New Techniques in Agricultural Biotechnology

172 Pages·2017·2.63 MB·English

by  European Commission

Scientific Advice
Mechanism (SAM)
New techniques in
Agricultural
Biotechnology
High Level Group of Scientific Advisors
Explanatory Note 02/2017
Research and
Innovation
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
Scientific Advice Mechanism (SAM)
INDEPENDENT SCIENTIFIC ADVICE FOR POLICY MAKING
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
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Internal document sources:
Pag. 26 Figure 1: "Challenges and opportunities for improving food quality and nutrition through plant biotechnology. Curr Opin Biotechnol.
2017", p. 44, Francis D, Finer JJ, Grotewold E., 2017 – http://www.sciencedirect.com/science/article/pii/S0958166916302658#gr1;
Pag. 71 Figure 7: "Chromosome engineering: Power tools for plant genetics. Trends Biotechnol. 2010", p. 28, Chan SWL., 2010 -
http://www.cell.com/trends/biotechnology/abstract/S0167-7799%2810%2900155-1
Explanatory note
New Techniques in Agricultural Biotechnology
Table of Contents
1. INTRODUCTION ..................................................................... 11
2. SUMMARY .............................................................................. 14
3. DESCRIPTION OF TECHNIQUES .............................................. 24
3.1. CONVENTIONAL BREEDING TECHNIQUES (CBT) .................. 29
3.1.1. Conventional breeding techniques in plants .............................. 29
3.1.2. Conventional breeding techniques in farm animals .................... 36
3.1.3. Conventional breeding techniques for microbial strain development
and improvement .............................................................................. 41
3.2. ESTABLISHED TECHNIQUES OF GENETIC MODIFICATION (ETGM)
IN BIOTECHNOLOGY ................................................................... 46
3.2.1. Plants .................................................................................. 49
3.2.2. Animals ............................................................................... 52
3.2.3. Microorganisms .................................................................... 53
3.3. NEW BREEDING TECHNIQUES (NBT) ................................... 56
3.3.1. Genome editing technologies .................................................. 56
3.3.2. Techniques introducing genetic material from same or sexually
compatible species: cisgenesis and intragenesis .................................... 67
3.3.3. Agro-infiltration .................................................................... 68
3.3.4. Epigenetic modification: RNA-dependent DNA methylation ......... 69
3.3.5. Grafting ............................................................................... 69
3.3.6. Reverse breeding .................................................................. 70
3.4. APPLICATION OF NBT IN GENE DRIVES AND IN SYNTHETIC
BIOLOGY ..................................................................................... 71
3.4.1. Synthetic biology .................................................................. 71
3.4.2. Gene drives .......................................................................... 73
SAM High Level Group of Scientific Advisors April 2017 5
Explanatory note
New Techniques in Agricultural Biotechnology
4. COMPARISONS ....................................................................... 77
4.1. GENERAL COMMENTS ........................................................... 77
4.2. COMPARISON OF NEW TECHNIQUES (NBT) AND CONVENTIONAL
BREEDING TECHNIQUES (CBT) ................................................... 87
4.2.1. Detectability/Identification ..................................................... 87
4.2.2. Unintended effects ................................................................ 88
4.2.3. Presence of exogenous DNA ................................................... 89
4.2.4. End products – characteristics ................................................ 90
4.2.5. Ease of use/efficiency ............................................................ 90
4.2.6. Speed and costs ................................................................... 91
4.2.7. Maturity ............................................................................... 92
4.3. NEW TECHNIQUES (NBT) AND ESTABLISHED TECHNIQUES OF
GENETIC MODIFICATION (ETGM) ............................................. 101
4.3.1. Detectability/Identification ................................................... 102
4.3.2. Unintended effects .............................................................. 103
4.3.3. Presence of exogenous DNA ................................................. 103
4.3.4. End-product ....................................................................... 104
4.3.5. Ease of Use and Efficiency .................................................... 105
4.3.6. Speed/Cost ........................................................................ 106
4.3.7. Maturity ............................................................................. 106
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 ......................................................................... 26
FIGURE 2 - MENDELIAN LAWS OF INHERITANCE ..................................................................................... 30
FIGURE 3 - GENE EXPRESSION ............................................................................................................ 47
FIGURE 4 - RECOMBINANT FORMATION OF PLASMIDS ............................................................................. 48
FIGURE 5 - TRANSFORMATION WITH AGROBACTERIUM TUMEFACIENS ........................................................ 50
FIGURE 6 - GENOME EDITING TIMELINE- APPLICATIONS IN CROPS AND FARM ANIMALS .................................. 57
FIGURE 7 - REVERSE BREEDING ........................................................................................................... 71
FIGURE 8 – TECHNIQUES FOR THE DETECTION AND IDENTIFICATION OF GENETIC ALTERATIONS......................... 83
FIGURE 9 - MINIMAL LENGTH FOR A FRAGMENT TO BE UNIQUE IN AN ORGANISM AS A FUNCTION OF ITS TOTAL
GENOME SIZE ........................................................................................................................... 85
FIGURE 10 - PUBLICATIONS REVIEWS OVER TIME BY TECHNIQUE (SCOPUS) - EXAMPLE OUTPUT FROM ANALYSIS BY
JRC USING TIM SOFTWARE ...................................................................................................... 122
FIGURE 11 - FLOW DIAGRAM OF LITERATURE SEARCH RESULTS AND SCREENING ......................................... 123

