GENETICS AND GENOMICS
BREEDOMICS: MARKER-ASSISTED BREEDING

Academic Year 2013/14
Structure AGRARIA [AG]
Course of Study SCIENZE E TECNOLOGIE AGRARIE (DM270) [AG0056 2008]

Prerequisites: The student needs to know the basic aspects of cell biology and reproductive biology, with particular reference to the main livestock and crop species.

Basic knowledge and abilities: The student is expected to gain basic knowledge and expertise of formal genetics useful for improving and breeding livestock and crop species, with particular reference to the inheritance of phenotypic variation and its heritability. The student should be able to examine the genetic aspects of the expression of both qualitative and quantitative traits, to analyze the genetic structure of populations and to evaluate the genetic traits of reproductive systems mainly affecting the characterization, selection and conservation of populations.

Examination procedures: Students will deal with both a written test (in progress) and an oral examination (at the end of the course).

Evaluation parameters: The student will be evaluated on the basis of theoretical knowledge on the genetics of mendelian and quantitative traits, population genetics, molecular genetics and cytogenetics, including elements of genetic mutations and biotechnologies.

Topics: Mendelism and inheritance of qualitative traits. Molecular genetics: The structure of nucleic acids. Mechanisms of replication, transcription and synthesis of proteins. Sources of genetic variation: recombination and mutation. Molecular bases of gene expression. Genetic control of quantitative traits and heritability estimates. Population genetics: Hardy-Weinberg equilibrium.

Genetics of reproductive systems: Processes of sporogenesis, gametogenesis and embryogenesis in the Angiosperms. Anfimixis: autogamy, allogamy and their effects on the genetic structure of populations. Apomixis and clonal populations. Reproductive barriers: genetics of incompatibility and malesterility.

Genetic breeding: Fundamentals of selection and methods for the constitution of varieties in the major crops. Varieties based on pure lines, hybrids, synthetics and clones. Registration of varieties. Conservative varietal selection and commercial seed production.

Genetic biotechnologies: Elements of molecular biology and genetic engineering. Genetically modified organisms (GMO) and transgenic varieties. Molecular marker-assisted breeding (MAB). The genetic identity of varieties and genetic traceability of agrifood products and derivatives.

Activities of learning and teaching: The course includes classroom lectures of general genetics and practical laboratory activities of molecular genetics, for a totale of 64 hours.

Supplementary materials for studying: The materials used for frontal lessons and practical activities (pdf files of presentations) of Genetics will be made available on request.

Reference books:
1) Gianni Barcaccia e Mario Falcinelli (2008). Genetica e Genomica. Vol. 1 Genetica generale. Napoli: Liguori Editore.
2) Gianni Barcaccia e Mario Falcinelli (2012). Genetica e Genomica. Vol. 2 Miglioramento genetico. Napoli: Liguori Editore.

Academic Year 2013/14
Structure MEDICINA VETERINARIA [MV]
Course of Study BIOTECNOLOGIE PER L'ALIMENTAZIONE (DM270) [IF0362 2011]

Prerequisites: Genomics: The student needs to know the basic aspects of formal genetics and especially of molecular genetics, with particular reference to genes as hereditary units that govern transcriptional and/or translational processes. Bioinformatics: The student needs to know the main characteristics of DNA, RNA, amino acids, genes and genomes. Basic knowledge of personal computer.

Basic knowledge and abilities: Genomics: Acquire a theoretical and technical knowledge of genomics for the analysis of genome structure and gene function, with particular reference to agri-food species. Bioinformatics: Acquire a general overview of the current bioinformatics tools used for biotechnological applications. Learn the use of the available main bionformatic programs.

Examination procedures: Genomics: Students will deal with both a written test (in progress) and an oral examination (at the end of the course). Bioinformatics: Written examination of bioinformatics at the end of the course.

Evaluation parameters: Genomics: The student will be evaluated on the basis of theoretical knowledge on structural and functional genomics, and the ability to use this knowledge to plan experiments of genomics applied to specific questions of the agro-food area. Bioinformatics: The student will be evaluated on the basis of the knowledge and the ability to use the programs presented in class and to perform bioinformatic analyses.

