In the global agroeconomy, grapevine occupies one of the first positions in the ranking of commercial crops with the highest impact on the market, thanks to its many products, but especially for wine production. As for many other crops, also grapevine cultivation is afflicted by environmental changes. Long-term studies on climatology and grapevine phenology revealed that global warming is affecting the onset and duration of phenological events, with an acceleration in their timing in many areas. All these processes depend on environmental conditions and cultivar features. The timing with which phenological stages occurs, especially ripening, is highly relevant and critical for berry development. More in detail, too high temperatures during ripening lead to negative biochemical effects, that all together result in an alteration of fruits development and wines quality. While previous studies have demonstrated the strong influence of environment on these biochemical changes, the genetic control of these processes are for the most part still unknown. Adapting local economically relevant varieties to future environment conditions is gaining relevance to preserve the peculiarities of grapes and wines grown in specific area like Corvina, a red berry grape cultivated in Verona’s area to produce prestigious and world-wide recognized DOC wines like Valpolicella and Amarone. Therefore, many research teams have attempted to elucidate genetic determinants of veraison time to provide useful information with the aim of developing local varieties better adapted to future climatic conditions. The final aim of this project is the identification of such candidate genes as genetic determinants for quality and phenological traits in V. vinifera, especially veraison time, flowering time and the interval among these. The future perspective is to use this genetic information to start breeding programs aimed to adapt the phenology of such relevant local varieties to new climate through the use of new breeding techniques, like CRISPR-Cas9 (Rao et al., 2021) or genomic prediction (Brault et al., 2022). In grapevine, as in many other crops, phenotypic traits show a complex quantitative inheritance with small additive or dominance effects of individual genes. By applying a quantitative trait loci (QTLs) analysis it is possible to identify segments of genome linked to observed variation that include candidate genes potentially involved in the traits. In this study, the dissection of genetic determinants has been attempted by combining two genetic approaches: QTL mapping and Genome-Wide Association Study (GWAS). The thesis is divided in two chapters: in the first chapter is described a QTL analysis performed with a QTL mapping approach, which required phenotypic (traits measurement) and genotypic (molecular markers) information on a bi-parental segregant population to find statistical association between markers and phenotypes and to explain the genetic basis of variation of complex traits. To this purpose, a large segregant population obtained by crossing Corvina with the international variety Cabernet Sauvignon (CsxC) was considered to perform the QTL mapping. CsxC population was propagated in few copies in two locations, genotyped with Vitis18KSNP chip (Le Paslier et al., 2013) and phenotyped for 2 years to assemble a consensus linkage map and a QTL map by using traits measurement collected in two vintages. In the second chapter, the results of a previous GWAS analysis were validated, as a complementary approach for QTLs identification. GWAS requires a larger fraction of diversity within a species for the analysis. In a previous study of our laboratory, a core collection composed by 132 individuals of the CREA-VE Conegliano (TV, Italy) grapevine germplasm collection was created after genotyping and phenotypic assessment, as minimal number to represent its genetic diversity. Association analysis was then performed by integration of genetic data provided from GrapeReSeq Vitis18KSNP Chip and phenotypic data (flowering time, veraison time and interval flowering-veraison) using different software. Fifteen SNPs significantly associated to veraison time and to the interval flowering-veraison were found. In this study, 3 of these 15 SNPs were validated as significantly associated to the phenotypic trait flowering–veraison interval on a subset of 94 individual of the collection with extreme phenotype.

Dissection of genetic determinants of phenology and qualitative traits in Vitis vinifera through two complementary genetic approaches

Mora, Riccardo
2022

Abstract

In the global agroeconomy, grapevine occupies one of the first positions in the ranking of commercial crops with the highest impact on the market, thanks to its many products, but especially for wine production. As for many other crops, also grapevine cultivation is afflicted by environmental changes. Long-term studies on climatology and grapevine phenology revealed that global warming is affecting the onset and duration of phenological events, with an acceleration in their timing in many areas. All these processes depend on environmental conditions and cultivar features. The timing with which phenological stages occurs, especially ripening, is highly relevant and critical for berry development. More in detail, too high temperatures during ripening lead to negative biochemical effects, that all together result in an alteration of fruits development and wines quality. While previous studies have demonstrated the strong influence of environment on these biochemical changes, the genetic control of these processes are for the most part still unknown. Adapting local economically relevant varieties to future environment conditions is gaining relevance to preserve the peculiarities of grapes and wines grown in specific area like Corvina, a red berry grape cultivated in Verona’s area to produce prestigious and world-wide recognized DOC wines like Valpolicella and Amarone. Therefore, many research teams have attempted to elucidate genetic determinants of veraison time to provide useful information with the aim of developing local varieties better adapted to future climatic conditions. The final aim of this project is the identification of such candidate genes as genetic determinants for quality and phenological traits in V. vinifera, especially veraison time, flowering time and the interval among these. The future perspective is to use this genetic information to start breeding programs aimed to adapt the phenology of such relevant local varieties to new climate through the use of new breeding techniques, like CRISPR-Cas9 (Rao et al., 2021) or genomic prediction (Brault et al., 2022). In grapevine, as in many other crops, phenotypic traits show a complex quantitative inheritance with small additive or dominance effects of individual genes. By applying a quantitative trait loci (QTLs) analysis it is possible to identify segments of genome linked to observed variation that include candidate genes potentially involved in the traits. In this study, the dissection of genetic determinants has been attempted by combining two genetic approaches: QTL mapping and Genome-Wide Association Study (GWAS). The thesis is divided in two chapters: in the first chapter is described a QTL analysis performed with a QTL mapping approach, which required phenotypic (traits measurement) and genotypic (molecular markers) information on a bi-parental segregant population to find statistical association between markers and phenotypes and to explain the genetic basis of variation of complex traits. To this purpose, a large segregant population obtained by crossing Corvina with the international variety Cabernet Sauvignon (CsxC) was considered to perform the QTL mapping. CsxC population was propagated in few copies in two locations, genotyped with Vitis18KSNP chip (Le Paslier et al., 2013) and phenotyped for 2 years to assemble a consensus linkage map and a QTL map by using traits measurement collected in two vintages. In the second chapter, the results of a previous GWAS analysis were validated, as a complementary approach for QTLs identification. GWAS requires a larger fraction of diversity within a species for the analysis. In a previous study of our laboratory, a core collection composed by 132 individuals of the CREA-VE Conegliano (TV, Italy) grapevine germplasm collection was created after genotyping and phenotypic assessment, as minimal number to represent its genetic diversity. Association analysis was then performed by integration of genetic data provided from GrapeReSeq Vitis18KSNP Chip and phenotypic data (flowering time, veraison time and interval flowering-veraison) using different software. Fifteen SNPs significantly associated to veraison time and to the interval flowering-veraison were found. In this study, 3 of these 15 SNPs were validated as significantly associated to the phenotypic trait flowering–veraison interval on a subset of 94 individual of the collection with extreme phenotype.
Grapevine, QTL, genetics, GWAS, phenology, veraison, mapping,
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11562/1075187
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