MASTERS’ DEGREE IN AGRICULTURAL AND ENVIRONMENTAL BIOTECHNOLOGY SYLLABUS 2020-2021
Year 1, Semester 1, 6 ECTS
Learning outcome
The aim of the course is to provide knowledge about the development and structure of plants, useful for the definition and organization of complex experiments of plant biotechnology. The main knowledge acquired will be:
- Knowledge concerning the mechanisms of development and differentiation in Angiosperms;
- Knowledge regarding the mechanisms of plant-environment interaction (ie floral induction). The main skills acquired will be:
- Ability to evaluate which methodologies to use for the study of different aspects of plant biology;
- Ability to use the knowledge concerning the genes involved in plant development, provided
by the course, for the evaluation of experimental data and the resolution of practical problems.
- Ability to critically evaluate the recent scientific literature related to the covered
Contents
Lectures. Cell wall structure and molecular mechanisms driving cell expansion. The seed: endosperm development and its characteristics. Seed germination and dormancy; influence of temperature in plant growth and distribution. Plant embryogenesis: molecular and cyto- histological mechanisms. Totipotency and plasticity of plant cell: cell fate according to position. Meristems: role, type and functioning. Coordination between rates of cell division and elongation during organogenesis. Root development: hormonal and genetic control. Shoot apical meristem and shoot development. Photomorphogenesis and plant light responses.
Leaves differentiation and phyllotaxis. Flower induction, photoperiodism and circadian clock. Flower organs differentiation: microsporogenesis, megasporogenesis and gametogenesis.
Pollination and pre-gamic phases: sporophytic and gametophytic incompatibility; pollen tube development and double fertilization. Post-gamic phase and fruit development from cyto- histological point of view. Different kind of fruits.
Practicals. Protocols for preparation of plant material (sampling, fixation and inclusion) for cyto-histological studies with light and electron microscopy. Cyto-histochemical techniques: in situ hybridization and immunolocalization. Samples sectioning using microtome and ultramicrotome (execution of "semi thin" and "thin" sections with a Reichert ultramicrotome). The activities of samples preparation and sectioning will be realized in the laboratory of Anatomy and Cytology of the Applied Biology Department, investigations in optical microscopy (bright field and epifluorescence) will be held in the Polo educational Microscopy, while the SEM-TEM investigations will be carried out in the CUME center of the University.
Year 1, Semester 1, 6 ECTS
Learning outcome: provide students with insights to understand the effect of selection and other evolutive forces operating in natural and human managed populations, upon qualitative and quantitative traits; provide the essential knowledge to deal with conventional and advanced genetic improvement programs. The course also provides a detailed knowledge of techniques based on molecular markers, gene expression and cloning to be used in assisted genetic improvement. Elements of bioinformatics will also be given through applications in Bash language applied to both SNPs-based genomic (GWAS) and DNA methylation analysis in crop plants.
Study unit: Quantitative Genetics
Contents
Part 1: Population genetics. Hardy-Weinberg equilibrium for: multiple alleles, sex linked traits, polyploid organisms, several loci (linkage equilibrium). Inbreeding and Outbreeding, Sewall Wright balance. Effect of mutations, migration and selection. Genetic drift, F Statistics, gene flow among fragmented populations.
Part 2: Quantitative genetics. Genotypic value and number of loci involved. Types of gene actions and Mather model. Mean and variance of the genotypic values of a population in EHW
and the effect of dominance and overdominance, as well as the changes of allele frequencies. Breakdown of the phenotypic and genetic variance. Estimates of additive variance and heritability through experimental designs. Breeding values. Phenotypic plasticity. G×E Interaction. Breeding for adaptation and yield stability. Correlation between characters.
