Master in plant and animal biotechnology

UNIVERSITY OF
乌迪内大学 UDINE

MASTER COURSE
IN PLANT AND ANIMAL BIOTECHNOLOGY
(IN ENGLISH)

Master Course in Plant and Animal Biotechnology

Objective

• Biotechnology is worldwide regarded as a strategic field for social development and progress. This view is
particularly true in a region that retains Life Science one of the avenues for development and therefore
made substantial structural investments in recent past. This process created a large and stimulating
background where a graduated in Plant and Animal Biotechnology finds perfect integration. This course has
the ambitious purpose of the education of those who will have the responsibility to move up biotechnology
from the present pioneer status to mass production and it is therefore focused on the extreme care of
individual student potentials in order to provide the future leadership for a yet-to-be-exploited field.

• This course aims to attract students wishing to apply in their professional activity the concepts and
technologies that have characterized one of the fastest scientific advancing field in the last twenty years.
The student will be the focus of the faculty activity devoted not only to concept transfer, but also to
development of the cultural maturity that leads to blend a critical approach together with permeability to new
information, whose rapid accumulation is a characteristic of this field. The build up of such a complex
cultural sensibility will be achieved through new and sometime non-conventional teaching approaches and
the development of practical/theoric projects by which student resources will be exploited.


Objective

• At graduation, the student in Plant and Animal Biotechnology not only will have acquired a large and
comprehensive knowledge of the notions relevant to specific scientific field, but he/she will also have
identified and practiced the peculiar ways to acquire, elaborate and analyze information in this field, as well
as the ability to synthesize and expose the results of the analysis. Thanks to the topics treated and the
teaching models used, the acquired professional will be recognizable in an international context, as it is
necessary for this particular field. A relevant and specific characteristic of this course will be the continuous
stimulus to the abilities to project and organize: a central point in the formation of the graduate will be the
understanding of the need to approach non-obvious context problems and to provide innovative and original
answers.

• The course will include contacts with various components of international research through participation in
seminars, in order to permeate the supranational dimension of the context in which the professional
graduate will have to move. The educational objectives will be achieved through activities that include
lectures, exercises and practical laboratory training. Students personal involvement will be stimulated
through the preparation and presentation of short reports or projects and the preparation of the thesis. The
training activities will be fully developed in English, placing the course in an international context.


Admission criteria

• The application and admission procedure differs for Italian university students and international students. In
order to be eligible for admission to the Master programme, international students must have completed at
least a relevant Bachelor's education with a major in biotechnology, agricultural, or veterinary science.
Admission requisites will be evaluated individually; detailed information may be found in the F.A.Q. page of
the Master programme web site (http://pab.uniud.it).

• The master course develops over two full academic year (four semesters) with a total of 120 ECTS (60
ECTS each academic year).


First year

• Biotechnology and genetics legislation (6 credits)
• Biotechnology in animal reproduction (8 credits)
• Genome analysis and bioinformatics (6 credits)
• Molecular nutrition of plants and animals 1(first module) (6 credits)
• Molecular nutrition of plants and animals 2 (second module) (6 credits)
• Plant-pathogen interaction (6 credits)
• Plant biotechnology (8 credits)
• Protein structure and function (6 credits)
• Animal physiology and welfare or Plant cell physiology and tissue culture (6 credits)

Credits: degree courses are usually structured in credits (crediti formativi universitari - CFU). A university credit generally corresponds to 25 hours of global work per
student, time for personal study included. The average workload of a full time student is conventionally fixed at 60 credits/year.


Second year

• Genetic resources (6 credits)
• Food safety (8 credits)

12 credits chosen from among the following:
Principles of crop breeding (6 credits)
Tree genetics and breeding (6 credits)
Livestock Production 1 (6 credits)
Livestock Production 2 (6 credits)

• Other Activities (26 credits)
• Training activities (2 credits)
• Final exam (24 credits)

Credits: degree courses are usually structured in credits (crediti formativi universitari - CFU). A university credit generally corresponds to 25 hours of global work per
student, time for personal study included. The average workload of a full time student is conventionally fixed at 60 credits/year.

