1. Genome size and organization:
• Comparing prokaryotic and eukaryotic genomes: the C-value paradox described through examples of various Angiosperm plants;
• Forces that influence genome size and expansion-contraction mechanisms (unequal crossing-over; illegitimate recombination).

2. Types, abundance and organization of genic and non-genic sequences in the eukaryotic chromosome:
a) Non-gene sequences
• Telomeric, centromeric and intercalary highly repeated sequences; micro- and mini-satellites;
• Transposable elements (TE) in Eukaryotes: comparison with prokaryotic IS elements; classes of TE and relative mode of transposition di ET and abundance in various Eukaryotic genomes: DNA TE (e.g. Ac-Ds) and RNA TE or retroelements, with (retrotransposons) or without LTR motifs (e.g. Gypsy, Copia, Alu, SINEs, LINEs); effect of TE on size and structure of Eukaryotic genomes; amplification of TE through intra- and inter-element unequal crossing-over;
b) Eukaryotic genes:
• Fine structure and structural variability (e.g. intron abundance and size) among taxa; exon re-shuffling and development of novel genes;
• Gene families and super-families: gene duplication and divergence (neo- and sub-functionalization): examples of the histone gene family, of resistance gene families in plants and of the human globin super-family.

3. Genome compartmentalization: mosaic organization (isochores) of the human genome and of plant genomes; “gene-rich” and “gene-poor” regions; TE as main components of inter-genic spaces; comparison between genetic and physical maps: uneven distribution of recombination along the Eukaryotic chromosome (“hot” and “cold” spots of recombination and their correlation with gene density and transcription).

4. Comparative genomics:
• Intergenomic and interspecific micro- and macro-synteny and colinearity; the “circle diagram” of grass genomes; levels of conservation: homoeologous chromosomes and orthologous genes;
• Chromosome rearrangements and disruption of synteny and colinearity: evidence from comparative mapping and comparative sequencing.

5. Evolution and adaptive mechanisms of plant genomes, with particular focus on polyploidy; rapid genome changes following the polyploidization event: maintenance and elimination of duplicated genes/sequences: examples from natural and neo-synthesized Triticum polyploids; gene silencing.

6. Epigenetics and epigenomics: modifications of chromatin structure (chromatin remodelling) mediated by DNA methylation, histone methylation/acetylation, RNA molecules; epigenetic changes associated with polyploidization.

7. Plant genome manipulations aimed at practical applications
• Targets of manipulations for breeding purposes: utilization of genetic variability outside the “target” species
• From creation of amphidiploids to single chromosome addition and substitution lines to targeted interspecific transfer of chromosome segments (chromosome engineering) in agriculturally relevant plant species: strategies and case-studies, with particular focus on Triticeae species (wheat and related species), Solanum spp., Medicago spp., Lolium-Festuca complex.

- Teaching material (e.g. lesson slides) and scientific articles provided by the teacher and available on the institutional website;
- Additional scientific articles on students' request, both for the preparation of the exam test and for the deepening of aspects of specific, individual interest;
- Chapters selected from:
- Barcaccia - Falcinelli – Genetica e genomica (Liguori ed.), vol. I, II e III;
- Hartwell et al. - Genetica - dall'analisi formale alla genomica (McGraw-Hill);
- Russell PJ - Genetica: un approccio molecolare (Pearson)

PROGRAM The program is divided in three modules: 1) Structural Genomics, 2) Bioinformatics and 3) Functional Genomics. 1) STRUCTURAL GENOMICS (10 hours of lesson) - Sequencing methods: 1) Second generation sequencing: ILLUMINA, Pyrosyquencing (ROCHE 454), SOLiD; 2) Third Generation Sequencing: HELICOS (Helicos Biosciences); PacBio (Pacific Biosciences); Nanopore (Oxoford Nanopore); 2) Comparison of next generation and next-netx generation sequencing methods. - Full genome sequencing strategies: hierarchical method and WHOLE GENOME SHOTGUN; - Gene Annotation; - Functional annotation; - Projects for the sequencing of whole genomes in plant species of agricultural interest. - Illustration of major databases (NCBI, EMBL, DDBJ), searches in biological databases (BLAST), sequencing software and for the design of oligonucleotides; 2) BIOINFORMATICS (8 hours of lesson) - Analysis of genomics, transcriptomics, proteomics and metagenomics data using R & RMarkdown. 3) FUNCTIONAL GENOMICS (12 hours of lesson) - The genetic transformation of plant species. Transformation mediated by Agrobacterium or by biolistic method. Preparation of plasmid vectors. - Study of gene function: gene overexpression and knock-out (RNA antisense, RNA interference) in transgenic plants; - Preparation of constructs for the realization of cis-genic plants. - Chemical mutagenesis and TILLING; physical mutagenesis with fast ions and neutrons; insertional mutagenesis: T-DNA and transposons; - Application of mutagenesis for functional studies and breeding programs. - Site-specific modifications. Methods of "genome editing": 1) zinc-finger nucleases (ZFN), 2) transcription activator-like effector nucleases (TALENs), and 3) Clustered Regularly Interspaced Short Palindromic Repeats-associated (Cas) proteins (CRISPR / Cas) - Application of "genome editing" methods for the genetic improvement of species of agrarian interest. Laboratory exercises will focus on the following topics: 1) Search in databases of nucleotide and protein sequences. Use of bioinformatics tools to open sequence files (DNAMAN, FINCH TV, GENEIOUS). Use of the BLAST algorithm to search nucleotide or protein sequences in databases. Alignment of nucleotide and acidic amino acids through the CLUSTAL OMEGA and GENEIOUS programs. Construction of phylogenetic trees (2 hours) 2) Identification of SNPs on genes of interest by TILLING in durum wheat (4 hours) 3) Preparation of constructs for genetic transformation by cis-genic approach: Insertion of the recombinant cassette into a bacterial vector; Transformation of bacterial cells; Extraction and digestion of the recombinant plasmids with restriction enzymes (8 hours) 4) Use of molecular marker to select transgenic plants (4 hours)

GENETICA un approccio molecolare. Quarta edizione Peter J. Russell Edizione italiana a cura di Carla Cicchini e Alessandra Marchetti ISBN:9788865186176 Biotecnologie e Genomica delle Piante. Rosa Rao e Antonietta Leone. Editor IDELSON-GNOCCHI. Power Point presentations and papers provided by the professor.