Study unit: Genomic Analysis and Elements of Bioinformatics
Contents
Restriction enzymes. Polymerase chain reaction (PCR). Southern electrophoresis and hybridization. Sanger and new sequencing technologies. Molecular markers based on hybridization (RFLP). Molecular markers based on PCR (RAPD, AFLP, STS, SSR, SNP). Markers based on Next Generation Sequencing (NGS) techniques: RRL, RAD-seq and GBS. Mapping theory. Detection of molecular data and their use in the construction of association maps (GWAS). Map-based cloning. Building classical and NGS genomic libraries. Fundamentals of Bioinformatics for the analysis and management of datasets deriving from NGS sequencing (methylation and SNP calling). Breeding assisted by molecular markers. Applications and impact of new sequencing technologies on plant breeding.
EXPERIMENTAL METHODOLOGY IN AGRICULTURE
Year 1, Semester 1, 6 ECTS
Learning outcome
The course will give students the theoretical background and practical tools to (1) design scientifically sound experiments as well as proceed to correct analysis and presentation of results; (2) simulate the outcome of agricultural systems, with specific reference to crop productivity.
The students will acquire knowledge on: basic aspects on experimental design, the main experimental designs, ANOVA, linear regression, multiple comparison procedures, and non- linear regression.
Practical skills will include the ability of (1) designing an experiment, (2) analysing the results of an experiment by using a statistical software, (3) checking the basic assumptions for linear non-linear models, (4) building and fitting basic nonlinear regression models, (5) using the statistical software R, at a basic level.
Contents
The course is based on the fact that there are two main ways to obtain scientific information that is not already found in literature, i.e. (1) organize scientifically sound experiments and (2) appropriately use simulation models.
Lectures
- - Measuring biological phenomena; variability of experimental Population, sample and sampling. Estimation methods and criteria. Statistical inference. Experimental units.
Replication and pseudoreplication. Independence.
- - Experimental Completely randomised designs (CR). Randomised complete block designs (RCB) and Latin square designs. Factorial experiments.
- - Split-plot, split-block and nested Repeated measures and repeated experiments. 4 - ANOVA on CR and RCB designs.
- - Problems with basic Graphical analyses of residuals. Stabilising transformations. Examples.
- - Multiple comparison
- - ANOVA on split-plot, split-block and repeated measures
- - Regression and Polynomial regression. Statistical inference on regression analyses. Examples.
- - Nonlinear regression Biologic assay.
- - Nonlinear regression Degradation of xenobiotics. Crop growth curves. Goodness and lack of fit.
Practicals: students will be exposed to some selected case studies and will be guided to their solution, by using the most appropriate statistical software.
EVOLUTION OF PLANT BIODIVERSITY
Year 1, Semester 2, 6 ECTS
Learning outcome
The objective of this course is to provide the students with detailed cytogenetic knowledge for understanding evolutionary mechanisms leading to the extant biodiversity. The students will learn to connect the cytogenetic aspects to the evolutionary pathways of plants, particular attention will be directed to the origin of the cultivated species. The importance of the wild flora for studying evolutionary processes and cytogenetic variants will be discussed. The learning objectives will be realized by lectures, practicals and reading of recent scientific articles. Students will be encouraged to propose plant material of their interest for practicals.
Contents
Lectures will be focused on the importance of cytogenetics for understanding the origin of biological diversity and the role of chromosomes in the evolution of the living forms. The following topics will be treated with particular emphasis: genome and chromosome evolution, chromosome number variations such as polyploidy and dysploidy, cytotypes and meiotic mutants. Recent strategies dealing with the search of the ancestral karyotype will be also described. Special attention will be given to particular evolutionary events such as plant and animal domestication. Advanced molecular cytogenetic techniques will be carefully described. Practicals will be prevalently directed to the application of these techniques. However time will be reserved for discussion of scientific articles to help understanding the use of these techniques in the study of evolution and biodiversity.
Year 1, Semester 2, 12 ECTS
Learning outcome
The objective of this course is to provide students with detailed knowledge of techniques and strategies to improve agricultural plants and livestock animals by means of conventional methods and advanced genetic biotechnologies. The learning outcome will be realized by lectures, practicals, reading and commenting recent scientific literature and field trips.