Syllabus for classes in the Master programme in Plant and Animal Biotechnology

Programme
Biotechnology in Animal Reproduction

• The aims of the course are to provide the essential knowledge for understanding and manipulating the biology of reproduction of domestic and laboratory
animals. The course will also address major biotechnology applied to animal reproduction.

• The estrous cycles of females and, in particular, the techniques for synchronization and superovulation of the embryo’s donor and recipient females will be
described. During the course gametogenesis, in vivo fertilization, embryonic and fetal development will also be described.

• The procedures for in vivo and in vitro gametes and embryo collection, for in vitro oocyte maturation and fertilization, will be also treated in both domestic and
laboratory animals. The course will deal with techniques for oocyte nuclear transfer (cloning), for obtaining transgenic animals and their possible use in animal
production and biomedicine, for the embryo and sperm sexing, for the cryopreservation of gametes and embryo, the cry banking of the genetic resource, and
the principal pathologies due to the application of biotechnologies of reproduction (epigenetic defects).

• Laboratory activity on rabbit superovulation and embryo collection and evaluation will be also organized.


Programme
Genome analysis and bioinformatics

• The course focuses on the use of Next Generation Sequencing Technologies for analyzing genome structure, diversity and function and on the bioinformatics
tools required for these analyses, taking a problem-solving approach. The goal is to provide students with the basic skills required to utilize the vast amount of
information which is currently being produced in plants and animals using sequencing technologies and to apply these methods to the biological problems of
their interest. The course has a strong hands-on component with informatics laboratory sessions and tutorials aimed at familiarizing students with the Linux
operating system, simple scripting and the different software packages used for the analysis of NGS data.

• The topics addressed in the course are:
• Introduction to eukaryotic genome structure. Next Generation Sequencing Technologies: technical specificities, pros and cons. Analytical pipelines for NGS
data: from the sequencer to the scientist. Quality checking and filtering of sequences. Assembling genomes de novo. Gene prediction methods and algorithms.
Aligning sequences against a reference genome: principles and softwares. Detecting single nucleotide polymorphisms. Detecting structural variants: paired end
mapping and depth of coverage approaches. Estimating linkage disequilibrium and inferring haplotypes. Detecting rare variants in populations. Genotyping by
sequencing methods. Gene expression analysis through RNA sequencing: detecting transcripts and estimating their abundance. SmallRNA analysis: detecting
and estimating abundance of siRNA, miRNA and ta-siRNAs. Detecting epigenetic variation: analysis of DNA methylation through bisulfite sequencing; analysis
of chromatin modifications through ChIP sequencing. Going from a reference genome sequence to a reference pan-genome sequence.


Programme
Molecular nutrition of plant and animals 1 (first module)
The students will learn basic and applied concepts of plant nutrition; in particular mechanisms and regulatory principles of nutrient uptake and plant response to abiotic
stresses will be elucidated considering approaches from biochemistry and molecular biology; the role of secondary metabolites in plant adaptation to adverse conditions
will also be considered. Applied objectives are the identification of processes contributing to nutrient efficiency and stress tolerance in crop plants, and possible
improvements by biotechnological approaches.

Definition of stress. Importance of mineral nutrition. Chemistry and biochemistry of nutrients in the soil-plant system; exogenous and endogenous factors affecting
nutrient availability; biochemical interactions at the soil-plant interface (the rhizosphere). Nutrient acquisition: physiological, biochemical and molecular aspects.
Mechanisms for the acquisition of the main macro- and micro-nutrients. Effects of different kinds of stresses on plants; physiological, biochemical, genetic and
molecular aspects of adaptation (tolerance and resistance). Adaptive responses of plants to nutritional disorders and to adverse soil conditions (acidic soils, alkaline
and calcareous soils, water stress, water logging, flooding and presence of heavy metals).

