Genetic dissection of grape berry ripening and composition Sara - PowerPoint PPT Presentation

Genetic dissection of grape berry ripening and composition Sara Zenoni

Fruit ripening Fruit is the organ specialized for seed dispersal and the transition from unripe to ripe fruit represents a crucial survival strategy Ø irreversible phenomenon Ø tightly coordinated with seed development TOMATO Ø genetically and epigenetically programmed system model for flesh fruit ripening _phytohormone signalling pathways climateric fruit _transcription factor networks

Grape berry ripening Ø non climateric fruit Ø very long ripening, almost 3 months Ø strongly affected by environment Ø ripening in the grape berry originates in pulp near the stylar end Ø the onset of ripening is characterized by an accumulation of specific reactive oxygen species (ROS) Pilati et al., 2014 Castellarin et al., 2011

Chemical and physiological changes during berry development Rogiers et al., 2017

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al., Genome-wide GRAPEVINE GENOME transcriptome profiling JAILLON et al., SEQUENCING Bioinformatic tools System biology approaches CONSTANT IMPROVEMENT OF TRANSCRIPTOMIC PLATFORMS cDNA-AFLP microarrays RNA-seq macroarrays

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al., hydroxyproline-rich proteinGRIP3 early nodulin GRIP13 Identification and definition of “ GRIP” early nodulin GRIP15 grape ripening-induced protein unknown GRIP22 cell wall related GRIP28

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al., Expression profile of the principal molecular events during berry development

Transcriptomic rearrangement during the ripening transition ○ Secondary metabolism ○ Photosynthesis ○ Sugar metabolism ○ Cell cycle ○ Starch degradation ○ Cellular component ○ Regulation of gene organization expression ○ Hormone (auxin) signalling ○ Biotic stress response responsive transcripts ○ Cell wall metabolism THE SHIFT FROM THE GROWTH TO RIPENING PHASE IN BERRY INVOLVES A PROFOUND TRANSCRIPTOMIC REARRANGEMENT

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al., Transcriptomic changes during berry development in pulp and skin separately

Ripening program is anticipated in pulp Wax biosynthesis Oxidative stress Flavonoids/ response anthocyanins biosynthesis Oil body organization Stilbenoid biosynthesis Ethylene signalling and flavor pathways PULP TRANSCRIPTOMIC PROGRAM IS ANTICIPATED IN PULP IN COMPARISON TO THE SKIN SKIN Lijavetzky et al., 2012

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al., RNA-seq approach to dissect the transcriptional complexity during berry development

Ripening transcriptomic program in red and white grapevine varieties Massonnet et al., 2017

Number of expressed genes and biomarkers THE NUMBER OF EXPRESSED GENES DECREASES DURING BERRY DEVELOPMENT BIOMARKERS OF BERRY DEVELOPMENT STAGES AND PHASES WERE DEFINED

Core transcriptomic traits during berry development Harvest Pea size Pre-veraison End of veraison CORE TRANSCRIPTOMIC TRAITS WERE PROFILED Massonnet et al., 2017

Relation with anthocyanin accumulation and ripening progress at transcriptional level TRANSCRIPTOMIC PROGRAM OF FRUIT RIPENING SEEMS MORE DIRECTLY RELATED TO ANTHOCYANIN ACCUMULATION RATHER THAN SUGAR CONTENT Massonnet et al., 2017

Relation with anthocyanin accumulation and ripening progress at transcriptional level Syrah Rinaldo et al., 2015 About 6000 genes are responsible for transcriptional differences among red varieties at harvest DEGs Secondary metabolic process Transport ANTHOCYANIN LEVELS MAY INFLUENCE MANY OTHER PROCESSES Carbohydrate metabolism Transcription factor activity INCREASE OF SKIN OPACITY TO SUNLIGHT • INVOLVEMENT IN SIGNALLING PATHWAYS NOT YET DESCRIBED • Massonnet et al., 2017

Correlation of gene expression between genotypes increases as haplotype distance decreases ü Sequencing of ten genomes ü Pairwise comparison to define the haplotype distance ü Identification of local IBD (segment identical by descent) Shared chromosome segments between ‘Garganega’ and ‘Passerina ’ Two shared haplotypes IBD2 One shared haplotype IBD1 No shared haplotypes IBD0 Shared chromosome segments between ‘Passerina’ and ‘Vermentino’ Magris et al., unpublished

Correlation of gene expression between genotypes increases as haplotype distance decreases Genes for which the pair of individuals are IBD0 ( Sharing 0 ) • Genes for which the pair of individuals share one haplotype (IDB1- Sharing 1 ) • Genes for which the pair of individuals share two haplotypes (IDB2- Sharing 2 ) • Correlation of transcript expression level Fraction of non differentially expressed genes Developmental stages HAPLOTYPE SHARING ACCOUNTS FOR CORRELATION OF GENE EXPRESSION Magris et al., unpublished

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al.,

Molecular dissection of the grapevine GXE interaction Changes in performance of genotypes in different environments are defined as genotype X environment ( GXE ) interaction 2 Genotypes Sangiovese Sangiovese and Cabernet sauvignon Cabernet S. Cabernet S. 4 Developmental stages Sangiovese 2 Years Cabernet S. 3 Areas Adjacent Vineyards Sangiovese per each Area Pea Size Pre-Veraison Mid-Ripening Ripe Dal Santo et al., 2018

Molecular dissection of the grapevine GXE interaction Data Mining Pipeline Whole Transcriptome Screening ↓ 18122 genes Profiles definition K-means clustering → 300 clusters Variable Importance Measure ( VIM ) measure of how each variable affects the expression Profiles characterization STAGE GENOTYPE YEAR AREA Cabernet Sauvignon Sangiovese SANGIOVESE RESULTED MORE RESPONSIVE THAN CABERNET SAUVIGNON Dal Santo et al., 2018

Variable-specific clusters Median VIM of each Variable Photosynthesis Median VIM of each Variable R-proteins Dal Santo et al., 2018

GxE clusters are enriched in secondary metabolism, signal transduction and abiotic stress response IDENTIFICATION OF SEVERAL CANDIDATE GENES THAT COULD BE USED AS MARKERS OF BERRY QUALITY TRAITS IN GXE INTERACTIONS Stilbene Sythases (VvSTSs) Linalool Sythases (VvSPSs) Dal Santo et al., 2018

Large-scale transcriptional changes during berry development AGUDELO-ROMERO et al., PILATI et al., DAL SANTO et al., DAL SANTO et al., FORTES et al., DELUC et al., FASOLI et al., RINALDO et al., GUILLAUMIE et al., GRIMPLET et al., DAVIES AND ROBINSON MASSONNET et al., PALUMBO et al., LUND et al., SWEETMAN et al., GHAN et al., TERRIER et al., CRAMER et al., ZAMBONI et al., WATERS et al., LIJAVETZKY et al., ZENONI et al., ZENONI et al., FASOLI et al., BURGER et al., Expression profile of the principal molecular events during postripening phase

Transcriptional changes during berry post-harvest ~ 30% weight loss Syrah Cabernet Sauvignon Oseleta Merlot Sangiovese Corvina Zenoni et al., 2016