Contents
Study unit: Advanced plant breeding (6 ECTS)
Lectures will deal with the objectives of plant breeding, the reproductive systems and genetic structure of plant populations. Next, the sources of genetic variation for plant breeding will be examined and the plant breeding methods will be recalled. Genetic engineering techniques and their application will be thoroughly presented, including the most advanced genome editing tools, with case studied from the recent scientific literature. Practicals will be devoted to the discussion of scientific literature on the biotech breeding topics and to hand crossing techniques.
Study unit: Advanced animal breeding (6 ECTS)
Lectures will provide basic knowledge of the anatomy and physiology of the reproductive systems of livestock animals necessary to carry out reproductive biotechnology procedures, considering their potential in the context of animal breeding. Then, the most recent applications of molecular technologies to animal breeding and selection will be presented, considering all the main animal species of economic interest. Practicals will include macro and microscopic analyses of seminal material, molecular characterization of genes under selection, for embryo sexing and molecular traceability of animal products.
Year 1, Semester 2, 12 ECTS
Learning outcome
Provide students with knowledge related to innovative biotechnological processes in the microbial biotechnology sector applied to food, nutraceutical, pharmaceutical and food additives industries; develop the aspects related to the use of selected microorganisms for innovative biotechnological processes. Provide students with knowledge related to the concept of microbial diversity and diffusion in the natural habitats and in the environmental technologies, in relation to their metabolic capacity and by observing the main factors that influence their survival.
Contents
Study unit: Industrial Microbiology (6 ECTS)
- Overview of microbial biotechnologies (traditional and innovative) and microbial biocatalysis
- Selection and conservation of microorganisms of biotechnological interest (bacteria, yeasts, filamentous fungi), microbial collections (BRCs). Screening, genetic improvement, optimization, modelling and scale-up
- Use of bioreactors (with mechanical, pneumatic and hydraulic agitation) and control systems for operating Closed, semi-open and open systems. Cell immobilization techniques.
- Balance control systems in open systems (chemostat and turbidostat). Industrial culture media, substrate utilization kinetics, biomass
- Examples of industrial use of selected microorganisms for biomass or compound production processes for industry (e.g. food and pharmaceutical industry: yeast biomass, ethanol, enzymes, vitamins, organic acids, glycerol, polysaccharides, VOCs).
- Microorganism screening techniques for the production of molecules of industrial interest (e.g. enzymes, vitamins, antibiotics, organic acids).
- Downstream processing techniques and determination of the biological activity of molecules of microbial origin
Study unit: Environmental Microbiology (6 ECTS)
- Factors that influence microbial
- Metabolic diversity of microorganisms: phototrophy, chemotrophy, autotrophy and
- Role of microorganisms in the biogeochemical cycles of the elements: carbon, nitrogen and sulphur
- Microbial
- Silage: microbial ecology in silage, ensiling techniques, use of additives and microbial starters, evaluation of the state of
- Composting: composting process, microflora during the process, evaluation of the state of
- Energy production in the form of methane: methanogenesis, ecology of methanogenic microorganisms, process biochemistry,
- Energy production in the form of hydrogen: production of hydrogen by fermentation, production in plants, production of hydrogen from photosynthetic
- Biological water purification: structure of a purification plant, microbial ecology of activated sludge, biochemistry of microbiological
- Bioremediation of contaminated soils: role of microorganisms in the degradation processes of pollutants in the soil, influence of environmental factors, bioremediation in situ, bioremediation
Year 2, Semester 1, 6 ECTS
Learning outcome:
To know the impact of pesticides on the soil/plant system and on the human health. To know the impact of pesticides on the water system; to know the rules for pesticides utilization; to calculate the predicted environmental concentrations of pesticides in soil and water; to know new sustainable pest control strategies as alternative of the chemical pesticides; to know the biotechnological methods to manage the organic wastes and byproducts to produce organic fertilizers promoting circular economy.
Contents:
Classification of pesticides. Risk assessment. Fate and behaviour of pesticides in soil-water-plant system. Main classes of herbicides, fungicides and insecticides. Methods of pesticides analysis. Pesticides metabolites. Integrated Pest Management (IPM). Biopesticides. Biotechnological treatments of wastes. Aerobic, anaerobic and integrated treatments.