List of Tables
TABLE 1A - NBT COMPARED WITH CBT - DETECTABILITY/IDENTIFICATION ................................................. 94
TABLE 2A - NBT COMPARED WITH CBT – UNINTENDED EFFECTS ............................................................. 95
TABLE 3A - NBT COMPARED WITH CBT – PRESENCE OF EXOGENOUS DNA MOLECULE ................................. 96
TABLE 4A - NBT COMPARED WITH CBT – END-PRODUCTS ...................................................................... 97
TABLE 5A - NBT COMPARED WITH CBT – EASE OF USE /EFFICIENCY ......................................................... 98
TABLE 6A - NBT COMPARED WITH CBT - SPEED-COST ........................................................................... 99
TABLE 7A - NBT COMPARED WITH CBT - MATURITY............................................................................ 100
TABLE 1B - NBT COMPARED WITH ETGM - DETECTABILITY/IDENTIFICATION ............................................ 109
TABLE 2B - NBT COMPARED WITH ETGM – UNINTENDED EFFECTS ........................................................ 110
TABLE 3B - NBT COMPARED WITH ETGM – PRESENCE OF EXOGENOUS DNA MOLECULE ........................... 111
TABLE 4B - NBT COMPARED WITH ETGM– END-PRODUCTS ................................................................. 111
TABLE 5B - NBT COMPARED WITH ETGM – EASE OF USE /EFFICIENCY ................................................... 112
TABLE 6B - NBT COMPARED WITH ETGM - SPEED-COST ...................................................................... 112
TABLE 7B - NBT COMPARED WITH ETGM – MATURITY ....................................................................... 113

ANNEXES
ANNEX 1 – SCOPING PAPER ............................................................................................................. 116
ANNEX 2 - METHODOLOGY FOR THE EVIDENCE REVIEW ........................................................................ 120
ANNEX 3 – REFERENCES .................................................................................................................. 124
ANNEX 4 – GLOSSARY .................................................................................................................... 141
SAM High Level Group of Scientific Advisors April 2017 7
Explanatory note
New Techniques in Agricultural Biotechnology
High Level Group of Scientific Advisors
Janusz Bujnicki
Professor, Head of the Laboratory of
Bioinformatics and Protein Engineering,
International Institute of Molecular and Cell
Biology, Warsaw

Pearl Dykstra
Deputy Chair
Professor of Sociology, Erasmus University
Rotterdam

Elvira Fortunato
Professor, Materials Science Department of the
Faculty of Science and Technology, NOVA
University, Lisbon

Rolf-Dieter Heuer
Chair
Former Director-General of the European
Organization for Nuclear Research (CERN)
Carina Keskitalo
Professor of Political Science, Department of
Geography and Economic History, Umea University

Paul Nurse
Director, Francis Crick Institute, London

Cédric Villani
Director, Henri Poincaré Institute, Paris

8 April 2017 SAM High Level Group of Scientific Advisors
Explanatory note
New Techniques in Agricultural Biotechnology
ACKNOWLEDGEMENTS
This Explanatory Note was presented by the SAM High Level Group (SAM
HLG) of Scientific Advisors to the European Commissioner for Research,
Science and Innovation, Carlos Moedas on 28 April 2017.
The HLG Members1 Janusz Bujnicki, Pearl Dykstra and Henrik Wegener2
authored this Note which is endorsed by the full SAM HLG. The SAM HLG
received extensive support from scientific experts in a steering group,
namely Professors Alain Boudet, Paul Hooykaas, Heiner Niemann, Peter
Ruhdal Jensen and Joachim Schiemann. These experts were nominated by
the Science Advice for Policy by European Academies (SAPEA) consortium3.
Additional scientific support to the Steering Group was provided by Guy van
den Eede representing the Directorate General Joint Research Centre. The
HLG wishes to thank these experts for the invaluable support they have
provided in the production of this Note.
The HLG also wishes to thank the scientific support team (EC's Scientific
Advice Mechanism Unit, in particular Sigrid Weiland, Dulce Boavida, Stuart
Kirk and Jeremy Bray) and staff members of SAPEA (Louise Edwards,
Thomas Stehnken and Céline Tschirhart). Finally, the SAM HLG also wishes
to thank other EC staff, and in particular those from Directorates General
(DG) Joint Research Centre, Health and Food Safety, Environment,
Agriculture and Rural Development, and Internal Market, Industry,
Entrepreneurship and SMEs.

1 Current HLG members are listed in the Commission's Register of Expert Groups,
http://ec.europa.eu/transparency/regexpert/
2 HLG Chair and Member of HLG until 28 February 2017.
3 SAPEA brings together the outstanding knowledge and expertise of Fellows from over 100 Academies and
Learned Societies in over 40 countries across Europe. Funded through the EU’s Horizon 2020 programme,
the SAPEA consortium comprises Academia Europaea (AE), All European Academies (ALLEA), the
European Academies Science Advisory Council (EASAC), the European Council of Academies of Applied
Sciences, Technologies and Engineering (Euro-CASE) and the Federation of European Academies of
Medicine (FEAM).
SAM High Level Group of Scientific Advisors April 2017 9
Explanatory note
New Techniques in Agricultural Biotechnology

Introduction

10 April 2017 SAM High Level Group of Scientific Advisors