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Vitis Vinifera) Genetic Resources from Caucasus Using an Integrative Approach

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Vitis Vinifera) Genetic Resources from Caucasus Using an Integrative Approach University of Milan Department of Agricultural and Environmental Sciences Production, Landscape, Agroenergy PhD Course of: Agriculture, Environment and Bioenergy (XXIX cycle) Insight into grapevine (Vitis vinifera) genetic resources from Caucasus using an integrative approach Thesis supervisor Dr. Osvaldo Failla Università degli studi di Milano Thesis co-supervisor Dr. Maria Stella Grando Fondazione Edmund Mach, San Michele all’Adige Ph.D student Maria Lucia Prazzoli Matr. n° R10455 Contents CONTENTS Riassunto ii-iii Abstract iv-v Abbreviations vi-viii Chapter 1 General introduction 1-11 Chapter 2 Phylogenetic reconstruction of Caucasian germplasm 12-36 Chapter 3 Genetic mapping and QTL analysis in Mgaloblishvili Noir 37-63 Chapter 4 Gene expression assays 64-91 Chapter 5 General discussion 92-93 Appendix 94-96 References 97-105 Acknowledgements 106 i Riassunto RIASSUNTO La vite europea, Vitis vinifera L., è una delle colture arboree più importanti al mondo sia per il valore economico che per la superficie coltivata. Negli ultimi anni una maggiore sensibilità alle problematiche ambientali insieme alle opportunità di mercato hanno stimolato l’avvio di nuovi programmi di miglioramento genetico per ottenere cultivar resistenti alle malattie, in particolare peronospora e oidio. Questo ha comportato anche una maggiore attenzione verso la conservazione della risorse genetiche come fonti di caratteri utili. Allo stato attuale, i metodi tradizionali di miglioramento genetico, che includono l’utilizzo di altre specie di Vitis per la produzione di varietà ibride resistenti, possono essere complementati dalle nuove tecnologie quali la selezione assistita da marcatori molecolari (MAS) e la possibilità di identificare geni di interesse agronomico tramite analisi di popolazioni sperimentali (QTL mapping) o naturali (GWAS , association mapping). Recentemente una maggiore attenzione è stata volta alla valorizzazione dei vitigni coltivati e delle viti selvatiche del Caucaso, considerato il centro primario di domesticazione della vite e contraddistinto da un’elevata diversità genetica dei materiali. Il presente progetto di ricerca è improntato sulla caratterizzazione di un germoplasma ancora inesplorato di origine caucasiaca composto da 25 accessioni di Vitis vinifera, sia coltivate che selvatiche, che presentano una bassa suscettibilità alla peronospora, come descritto in Toffolatti et al., 2016 [1]. Al fine di definire una eventuale introgressione di tratti di resistenza provenienti da viti americane o asiatiche, è stato condotto un primo screening con marcatori molecolari associati ai loci Rpv noti, che apparentemente ha escluso tale evenienza. Una prima analisi filogenetica, tramite l’utilizzo di 21 marcatori microsatelliti, ha permesso di comparare queste accessioni con una collezione di cultivar di varia provenienza geografica precedentemente descritte (Vv1, Vv2, Vv3, Vv4) insieme ad altre varietà Georgiane e ad alcuni portainnesti, posizionandole all’interno della specie V. vinifera. Utilizzando un più ampio database composto da accessioni provenienti dall’Europa, Caucaso, Israele, America ed Asia, una seconda analisi ha permesso di collocare queste accessioni all’interno della regione Georgia caratterizzata da una forte diversità genetica, un numero elevato di varianti alleliche e di alleli privati. L’analisi delle componenti principali (PCoA) e l’analisi di struttura di popolazione hanno inoltre identificato all’interno del germoplasma georgiano una certa percentuale di “admixture” tra le varietà coltivate e le accessioni selvatiche. Allo scopo di approfondire questi risultati, è stata impostata un’analisi filogenetica basata su marcatori plastidiali descritti in letteratura, suddividendo la collezione sulla base dei diversi clorotipi. In accordo con i dati ottenuti, alcune cultivar georgiane, di particolare interesse per la loro bassa suscettibilità alla peronospora hanno mostrato una elevata omozigosità e un clorotipo molto simile a quello delle viti sylvestris Europee, lasciando presupporre la presenza di caratteri ancestrali tipici di varietà ibride di viti coltivate ed accessioni selvatiche. Tra queste accessioni una cultivar georgiana, nota come ‘Mgalobshivili N.’, è stata maggiormente approfondita per la sua bassa suscettibilità alla peronospora. Al fine di studiare questa tolleranza, è stata costruita una mappa genetica derivata da una popolazione segregante, composta da 154 genotipi, ottenuta da un’ autofecondazione della cultivar. Nonostante l’alta omozigosità della cultivar, sono stati ottenuti tutti i 19 cromosomi, utilizzando 177 marcatori molecolari (SSRs e SNPs). La mappa ottenuta è stata integrata a dati