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Epidemiology of Herbicide Resistance Evolution in Rice Weeds and Variability in Echinochloa Spp

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Epidemiology of Herbicide Resistance Evolution in Rice Weeds and Variability in Echinochloa Spp Sede Amministrativa: Università degli Studi di Padova Dipartimento di Agronomia Animali Alimenti Risorse Naturali e Ambiente (DAFNAE) ___________________________________________________________________ CORSO DI DOTTORATO DI RICERCA IN: CROP SCIENCE CICLO XXXI Epidemiology of herbicide resistance evolution in rice weeds and variability in Echinochloa spp. Tesi redatta con il contributo finanziario di Dow Agrosciences Coordinatore: Ch.mo Prof. Giuseppe Zanin Supervisore: Maurizio Sattin Co-Supervisore: Prof. Roberta Masin Dottorando : Elisa Mascanzoni Declaration I hereby declare that this submission is my own work and that, to the best of my knowledge and belief, it contains no material previously published or written by another person nor material which to a substantial extent has been accepted for the award of any other degree or diploma of the university or other institute of higher learning, except where due acknowledgement has been made in the text. November 29th 2018 Elisa Mascanzoni A copy of the thesis will be available at http://paduaresearch.cab.unibo.it Dichiarazione Con la presente affermo che questa tesi è frutto del mio lavoro e che, per quanto io ne sia a conoscenza, non contiene materiale precedentemente pubblicato o scritto da un’altra persona nè materiale che è stato utilizzato per l’ottenimento di qualunque altro titolo o diploma dell’ università o altro istituto di apprendimento, a eccezione del caso in cui ciò venga riconosciuto nel testo. 29 Novembre 2018 Elisa Mascanzoni Una copia della tesi sarà disponibile presso http://paduaresearch.cab.unipd.it Alice ed Irene Look wide, and even when you think you are looking wide, look wider still. Robert Stephenson Smyth Baden Powell, Lord of Gilwell. TABLE OF CONTENTS CHAPTER I – INTRODUCTION 1.1 Man vs weed ............................................................................................................................. 8 1.2 Herbicide brief history ............................................................................................................... 8 1.3 Herbicide Classification ............................................................................................................. 9 1.4 Herbicide resistance ................................................................................................................ 11 1.4.1 Definitions of herbicide resistance ........................................................................................... 11 1.4.2 Factors influencing resistance evolution .................................................................................. 12 1.4.3 Resistance Mechanisms ........................................................................................................... 14 1.4.4. Herbicide resistance: current situation worldwide and in Italy ................................................. 15 1.4.5 Resistance Management .......................................................................................................... 18 1.4.6 Epidemiology in herbicide resistance studies ........................................................................... 19 1.5 Rice, a key crop worldwide and in Italy .................................................................................... 21 1.5.5 Weed flora in rice fields ........................................................................................................... 23 1.5.6 Echinochloa spp., rice’s worst weed ......................................................................................... 24 1.5.6.1 Echinochloa spp. morphological classification ......................................................................... 25 1.5.6.2 Echinochloa spp. discrimination through molecular markers .................................................. 28 1.5.6.3 DNA barcoding: an innovative tool for weed species discrimination ....................................... 29 1.5.6.4 Echinochloa spp. and herbicide efficacy .................................................................................. 32 1.5.7 Herbicide Resistance in rice in Italy .......................................................................................... 33 1.5.8 Weed management in rice fields .............................................................................................. 34 1.5.8.1 New molecule for weed control in rice ..................................................................................... 36 1.6 AIMS of the RESEARCH ............................................................................................................ 37 CHAPTER II – MATERIALS and METHODS 2.1 Epidemiology of herbicide resistance in rice in Italy ................................................................ 39 2.1.1. Definition of the area in the study ........................................................................................... 39 2.1.2. Database building .................................................................................................................... 39 2.1.2.1 Resistance data ....................................................................................................................... 40 2.1.2.2. Soil data ................................................................................................................................... 42 2.1.2.3. Water seeding data ................................................................................................................. 43 2.1.2.4 Rotation Rate data .................................................................................................................. 43 2.1.3 Mapping .................................................................................................................................. 43 2.1.4 Statistical analyses ................................................................................................................... 44 2.1.4.1 Discriminant analyses .............................................................................................................. 45 2.1.4.2 Logistic regression ................................................................................................................... 45 2.1.4.3 Neural network approach ........................................................................................................ 46 2.1.5 Echinochloa spp. random survey ............................................................................................. 48 2.2 Echinochloa spp. case study .................................................................................................... 51 2.2.1 Seed samples collection and morphological classification on original accessions. .................... 51 2.2.2 Preliminary screening .............................................................................................................. 52 2.2.3 Accessions reproduction ......................................................................................................... 53 2.2.4 Collaboration with the Meise Botanic Garden (Belgium) .......................................................... 55 2.2.4.1 Analyses of morphological data .............................................................................................. 55 2.2.5 DNA barcoding ........................................................................................................................ 57 2.2.5.1 gDNA extraction ...................................................................................................................... 57 2.2.5.2 cpDNA genes amplification and sequencing ............................................................................ 58 2.2.6 Specie specific PCR ................................................................................................................... 62 2.2.7 Herbicide efficacy on different Echinochloa species ................................................................ 63 2.2.7.1 Greenhouse preliminary screening .......................................................................................... 64 2.2.7.2 DR experiments design ............................................................................................................ 65 2.2.7.3 Statistical analyses .................................................................................................................. 66 CHAPTER III – RESULTS and DISCUSSION 3.1 Epidemiology of herbicide resistance in rice in Italy ................................................................ 68 3.1.1 Database analyses ................................................................................................................... 68 3.1.2 Discriminant analysis and logistic regression ........................................................................... 70 3.1.3 Neural network analyses ......................................................................................................... 73 3.1.4 Echinochloa spp. resistance screening ..................................................................................... 76 3.1.5 Association between resistance in collected populations and initial infestation density .......... 82 3.1.6 Specific conclusions ................................................................................................................. 84 3.2 Echinochlos spp. case study ..................................................................................................... 86 3.2.1 Discrimination of Italian accession performed in 2015 ...........................................................
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