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Innate Potatoes Title Petition for Determination of Nonregulated Status for InnateTM Potatoes with Late Blight Resistance, Low Acrylamide Potential, Reduced Black Spot, and Lowered Reducing Sugars: Russet Burbank Event W8 We submit this petition under 7 CFR 340.6 to request that the Administrator make a determination that the articles should not be regulated under 7 CFR Part 340. Submitted by Pete Clark Ph.D. J.R. Simplot Company Prepared by Pete Clark Ph.D.*, Jeff Habig Ph.D., Jingsong Ye Ph.D., and Susan Collinge Ph.D. J.R. Simplot Company Submitted on March 28, 2014 By J.R. Simplot Company Petition USDA Petition 14-093-01p OECD Unique identifier: SPS-W8-4 *Corresponding Author: Pete Clark Ph.D. J.R. Simplot Company 5369 West Irving Street Boise, ID 83706 Tel.: (208) 780-6066 This Document (Including Appendices) Does Not Contain CBI J.R. Simplot Company Page 1 of 199 Release of Information J.R. Simplot Company is submitting the information in this assessment for review by the USDA as part of the regulatory process. By submitting this information, J.R. Simplot Company does not authorize its release to any third party except to the extent it is requested and required under the Freedom of Information Act, 5 U.S.C., paragraph 552; USDA complies with the provisions of FOIA and USDA’s implementation regulations (7 CFR Part 1.4). Except in accordance with the Freedom of Information act, J.R. Simplot Company does not authorize the release, publication or other distribution of this information without J.R. Simplot Company’s prior notice and consent. J.R. Simplot Company Page 3 of 199 Table of Contents Title ............................................................................................................................................................... 1 Table of Contents .......................................................................................................................................... 4 List of Tables ................................................................................................................................................. 8 List of Figures ................................................................................................................................................ 9 List of Appendices ....................................................................................................................................... 10 List of Abbreviations, Acronyms, Definitions, and Commonly Used Terms ............................................... 11 Summary ..................................................................................................................................................... 14 1.0 Rationale for Potatoes with Late Blight Resistance, Low Acrylamide, Reduced Black Spot, and Lowered Reducing Sugars ........................................................................................................................... 18 1.1 Basis for Determination of Nonregulated Status ....................................................................... 18 1.2 Rationale and Benefits of Developing Potatoes with Late Blight Resistance ............................. 19 1.3 Rationale and Benefits of Developing Potatoes with Low Acrylamide Potential ....................... 20 1.4 Rationale and Benefits of Developing Potatoes with Reduced Black Spot ................................ 22 1.5 Rationale and Benefits of Developing Potatoes with Reduced Levels of Reducing Sugars ........ 23 1.6 Conclusions: Rationale for Potatoes with Late Blight Resistance, Low Acrylamide, Reduced Black Spot, and Lowered Reducing Sugars ............................................................................................. 24 1.7 References .................................................................................................................................. 25 2.0 The Biology of Potato ...................................................................................................................... 28 2.1 History of Potato ......................................................................................................................... 28 2.2 Use of the Potato as Food and Feed in the USA ......................................................................... 28 2.3 Taxonomy of the Genus Solanum ............................................................................................... 29 2.4 Genetics of Potato ...................................................................................................................... 29 2.5 Potato Growth and Life Cycle ..................................................................................................... 30 2.6 Seed Propagation ........................................................................................................................ 30 2.7 Variety Development .................................................................................................................. 31 2.8 Recipient Potato Varieties .......................................................................................................... 33 2.9 Typical Agronomic Practices ....................................................................................................... 33 2.10 Pollination and Outcrossing ........................................................................................................ 33 2.11 Wild potatoes in the U.S. ............................................................................................................ 34 2.12 Weediness .................................................................................................................................. 35 2.13 Characterization of the Recipient Potato Cultivar ...................................................................... 36 2.14 Conclusions: The Biology of Potato ........................................................................................... 37 2.15 References .................................................................................................................................. 38 3.0 Development of W8 Russet Burbank: Description of Marker-Free DNA Transformation .............. 40 3.1 Introduction ................................................................................................................................ 40 3.2 Description of the Transformation System ................................................................................ 40 3.3 Transformation Method ............................................................................................................. 40 3.4 References .................................................................................................................................. 42 4.0 Donor Genes and Regulatory Sequences ........................................................................................ 43 4.1 Plasmids used for Transformation .............................................................................................. 43 4.2 References .................................................................................................................................. 50 5.0 Genetic Characterization of Russet Burbank Event W8 .................................................................. 51 5.1 Introduction ................................................................................................................................ 51 5.2 Copy number and structure of the DNA Inserts ......................................................................... 51 5.2.1 Characterization of insertion number for pSIM1278 and pSIM1678 ................................. 54 5.2.2 Structure of the pSIM1278 DNA insert ............................................................................... 57 5.2.3 Structure of the pSIM1678 DNA insert ............................................................................... 63 J.R. Simplot Company Page 4 of 199 5.2.4 Conclusions: Copy number and structure of the DNA Inserts ........................................... 79 5.3 Flanking Regions of Inserted Sequences .................................................................................... 79 5.4 Absence of Plasmid Backbone Sequence ................................................................................... 80 5.4.1 Selection of Backbone-free Plants ...................................................................................... 80 5.4.2 Molecular Evidence for Backbone-free Plants .................................................................... 81 5.4.3 Conclusions: Absence of Plasmid Backbone ...................................................................... 86 5.5 Genetic stability of W8 over three generations ......................................................................... 86 5.5.1 Molecular Evidence for Stability of the DNA Insert ............................................................ 86 5.5.2 Phenotypic Evidence for Stability of the DNA Insert .......................................................... 91 5.5.3 Summary of Genetic Stability Studies ................................................................................. 91 5.6 Characteristics of Transferred DNA and Gene Regulation ......................................................... 91 5.7 Event-Specific PCR ...................................................................................................................... 91 5.8 Summary of the Genetic Characterization of Event W8 ...........................................................
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