fenotipici della popolazione segregante al fine di elaborare una preliminare analisi QTL. La popolazione mantenuta in vaso è stata valutata in anni differenti: 2013, 2014, 2015 (maggio e luglio) e 2016 in seguito a infezioni artificiali di peronospora. Tuttavia il comportamento delle piante non è risultato riproducibile nelle diverse annate e andrà valutato in condizioni di maggiore stabilità sulla popolazione adulta. L’analisi QTL effettuata ha individuato tre QTLs nel 2014 sui cromosomi 1, 7 e 11 ed un QTL minore nel 2016 coincidente con il locus Rpv11. Su tali cromosomi è stato effettuato un fine mapping per poter circoscrivere il più possibile i geni di interesse. All’interno di questi QTL sono stati identificati prevalentemente geni legati al pathway dell’etilene. E’ stato inoltre intrapreso un approccio integrativo basato su uno studio di espressione genica. Sono stati selezionati due genotipi della popolazione che durante gli anni hanno mostrato un comportamento differente in risposta all’infezione con P. viticola ed insieme alla linea parentale sono stati micropropagati, partendo da internodi. In un arco di sette mesi, sono state ottenute piantine sufficientemente grandi per poter effettuare un esperimento di espressione genica. Allo scopo di testare l’efficienza dell’inoculo e la risposta dei vari ii Riassunto genotipi a tale inoculo, sono stati eseguite delle valutazioni fenotipiche su dischetto fogliare indicative delle differenze di sporulazione tra i genotipi. Successivamente lo stesso inoculo è stato testato sulle diverse repliche biologiche delle intere piante e sono stati effettuati campionamenti a diversi tempi dopo l’inoculo (0h, 8h, 24h, 48h). Mentre la valutazione fenotipica su dischetto ha definito una chiara differenza tra i genotipi, quella sull’intera pianta ha evidenziato delle differenze significative tra repliche biologiche che hanno influenzato anche la successiva espressione genica. Una volta ottenuti i cDNA opportunamente restrotrascritti, è stata valutata l’espressione di diversi geni scelti sia sulla base dei geni individuati nelle regioni dei QTL, sia sulla base della letteratura con riferimento alle resistenze studiate nella vite selvatica, date le caratteristiche ancestrali della cultivar. Ogni esperimento è stato condotto in qRT-PCR e ne è stata confermata la significatività tramite appositi test statistici quali ANOVA e Tukey. I risultati ottenuti dall’esperimento di espressione genica hanno confermato, nel genotipo più resistente all’infezione da P. viticola, una risposta HR associata ad un’induzione di geni coinvolti nel pathway dell’etilene. Inoltre l’elevata espressione di fattori di trascrizione MYB e VvWRKY ha evidenziato una risposta immune legata alla produzione di fitoalessine e metaboliti secondari. In conclusione, questo lavoro ha permesso di caratterizzare un germoplasma di V. vinifera meno suscettibile alla peronospora rispetto alle cultivar commerciali e proveniente dalla Georgia, centro di domesticazione della vite, composto da alcune varietà filogeneticamente molto vicine a accessioni di viti selvatiche Europee. Questo ha suggerito una possibile natura “ibrida” di tali accessioni con tratti ancestrali molto accentuati. Le successive analisi sulla cultivar ‘Mgalobshivili N.’ fanno ipotizzare che questo interessante fenotipo (Toffolatti et al., 2016) [1] sia controllato da geni che inducono la produzione di fitoalessine e quindi prettamente legati ad un sistema di difesa basale influenzato dalla produzione di etilene. Questa ricerca evidenzia la presenza di caratteri di resilienza nelle viti coltivate che hanno mantenuto tratti ancestrali e che hanno, presumibilmente, assunto un ruolo primario nel processo di domesticazione, migliorando anche il processo di difesa della pianta dal patogeno. iii Abstract ABSTRACT European grapevine, Vitis vinifera L., is one of the most important tree crops worldwide for both economic value and cultivated area. The social-economic significance of Vitis vinifera led to the development of new cultivation techniques in order to produce hybrids characterized by the resistance to diseases like downy and powdery mildews typical of american and asian vitis and at the same time characterized by the quality of European grapevines. During the last years, a major sensitivity to environmental issues along with market demand led the research towards the crops genetic improvement and the greater attention over the biodiversity conservation. The advent of new technologies and the improvement of crop farming and winemaking made the wine growing activity very profitable. Indeed, traditional methods of breeding, which include the employment of rootstocks for the resistant hybrids production, together with the advent of new techniques such as marker assisted selection (MAS) and the chance to isolate gene of agronomic interest throughout experimental
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