Physiological role of secondary metabolites. Chemistry, biochemistry and biosynthesis of phenolic compounds, isoprenoids, alkaloids, terpenoids, lipids, S- and N-
containing secondary metabolites. Production and release in the soil of metabolites involved in signal exchange between plant and soil micro-organisms.
Genetic engineering of plant secondary metabolism for food and non-food application.

The course will include lectures and laboratory practices on the physiological, biochemical and molecular characterization of the main mechanisms involved in mineral
nutrition of plants and in their response to abiotic stress.


Programme
Molecular nutrition of plant and animals 2 (second module)

• - Rudiments of animal nutrition: chemical composition and analysis of feed;
• - Rudiments of digestion physiology and metabolism of feeds;
• - Energy, protein, minerals and vitamins requirements of animals;
• - Diet formulation;
• - Feeding techniques;
• - Useful laboratory techniques in structural and functional genomics;
• - Nutrigenetics;
• - Monogenic diseases in animals;
• - Nutrigenomics and pharmacogenomics;
• - Cellular nutrient homeostasis, proliferation and apoptosis;
• - Roles for nutrients in signal transduction, gene expression and proteolysis;
• - Nutrition and immune function;
• - Nutrition and stress response;
• - Molecular mechanisms of action of bioactive compounds in monogastrics and ruminants;
• - Molecular mechanisms of food allergy;
• - Ruminal and intestinal metagenomics;
• - Introduction to proteomics and metabolomics;
• - Bioinformatics laboratory: statistical analysis and data mining in animal nutrigenomics experiments;
• - Consultation of useful genetic databases in animal science.


Programme
Plant biotechnology

The course will include an introduction to theoretical aspects in Plant Biotechnology with emphasis on practical application.

Overview of the main issues relating to cell culture. Direct and indirect organogenesis, somatic embryogenesis. Use of protoplasts and
haploids culture in Agricultural Biotechnology. Principles of plant transformation, techniques and applications. Dominant and co-
dominant molecular markers. Analysis of electropherograms of SSR and AFLP markers. Development of molecular marker datasets
with specific software, descriptive analysis, calculation of genetic distances with different indices (Nei, Fst), PCA, construction of
dendrograms. Construction of genetic and physical maps, practical examples and applications. Molecular marker assisted selection
(MAS). Cytogenetics: In Situ Hybridization. Sequencing techniques and sequence analysis: base calling, editing, contig assembly by the
specific softwares. ORF scanning, organization of a genome of higher organism. Localization of genes in genome sequences. Analysis
in silico: searching for homology, comparison of gene sequences and CDS, similarity and homology between sequences. PCR
amplification of plastid sequences for the barcoding of plants. RNA Interference: Principles and Applications. Gene expression analysis.


Programme
Plant-pathogen interaction
• The students will develop a comprehension of the molecular mechanisms underlying the interaction of fungal and bacterial
pathogens with their host. They will be able to recognize the molecular signals that characterize plant diseases, the major
physiological and genetic aspects of pathogenesis and virulence in the microrganisms, the different aspects of innate immunity
and resistance in the plant. Within the general contexts of evolution, environmental fitness and competition among organisms, the
most recent research issues with potential for disease control will be acquired.

• Molecular methods used in the study of plant-microorganism relationships, transposons, gene disruption, yeast two hybrids,
differential display. Fungal genetics and fungal population dynamics: relevance in plant pathology. Molecular mechanisms of
fungal penetration, thigmotropism, appressorium formation. Auxonic diseases and hormonal unbalance in the host: the case of
olive knot. Infection, colonization and host transformation by Agrobacterium tumefaciens. Cell wall degrading enzymes. Role of
polygalacturonase inhibiting proteins in plant defence. Programmed cell death and hypersensitive reaction. Avirulence and gene
per gene theory. The secretion of virulence factors and the type III transport system. The harpin and the cluster hrp. Effectors.
Molecular basis of recognition and defence of plants. Innate immunity and cultivar specific resistance. Phytoalexins and
phytoanticipins. PR proteins and systemic acquired resistance. Molecular basis of hypovirulence in Chryphonectria parasitica.