Topics: Genomics: Classroom teaching: Techniques for the sequencing of genomes; Genome analysis using RFLP and PCR-derived molecular markers; Genetic characterization by means of fingerprinting and genotyping; Study of gene expression through Northern blot hybridization, RT-PCR and Real-Time PCR; Analysis of the trascriptome: identification of ESTs by SSH and DD techniques, and Microarrays; Analysis of proteome through the construction of 2D-PAG maps; Study of the gene function by using T-RNA and RNAi lines, and over-expression. Laboratory training: Activities related to DNA isolation, amplification by PCR, restriction and sequencing.  Bioinformatics: Classroom teaching: Biological databases; alignments of nucleic acids and proteins, primer design, identification of patterns and functional motifs, phylogeny and molecular evolution, and the analysis of protein structure, prediction of secondary structures of RNA molecules; bioinformatic analysis of genomes. Practical training: Use of programs related to the topics presented in the lectures.

Activities of learning and teaching: The course includes lectures in classroom and practical activities of genomics and bioinformatics, for a total of 80 hours.

Supplementary materials for studying: The materials used for frontal lessons and practical activities (pdf files of presentations) of Genomics will be made available on request. The material used for lessons (powerpoint slides) of Bioinformatics will be made available on the Moodle platform (https://elearning.unipd.it/scuolaamv/).

Reference books:
1) Gianni Barcaccia e Mario Falcinelli (2006). Genetica e Genomica. Vol. 3 Genomica e Biotecnologie genetiche. Napoli: Liguori Editore.
2) Giorgio Valle e coll. (2003). Introduzione alla bioinformatica. Bologna: Zanichelli Editore.

Academic Year 2013/14
Structure MEDICINA VETERINARIA [MV]
Course of Study BIOTECNOLOGIE PER L'ALIMENTAZIONE (DM270) [IF0362 2011]

Prerequisites: The student needs to know the basic aspects of genomics, with particular reference to the techniques suitable for the analysis of DNA polymorphisms using molecular markers.
Basic knowledge and abilities: Acquire a theoretical and technical knowledge on applied genomics and biotechnologies for the implementation of molecular tools for marker-assisted selection and diagnostic assays useful for the genetic identification of species, plant varieties and animal breeds, including the genetic traceability of their food derivatives.

Examination procedures: Students will deal with both a written test (in progress) and an oral examination (at the end of the course).

Evaluation parameters: The student will be evaluated on the basis of theoretical knowledge on structural analysis of genomic DNA, and the ability to use this knowledge to implement diagnostic assays aimed at the genetic traceability of agro-food products of animal and plant origin.

Topics: Genomics applied to marker-assisted selection (MAS) for the breeding of crop species. Genetic-molecular identification of species and populations by DNA profiling with RFLP and PCR-derived markers (SSR), and cpDNA and mtDNA barcoding; determination of genetic diversity, similarity and identity statistics, genetic differentiation and gene flow, genetic distance parameters, estimates of homozygosity and heterozygosity useful for the genetic characterization and identification of plant landraces and cultivars (hybrids, pure lines, and clones), and animal races and breeds; implementation of molecular diagnostic assays for the genetic traceability of agri-food products by means of DNA fingerprinting, SSR genotyping and SNP haplotyping. Genetically modified organisms (GMO). Methods of genetic transformation of plants and animals. Analysis of GMOs and traceability of their food derivatives by using Real-Time PCR assays. Legal aspects related to the production of GM plants and animals, and to the commercialization of GMO-derived products.

Activities of learning and teaching: The course includes lectures in the classroom and practice in the laboratory for a total of 80 hours, with the focus on specific case-studies.

Supplementary materials for studying: The materials used for theoretical lessons and practical case studies (pdf files of presentations) will be made available on request.

Related readings:
1) Gianni Barcaccia e Mario Falcinelli (2006). Genetica e genomica. Vol. III Genomica e biotecnologie genetiche. Napoli: Liguori Editore.