BIOTECHNOLOGIES FOR PLANT HEALTH
Year 2, Semester 1, 6 ECTS
Study unit: Molecular plant pathology
Learning outcome:
Students at the end of the course will know the molecular aspects of the infectious process of pathogenic fungi and bacteria, of race-specific resistance and of induced plant defense responses. They will also learn the principles of molecular diagnosis of plant disease. Students should be able to plan experiments, extract DNA from phytopathogenic bacteria and fungi, apply basic analytical methods for the study of plant-pathogen interactions, using molecular techniques for the diagnosis of plant disease.
Contents:
Molecular aspects of pathogenicity and virulence of phytopathogenic fungi and bacteria.
- Fungi: the role of melanin, hydrophobin, cutinases, signal transduction pathways, saponins, phytotoxins,
- Bacteria: Hrp pilus and pathogenicity, effector proteins, phytotoxins, pectic enzymes, extracellular polysaccharides, quorum sensing and quorum quencing, hormones and
Molecular aspects of race-specific resistance (resistance and virulence genes), induced resistance and defense responses in plants.
Biocontrol. Mechanism of action of biological control agents (BCA). Principles of plant disease diagnosis.
- Diagnosis of plant diseases caused by viruses, bacteria and fungi, with particular reference to the use of molecular
Molecular characterization of populations of pathogens.
Study unit: Insect biotechnology
Year 2, Semester 1, 6 ECTS
Educational objectives:
Achievement of knowledge on the following topics: main insects and other arthropods of applied relevance; conventional and molecular systematics and diagnostics in entomology; functional and molecular bases that regulate the ecological and physiological interactions of arthropods with other organisms; evaluation of insect biodiversity; exploitation of entomological resources; role of biotechnologies in integrated pest management. Laboratory abilities on insect applied biotechnologies, behaviour and chemical ecology.
Contents:
CLASSES. Introduction to the course; insects and man. Outlines of general and applied entomology; phylogeny, systematics, anatomy and physiology of insects and other arthropods; reproduction and development; main arthropods of applied importance; predators and parasitoids; bases of integrated pest management (IPM).
Molecular markers and diagnostic methods in entomology. PCR of mtDNA and rDNA, DNA barcoding, sequencing, next generation sequencing. Applications in: molecular systematics; molecular diagnostics of parasitoids in the host; molecular analysis of gut content in predators and phytophages; molecular diagnostics of phytopathogens in insect vectors; insect biodiversity.
Ethology and chemical ecology of insects and other arthropods. Pheromones and other semiochemicals, physical stimuli; perceptions of stimuli and mechanisms of behavioural responses; manipulation of insect behaviour in the field for management of pest species and in the laboratory for mass rearing of parasitoids and predators.
Insect-plant interactions; the resistance of plants to herbivorous insects and mites; constitutive and induced resistance, direct resistance (antixenosis, antibiosis) and indirect resistance. Induction mechanisms of plant resistance to arthropods. Implementation and
perspectives; resistance varieties, genetically modified plants, plant treatments with resistance inducers.
Biotech approaches in pest control. Sterile insect technique (SIT); enhancement of SIT and insect transgenesis; genome editing and gene drive in insects; RNAi applications.
Exploitation of entomological resources in agriculture, medicine and industry. Insects as a highly sustainable source of animal proteins for food and feed.
PRACTICALS: Rearing of phytophagous and entomophagous insects. Entomological collections: economically relevant species and tropical species.
Insect dissections and microscope observation of external and internal anatomy. Seminar on biological control using parasitoids and predators reared in biofactories.
Molecular identification of insect species. Molecular diagnostics: detection and molecular identification of prey in the gut content of predator; molecular detection and identification of parasitoids in the host; molecular diagnostics of phytopathogens in insect vector.
Behavioural (olfactometer) and electrophysiological (EAG, GC-EAD, SSR, SCR) bioassays; extraction of volatile organic compounds (VOCs) emitted by insects and/or plants attacked by insects. Plant resistance induced by insects: qRT-PCR for expression analysis of genes associated with plant defences. Visit to insect biotech facility; genetically modified insect cultures; seminar on gene-drive strategy and pest (pathogen vector) eradication.