• The course includes laboratory training on elicitation of hypersensitive response, induction of systemic acquired resistance and
phytoalexin production.


Programme
Protein structure and function

• Protein structure: definition of domain; levels of organization; protein folding and flexibility; properties of soluble and membrane-
bound proteins; examples of typical protein structures.
• Protein sorting: cytoplasm-localized proteins; protein sorting; proteolysis.
• Protein characterization: purification and enzymatic analysis; purification of membrane proteins; chromatographic techniques;
protein electrophoresis.
• Structural and conformational analysis: molecular mass determination; subunit composition; aminoacid analysis; aminoacid
sequence determination; x-ray crystallography and NMR techniques; reverse genetics; structure prediction; computer-assisted
protein analysis.
• Antibodies; structure of the antibodies; production and quality analysis of antibodies; antibody methods.
• Determination of protein function and prediction of structure, function, and localization: comparison between sequences;
recombinant DNA techniques; site-directed mutagenesis; heterologous expression; protein engineering.
• Phylogenetic analysis using protein sequences: substitution matrices (PAM and BLOSUM); alignment of protein sequences; tree-
building methods for protein phylogeny.
• Laboratory practicals: dedicated protocols are developed to show the main protein purification and protein analysis techniques.
Bioinformatic paracticals are provided by guided access to biological sites and protein databases on the web.


Programme
Animal physiology and welfare

The aim of the course is to make students acquire specific knowledge in order to provide a knowledge base of homeostasis, behavior,
animal welfare in order to the study new strategy to improve well-being and a better interaction between man and animal.

• Basic physiology concepts of organ system
• Major Senses ( Sight, Hearing, Taste, Smell, and Touch)
• Temperature control
• Basic physiology concepts of homeostasis, omeoresis, allostasi, resilience.
• Limbic system, Emotional intelligence and cognitive intelligence
• The pain.
• Stress.


Programme
Plant cell physiology and tissue culture

• Introduction and historical overview, importance of tissue culture system and biotechnology in modern agriculture.
• The metabolic regulation, the basis of metabolic control. Examples of metabolic control, the role of Ca2+ in metabolic regulation. Relations
between metabolic regulation and cell compartmentation.
• Plant cell growth and differentiation, regulation of differentiation, totipotency
• Plant growth regulators and their role in the tissue culture system
• Growth and development, overview of plants growth and development. The origins of polarity. The rate of cell elongation. Shoot and root apical
meristem.
• Programmed cell death (PCD) paradigms in animals and plants; PCD in the life cycle of plants, the senescence.
• The Control of flowering. Floral evocation: internal and external cues. Cicardian rhythms: the clock within. Vernalization: promoting flowering
with cold. Biochemical signalling involved in flowering.
• Tissue culture techniques: work in aseptic conditions; advantages of tissue culture techniques, tissue culture media and physical factors of
cultivation
• Regeneration of plants in tissue culture system; different types of cultures: meristematic, organ, callus cultures; regeneration systems: induction
of adventitious and axillary buds, induction of rooting; somatic embryogenesis; stages of plant regeneration in tissue culture system;
physiological aspects of adaptation processes – transfer from in vitro to in vivo conditions; cryopreservation; soma clonal variability
• Protoplast cultures, isolation of protoplast, regeneration of plants from protoplast, somatic hybridization
• Tissue cultures for production of secondary metabolites, bioreactors, biotransformations.


Programme
Genetic resources

• To provide students with knowledge about the centres of origin of the main species domesticated by the man; to provide as well
students with methodological tools suitable to understand the origin of genetic diversity and to evaluate it; to show how the
genetic diversity is the base of evolution and the base of the breeding as well; finally, to make students aware of the importance to
conserve the genetic diversity especially in the centres of origin of the specie.

