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New Techniques in Agricultural Biotechnology New Techniques in Agricultural Biotechnology EUROPEAN COMMISSION Directorate-General for Research and Innovation Unit RTD.01 – Scientific Advice Mechanism (SAM) E-mail: [email protected] [email protected] European Commission B-1049 Brussels EUROPEAN COMMISSION New Techniques in Agricultural Biotechnology High Level Group of Scientific Advisors Explanatory Note 02 Brussels, 28 April 2017 2017 Directorate-General for Research and Innovation EUROPE DIRECT is a service to help you find answers to your questions about the European Union Freephone number (*): 00 800 6 7 8 9 10 11 (*) The information given is free, as are most calls (though some operators, phone boxes or hotels may charge you) LEGAL NOTICE Neither the European Commission nor any person acting on behalf of the Commission is responsible for the use which might be made of the following information. The contents of this report are the sole responsibility of the High Level Group of Scientific Advisors. Although staff of the Commission services participated in the preparation of the report and provided information and assistance in assembling it, the views expressed in this report reflect the collective opinion of the Members of the High Level Group of Scientific Advisors, and may not in any circumstances be regarded as stating an official position of the European Commission. More information on the European Union is available on the Internet (http://europa.eu). Luxembourg: Publications Office of the European Union, 2016. Print ISBN 978-92-79-66223-2 doi: 10.2777/17902 KI-02-17-242-EN-C PDF ISBN 978-92-79-66222-5 doi: 10.2777/574498 KI-02-17-242-EN-N © European Union, 2017 Reproduction is authorised provided the source is acknowledged. Printed in Belgium. Image(s) © Francis D, Finer JJ, Grotewold E. – Figure 1 – 2017 – Source: Challenges and opportunities for improving food quality and nutrition through plant biotechnology. Curr Opin Biotechnol.2017; 44. doi:10.1016/j.copbio.2016.11.009. http://www.sciencedirect.com/science/article/pii/S0958166916302658#gr1 Chan SWL. – Figure 3 – 2010 - Chromosome engineering: Power tools for plant genetics. Trends Biotechnol. 2010;28(12):605-610. doi:10.1016/j.tibtech.2010.09.002. http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2810%2900155-1 Explanatory note New Techniques in Agricultural Biotechnology Table of Contents 1. INTRODUCTION ..................................................................... 14 2. SUMMARY .............................................................................. 18 3. DESCRIPTION OF TECHNIQUES .............................................. 29 3.1. CONVENTIONAL BREEDING TECHNIQUES (CBT) .................. 34 3.1.1. Conventional breeding techniques in plants ............................. 34 3.1.2. Conventional breeding techniques in farm animals .................... 41 3.1.3. Conventional breeding techniques for microbial strain development and improvement ............................................................................. 46 3.2. ESTABLISHED TECHNIQUES OF GENETIC MODIFICATION (ETGM) IN BIOTECHNOLOGY ................................................................... 51 3.2.1. Plants ................................................................................. 54 3.2.2. Animals .............................................................................. 57 3.2.3. Microorganisms ................................................................... 58 3.3. NEW BREEDING TECHNIQUES (NBT) ................................... 61 3.3.1. Genome editing technologies ................................................. 62 3.3.2. Techniques introducing genetic material from same or sexually compatible species: cisgenesis and intragenesis ................................... 72 3.3.3. Agro-infiltration ................................................................... 74 3.3.4. Epigenetic modification: RNA-dependent DNA methylation ......... 74 3.3.5. Grafting .............................................................................. 75 3.3.6. Reverse breeding ................................................................. 76 3.4. APPLICATION OF NBT IN GENE DRIVES AND IN SYNTHETIC BIOLOGY ..................................................................................... 77 3.4.1. Synthetic biology ................................................................. 77 3.4.2. Gene drives ........................................................................ 79 SAM High Level Group of Scientific Advisors April 2017 5 Explanatory note New Techniques in Agricultural Biotechnology 4. COMPARISONS ....................................................................... 83 4.1. GENERAL COMMENTS ........................................................... 