and implementation of the Global Information System. www.planttreaty.org 1 Author: Dr Norman Warthmann, Lecturer in Plant Biology, Genetics and Genomics at The Australian National University The designations employed and the presentation of material in this information product do not imply the expression of any opinion whatsoever on the part of the Food and Agriculture Organization of the United Nations (FAO) concerning the legal or development status of any country, territory, city or area or of its authorities, or concerning the delimitation of its frontiers or boundaries. The mention of specific companies or products of manufacturers, whether or not these have been patented, does not imply that these have been endorsed or recommended by FAO in preference to others of a similar nature that are not mentioned. This study reflects the technical opinion of its authors, which is not necessarily those of the FAO, or the Secretariat of the International Treaty on Plant Genetic Resources for Food and Agriculture. © FAO, 2014 FAO encourages the use, reproduction and dissemination of material in this information product. Except where otherwise indicated, material may be copied, downloaded and printed for private study, research and teaching purposes, or for use in non-commercial products or services, provided that appropriate acknowledgement of FAO as the source and copyright holder is given and that FAO’s endorsement of users’ views, products or services is not implied in any way. All requests for translation and adaptation rights, and for resale and other commercial use rights should be made via www.fao.org/contact-us/licence-request or addressed to [email protected]. 2 NOTE FROM THE SECRETARIAT This study is available on line at: http://www.planttreaty.org/content/background-study-paper-5 BACKGROUND 1. Through Article 12.1 of the Treaty, Contracting Parties agreed to facilitate access to plant genetic resources for food and agriculture under the Multilateral System and in accordance with the provisions of the Treaty. 2. Among the conditions of the transfer, Article 12.3.c. of the Treaty states that “All available passport data and, subject to applicable law, any other associated available non- confidential descriptive information, shall be made available with the plant genetic resources for food and agriculture provided”. 3. Article 12.4 of the Treaty provides that facilitated access under the Multilateral System shall be provided pursuant to a Standard Material Transfer Agreement (SMTA), which was adopted the Governing Body of the Treaty, in its Resolution 1/2006 of 16 June 2006. 4. Article 3 of the SMTA states: “The Plant Genetic Resources for Food and Agriculture specified in Annex 1 to this Agreement (hereinafter referred to as the “Material”) and the available related information referred to in Article 5b and in Annex 1 are hereby transferred from the Provider to the Recipient subject to the terms and conditions set out in this Agreement.” 5. Article 17 of the International Treaty states that “Contracting Parties shall cooperate to develop and strengthen a global information system to facilitate the exchange of information, based on existing information systems, on scientific, technical and environmental matters related to plant genetic resources for food and agriculture". 6. At its Fifth session in Muscat in September 2013, the Governing Body of the International Treaty adopted the Resolution 10/2013, Development of the Global Information System on plant Genetic Resources in the context of Article 17 of the International Treaty, and requested the Secretary to call for an expert consultation. 7. In preparation of the expert consultation scheduled on January 2015 in San Diego, California, USA, the Secretariat has requested the preparation of this study as a technical input. 8. The present document is intent to bring light to the importance of plant genomics for food and agriculture and present some suggestions for the consideration of technical experts and does not intent to make recommendations on the decisions that the Governing Body will need to take, but to provide information and technical analysis that may help identify both problems and opportunities, and so support the Consultation in its task of providing advice to the Secretary for the Development of the Vision that will be later on presented to the Governing Body in October 2015. 9. The author would like to thanks the Treaty Secretariat for this opportunity and have invited comments from other experts to further elaborate this preliminary study exploring the role of genomics in its potential impact in the development of the Global Information System. 3 Plant Genetic Resources for Food and Agriculture and Genomics : Mainstreaming Agricultural Research through Genomics Crop improvement is facilitated by harnessing the gene pool of the species and related species to find genotypes and recombine genes to deliver superior plant performance in agriculture, food, energy and biomaterial production. Henry, R. J. (2011). Next-generation sequencing for understanding and accelerating crop domestication. Briefings in Functional Genomics. I believe plant breeders and geneticists will drive the next agricultural revolution via the web by sharing the phenotypes and genotypes of crop plants using a system that can store, manage, and allow the retrieval of data. Zamir, D. (2013). Where have all the crop phenotypes gone? PLoS Biology, 11(6), e1001595. But the real revolutionary potential in this method lies in its power to open up the genetic bottleneck created thousands of years ago when our major crops were first domesticated. Goff, S. A., & Salmeron, J. M. (2004). Back to the future of cereals. Scientific American, 291(2), 42–49. 4 Table of Contents Introduction ...................................................................................................................................... 6 Motivation .................................................................................................................................................... 6 The opportunity - The genomics revolution .................................................................................... 7 The chance.................................................................................................................................................... 9 The challenge .............................................................................................................................................. 9 Genomes and genetic variation .......................................................................................................... 10 Genomics .......................................................................................................................................... 12 DNA Sequencing ....................................................................................................................................... 12 Technologies and machines ............................................................................................................................ 13 Sequencing strategies........................................................................................................................................ 15 SNP genotyping .................................................................................................................................................... 18 File formats ............................................................................................................................................................ 19 Data Analysis - Genomic information ............................................................................................... 22 Assembly vs. re-sequencing ............................................................................................................................ 22 Genome assembly ............................................................................................................................................... 23 Genome assembly quality ................................................................................................................................ 27 Genome Re-sequencing .................................................................................................................................... 28 The Transcriptome ............................................................................................................................................. 31 Transcriptomics - Gene Expression............................................................................................................. 33 Epigenetics ............................................................................................................................................................. 34 Data sharing ............................................................................................................................................... 36 Data sharing - Technical
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