Module I (3 cfu) INTRODUCTORY CONCEPTS - Plant organisms. The plant cell. Nuclear, mitochondrial and plastid genome of plants. Reproduction of plant organisms. -Basic concepts of genetics. Genetic polymorphisms. Genetic and molecular markers. Genetic and physical maps. Backcross and inbreeding. Heterosis. Recombinant Inbred Lines. Quantitative Trait Loci. ANALYSIS OF PLANT GENOMES AND USE OF GENOMICS IN PLANT BREEDING - Evolution of plant genomes. Repetitive DNA; polyploidy; sequencing of genomes; the genome of Arabidopsis thaliana. - Comparative genomics; identification of orthologous genes in different species, synteny. Databases of plant genomes. Genome-wide association studies. Development of new plant varieties through marker assisted selection. PLANT EPIGENETICS AND EPIGENOMICS - Epigenetic modifications: DNA methylation; histone changes; Non-coding RNAs: siRNA, microRNA; transcriptional and post-transcriptional gene silencing; role of silencing in maintaining the integrity of the genome. - Generation and maintenance of epigenetic modifications; epialleles; large-scale analysis of the epigenome; transposons. Module II (3 cfu) DIRECT AND REVERSE GENETICS - Analysis of gene function: direct and reverse genetic approaches in plants. Mutagenesis by insertion in plants. Overexpression and silencing. Map-based and deep sequence-based identification of mutations. (4 h). - From mutants to transgenic plants of biotechnological interest. Natural genetic variability as a source of characteristics of biotechnological interest. TILLING and ecoTILLING. Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype. (4 h) - Genome editing: CRISPR/Cas9 (2 h) - Chemical genomics in plant biology. "Click" chemistry. Single cell genomics. (2 h) TRANSCRIPTOME AND INTERACTOME ANALYSES IN PLANTS - ESTs, cDNA-AFLPs, Microarrays, DNA Chips, SAGE. RNA sequencing, sequence analysis and their applications (4 h) -Transcriptomic analysis on a single cell or individual tissues: laser capture; FACS on protoplasts labeled with fluorescent proteins. Databases of plant transcriptomes. (4 h) - Examples of networks and correlation analysis of the expression of multiple genes. (2 h) - Interactomics (2 h)

- Teaching material provided through E-Learning (articles, reviews, lectures slides); - Biotecnologie Sostenibili - Galbiati et al. – EDAGRICOLE - Biotecnologie e Genomica delle Piante - Rao e Leone - Idelson-Gnocchi (acronimo BGP) - Biochemistry and Molecular Biology of Plants, - Buchanan, Gruissem e Jones, 2° ed., Wiley Blackwell

Module I (3 cfu) INTRODUCTORY CONCEPTS - Plant organisms. The plant cell. Nuclear, mitochondrial and plastid genome of plants. Reproduction of plant organisms. -Basic concepts of genetics. Genetic polymorphisms. Genetic and molecular markers. Genetic and physical maps. Backcross and inbreeding. Heterosis. Recombinant Inbred Lines. Quantitative Trait Loci. ANALYSIS OF PLANT GENOMES AND USE OF GENOMICS IN PLANT BREEDING - Evolution of plant genomes. Repetitive DNA; polyploidy; sequencing of genomes; the genome of Arabidopsis thaliana. - Comparative genomics; identification of orthologous genes in different species, synteny. Databases of plant genomes. Genome-wide association studies. Development of new plant varieties through marker assisted selection. PLANT EPIGENETICS AND EPIGENOMICS - Epigenetic modifications: DNA methylation; histone changes; Non-coding RNAs: siRNA, microRNA; transcriptional and post-transcriptional gene silencing; role of silencing in maintaining the integrity of the genome. - Generation and maintenance of epigenetic modifications; epialleles; large-scale analysis of the epigenome; transposons. Module II (3 cfu) DIRECT AND REVERSE GENETICS - Analysis of gene function: direct and reverse genetic approaches in plants. Mutagenesis by insertion in plants. Overexpression and silencing. Map-based and deep sequence-based identification of mutations. (4 h). - From mutants to transgenic plants of biotechnological interest. Natural genetic variability as a source of characteristics of biotechnological interest. TILLING and ecoTILLING.. Genome-Wide Association Studies to identify regions of DNA important for influencing a desired phenotype. (4 h) - Genome editing: CRISPR/Cas9 (2 h) - Chemical genomics in plant biology. "Click" chemistry. Single cell genomics. (2 h) TRANSCRIPTOME AND INTERACTOME ANALYSES IN PLANTS - ESTs, cDNA-AFLPs, Microarrays, DNA Chips, SAGE. RNA sequencing, sequence analysis and their applications (4 h) -Transcriptomic analysis on a single cell or individual tissues: laser capture; FACS on protoplasts labeled with fluorescent proteins. Databases of plant transcriptomes. (4 h) - Examples of networks and correlation analysis of the expression of multiple genes. (2 h) - Interactomics (2 h)

- Teaching material provided through E-Learning (articles, reviews, lectures slides); - Biotecnologie Sostenibili - Galbiati et al. – EDAGRICOLE - Biotecnologie e Genomica delle Piante - Rao e Leone - Idelson-Gnocchi (acronimo BGP) - Biochemistry and Molecular Biology of Plants, - Buchanan, Gruissem e Jones, 2° ed., Wiley Blackwell