• Crop domestication and breeding. The emergence of agricultures in different parts of the world and their link with the centres of
origin of species. The domestication syndrome: genes gained/lost during the domestication process. The domestication of new
crops at the time of the great colonisations. The birth of genetics and crop breeding . Effect of domestication on genetic diversity.
• Population genetics. Origin of genetic diversity. Population genetic structure, the Hardy-Weinberg equilibrium and disruption
mechanisms: migration, genetic drift, founder effect, bottle neck, selection. Methods of estimation of genetic diversity. Molecular
taxonomy.
• Domestication cases study. Cereals (wheat, corn, rice), legumes (bean and soybean), potato, squash and zucchini, canola and
other brassicaceae, sunflower, sugarcane and sugar beat, fruit crops (apple, peach, grape, banana), other commodities (tea,
coffee, cocoa, cotton).
• Conservation of genetic diversity. Conservation in situ (biotopes, reserves, natural parks), conservation ex situ (base, active and
core collections). Institutions with the mission of preserving the genetic diversity (FAO, IPGRI, CGIAR, Governments, local
Administrations). Genetic resources and intellectual property.


Programme
Food safety
This course is devoted to the description of econometric and statistical tools which allow complex contexts modelling. The course structure may be described by the
expression “GLM + LMM = GLM”, because lessons will start treating generalized linear models (GLM) and linear mixed models (LMM), then linear generalized mixed
models will be described (GLMM).

Linear generalized models (GLM) represent a flexible generalization of linear regression as they allow the analysis of whichever response variable with distribution
belonging to the exponential family. The GLM approach represents a unified context for different statistical models, the linear model included.

Linear mixed models (LMM) represent an extension of linear models which allows to describe complex data with jerarchical structures affecting the observations
independence, through the inclusion of mixed effects inside the model formulation. Many fields of analysis, in fact, present data with jerarchical structures, longitudinal
dimension or repeated measures which make observations not independent.

Finally, if mixed effects have to be considered in generalized linear models formulation, the statistical econometric tools useful in this situations relate to the generalized
linear mixed models context: GLMM.

This course requires a good knowledge of base econometric methods and statistical inference, together with a good level of English language comprehension.


Programme
Principles of crop breeding

Nature and objectives of plant breeding, importance of the variety factor in modern agriculture, neolithic revolution, domestication of
species, food availability and starvation, centres of origin o the plant species, germplasm collections, introduction of new varieties and
species, main evolutionary schemes followed by plants, mutagenesis, interspecific hybridization, induced polyploidy, flower and flower
modifications, mating systems in plants, genetic structure in population of autogamous and allogamous species, self-incompatibility
systems, male sterility, inheritance of quantitative traits, heritability, possible responses to selection, methods of plant breeding in
autogamous, allogamous, vegetatively-propagated and apomictic plants, registration of new varieties, breeder’s rights, breeder’s
exemption, farmer’s privilege, seed categories, natural and artificial methods of plant cloning, totipotency of the plant cell, regeneration
methods, methods of genetic transformation of plants, transgenesis in plant breeding, expression vectors, reporter genes, selectable
markers, molecular cassettes for transgene expression in plants, elements controlling gene expression, selection of primary
transformants on the base of transgene expression levels, guidelines, rules and regulations at national and EU level for the deliberate
release and marketing of transgenic crops.


Programme
Tree genetics and breeding
The objective of this course is to illustrate the conventional methods used to select new varieties in vegetatively propagated crops with particular emphasis to fruit and
timber trees, as well as the most advanced techniques used to improve selection efficiency in wooden species. Aspects related to fruit tree breeding, including polyploid
inheritance, apomixis and genetic analysis of complex loci will be presented and discussed. The course will consist of lectures, practical exercises and visits to ongoing
field trials.
1. The Scope and Nature of Plant Breeding . What is Plant Breeding. Scope of the Modern Industry. Sources of Genetic Material. Germplasm Preservation.Botanic
Gardens, Plant Breeding Organisations, Research Bodies