83 4.2. COMPARISON OF NEW TECHNIQUES (NBT) AND CONVENTIONAL BREEDING TECHNIQUES (CBT) ................................................... 93 4.2.1. Detectability/Identification .................................................... 93 4.2.2. Unintended effects ............................................................... 94 4.2.3. Presence of exogenous DNA .................................................. 95 4.2.4. End products – characteristics ............................................... 96 4.2.5. Ease of use/efficiency ........................................................... 96 4.2.6. Speed and costs .................................................................. 97 4.2.7. Maturity ............................................................................. 98 4.3. NEW TECHNIQUES (NBT) AND ESTABLISHED TECHNIQUES OF GENETIC MODIFICATION (ETGM) ............................................. 107 4.3.1. Detectability/Identification .................................................. 108 4.3.2. Unintended effects ............................................................. 109 4.3.3. Presence of exogenous DNA ................................................ 109 4.3.4. End-product ...................................................................... 110 4.3.5. Ease of Use and Efficiency ................................................... 111 4.3.6. Speed/Cost ....................................................................... 112 4.3.7. Maturity ........................................................................... 112 6 April 2017 SAM High Level Group of Scientific Advisors Explanatory note New Techniques in Agricultural Biotechnology List of Figures FIGURE 1 - TIMELINE OF KEY EVENTS IN PLANT BREEDING ......................................................................... 31 FIGURE 2 - MENDELIAN LAWS OF INHERITANCE ..................................................................................... 35 FIGURE 3 - GENE EXPRESSION ............................................................................................................ 52 FIGURE 4 - RECOMBINANT FORMATION OF PLASMIDS ............................................................................. 53 FIGURE 5 - TRANSFORMATION WITH AGROBACTERIUM TUMEFACIENS ........................................................ 55 FIGURE 6 - GENOME EDITING TIMELINE- APPLICATIONS IN CROPS AND FARM ANIMALS .................................. 62 FIGURE 7 - REVERSE BREEDING ........................................................................................................... 76 FIGURE 8 – TECHNIQUES FOR THE DETECTION AND IDENTIFICATION OF GENETIC ALTERATIONS......................... 89 FIGURE 9 - MINIMAL LENGTH FOR A FRAGMENT TO BE UNIQUE IN AN ORGANISM AS A FUNCTION OF ITS TOTAL GENOME SIZE ........................................................................................................................... 91 FIGURE 10 - PUBLICATIONS REVIEWS OVER TIME BY TECHNIQUE (SCOPUS) - EXAMPLE OUTPUT FROM ANALYSIS BY JRC USING TIM SOFTWARE ...................................................................................................... 141 FIGURE 11 - FLOW DIAGRAM OF LITERATURE SEARCH RESULTS AND SCREENING ......................................... 142 List of Tables TABLE 1A - NBT COMPARED WITH CBT - DETECTABILITY/IDENTIFICATION ............................................... 101 TABLE 2A - NBT COMPARED WITH CBT – UNINTENDED EFFECTS ........................................................... 103 TABLE 3A - NBT COMPARED WITH CBT – PRESENCE OF EXOGENOUS DNA MOLECULE ............................... 105 TABLE 4A - NBT COMPARED WITH CBT – END-PRODUCTS .................................................................... 107 TABLE 5A - NBT COMPARED WITH CBT – EASE OF USE /EFFICIENCY ....................................................... 109 TABLE 6A - NBT COMPARED WITH CBT - SPEED-COST ......................................................................... 111 TABLE 7A - NBT COMPARED WITH CBT - MATURITY............................................................................ 113 TABLE 1B - NBT COMPARED WITH ETGM - DETECTABILITY/IDENTIFICATION ............................................ 123 TABLE 2B - NBT COMPARED WITH ETGM – UNINTENDED EFFECTS ........................................................ 125 TABLE 3B - NBT COMPARED WITH ETGM – PRESENCE OF EXOGENOUS DNA MOLECULE ........................... 127 TABLE 4B - NBT COMPARED WITH ETGM– END-PRODUCTS ................................................................. 127 TABLE 5B - NBT COMPARED WITH ETGM – EASE OF USE /EFFICIENCY ................................................... 129 TABLE 6B - NBT COMPARED WITH ETGM - SPEED-COST ...................................................................... 129 TABLE
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