Effect of food substrates on fatty acid composition of edible insects.
FIELD CROPS, SEED PRODUCTION AND BIOTECHNOLOGIES
Year 2, Semester 2, 6 ECTS
Learning outcome
The objective of the course is to provide students with basic knowledge on crop science and technology for the main groups of field crops, and with knowledge on seed biology and production as sectors where to apply biotechnologies. Considering that BSc background of students is heterogeneous and variable year by year, the teacher will evaluate case by case on whether just recall or explain in detail topics concerning crop science and technology. The learning outcome is achieved by means of lectures, practicals, analysis of scientific literature and field trips
Contents
Study unit: Crop Science and Technology
Crop ecology (climate and soil factors); Crop physiology (crop photosynthesis, growth, development and yield, competition between plants and plant organs, yield components, crop plasticity). Cultivation techniques (elements of soil drainage, tillage, sowing, fertilization, weed control, crop protection, harvest and product utilization, crop residues management) Classification of crops and description of peculiarities (botanical, biological, agronomical) of different groups: cereals, grain legumes, oil crops, fiber crops, sugar crops, forage crops, vegetables, herbs, ornamental crops.
Study unit: Seeds and seed production
Description of seeds of main field crop species; Seed biology: physiology of germination, seed vitality vigour, dormancy; Seed Technology: seed selection, chemical treatments, coating, pelletting, priming, storage. Regulations for seed production and marketing, cultivar registration and certification. Seed analysis. Seed production: seed crops of wheat, maize, sugarbeet and alfalfa as case studies.
Practicals
Identification of seeds and plants of studied species; Solving of practical cases concerning arable crops; Cultivation operations and management in the farm; Seed processing, machineries, assessment of process problems both at the seed lab of the DSA3 and in seed industries. Lab techniques for seed analysis
BIOTECHNOLOGY APPLIED TO PLANT NURSERY PRODUCTIONS
Year 2, Semester 2, 6 ECTS
Learning outcome
The teaching provides to the students theoretical knowledges and practical capabilities related to specific biotechnology applications for production of high quality woody plants through the vegetative propagation. The basics of in vitro cultures (as the totipotency, the regenerative processes and the growing conditions) and the main techniques, as the micropropagation, will be addressed with particular focus on their nursery applications. Innovative techniques and technologies to improve the management of vitro-derived plant material will be described.
Contents
Introduction to biotechnologies and woody plants. Basics on techniques of in vitro culture and micropropagation (totipotency and regenerative processes). In vitro cultures for vegetative propagation of woody species (trees and shrubs). Technical aspects and applications of micropropagation for nursery productions. Organization of a plant micropropagation laboratory in the nursery. Issues connected with the commercial micropropagation. Limits and potentiality of regenerative processes on tissue and organ cultures. Restoration of plant material.
Methodological innovations improving the nursery plant productions by micropropagation. New technologies for management, conservation, storage and exchange of plant germplasm.
Application potential of “multifunctional” beads and synthetic seeds. Innovations on management of vitro-derived plant material in ex vitro conditions. Practical activities at micropropagation laboratory. Evaluation of scientific papers and cases studies on in vitro culture. Field trips to nurseries and commercial laboratories. Workshops and lectures by experts.
Year 2, Semester 1, 6 ECTS
Learning outcome
The objective of this course is to provide students with knowledge and tools to understand the dynamics of the innovative processes of biotechnology companies, with a particular attention to the economic and management aspects. The learning outcome will be realized by lectures, practicals, case study analysis and field trips.
Contents
Lectures will deal with the objectives of business administration and management of biotechnology companies. Next, applications in the agricultural field will be examined, deepening the economic aspects concerning the supply and demand of genetically modified food, insect-resistant fibre, food processing. Economic characteristics and perspectives of the agricultural biotechnology industry will be thoroughly presented, including the economic tools to examine the strategies used by the most important biotechnology companies. Practicals will be devoted to the discussion of case studies.