2. Introduction to Genetics: a review. Review of Plant Genetics Linkage and Crossing Over. DNA. Homologous Chromosomes. Plant Genetics, Mendel's Principles and
Experiment. Genetic Terminology. Gene Linkages. Traits inherithance

3. Gamete Production, Pollination and Fertilisation in Plants: a review focused on trees. Phases of Plant Reproduction. Gamete Production. Gene Mutation: example of
commercial cultivars produced by bud mutation. Sources of Genetic Variation: Polyploidy, Bud Sports and Chimeras. Male Sterility, self incompatibility. Effect of
Environment. Terminology. Use of Pollination Biology in Plant Breeding: Pollination Process, Pollination Requirements, Cross Pollination, Fertilisation, Male/Female
Recognition, Overcoming incompatibilit, Post Fertilisation, Pollen Selection, Floral Introduction. Mitosis and Meiosi. Sexual Structures in Plants: Flowers, Fruit, Seed

4. Mono Hybrid and Dihybrid Inheritance in Trees. Mono hybrid Crosses. Dihybrid Crosses. Gene Linkages. Crossing Over. Recombination. Quantitative Traits

5. Practical Plant Breeding Techniques: examples in fruit and forest trees. Plant Breeding Program. Breeding Self Pollinated Crops (peach)Mass Selection. Pedigree
Breeding. Bulk Population Breeding. Breeding Cross Pollinated Crops (apple, kiwifruit, grape, poplar). Single Plant Selection.Mass Selection. Progeny Selection. Line
Breeding. Recurrent Selection. Backcross Breeding. Induced Polyploidy. Dormancy Factors Affecting Germination (eg. hard seeds, impermeability to water, Chemical
inhibitors, Undeveloped embryos, etc)

6. Current Developments in Tree Genetics. Plant Biotechnology. Genetic Engineering. DNA Markers. Somatic Hybridisation. Micropropagation. Breeding by design.
Plant Breeders Rights. Trade Marks, Patents


Programme
Livestock production 1

The course has the objective to provide to students the basic knowledge in breeding of domestic animals (cattle, horses, pigs, rabbits, chicken, etc.) and fish. During
the course, the main techniques of traditional selection and molecular biology will be explained and discussed in detail. These principles are applicable to farm animals,
companion animals, populations of rare breeds and zoo animals. The course comprises three types of teaching activities: lectures, a computer-supported practical and
a practical in a modern farm. In addition, there is a laboratory practical, during which the students become acquainted with the techniques of molecular genetics. This
course will also provide a foundation knowledge in the genetic-veterinary management and epidemiology of farm animals.

Basic molecular laboratory methods applied to farm animals: DNA and RNA analysis. Genetic markers. Genome mapping and linkage analysis. Genome
sequencing. Identification and analysis of SNPs. High-throughput marker genotyping. BACs and BAC libraries. Expressed sequence tags. DNA chips. Proteomics.
Bioinformatics

Genetic diseases of farm animal: Biochemical genetics. Chromosomes and chromosomal aberrations. Familiar disorders not due to single genes. Genetic control of
inhered disease

Quantitative genetics: Relationship and inbreeding. Selection within populations. Identification and analysis of a QTL. QTL mapping and marker assisted selection.
Genomic selection. Breed structure analysis. Crossing schemes


Programme
Livestock production 2

The aim of the course if to present the basis of animal biodiversity for domestic animals, giving an insight of
species and breeds, reporting the main productive traits and their relationship with the variability of genome.
Aspects concerning the conservation of animal biodiversity and breeding progress based on selection programs
and molecular genetics are also presented.

Biology of domestication. Origin, differentiation and ecological adaptation of animal species and breeds.
Molecular basis of animal biodiversity. Linking phenotypes to variability of animal genomes. Crossbreeds,
coadaptation, biodiversity and sustainable developments. Use of genomic technology for the selection and
maintenance of animal biodiversity. Description of breed traits of main species of domestic animals. Biology,
behavior and productive cycles of domestic animals. The dairy and meat production systems. Training,
education of animal and human-animal relationships.

Master in plant and animal biotechnology

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