Unit ANIMAL BREEDING AND GENETICS

MOLECULAR GENETICS APPLIED TO DOMESTIC ANIMALS

Code	85104202
CFU	2
Teacher	Katia Cappelli
Teachers	Katia Cappelli
Hours	26 ore - Katia Cappelli
Learning activities	Caratterizzante
Area	Discipline della zootecnica, allevamento e nutrizione animale
Academic discipline	AGR/17
Type of study-unit	Obbligatorio (Required)
Language of instruction	Italian
Contents	Introduction to genomics and genomes anatomy. Genome sequencing, Next Generation Sequencing, Molecular markers and their applications. Genes controlling ereditary diseases. Gene expression and epigenetic regulation. Brief overview of Bioinformatics and data management. Genetic predisposition to deseases; gene editing
Reference texts	Genomi 3 "T.A. Brown" Edises. Introduzione alla Bioinformatica "Arhur M.Lesk" McGraw-Hill. Sides of the lectures
Educational objectives	The course aims to illustrate molecular genetics and main applications in livestocks. D1 - KNOWLEDGE AND UNDERSTANDING¿ The student is expected - to obtain knowledge and independence in interpreting and planning molecular tests for diseases; - to acquire information on unknown disease through the employment of data analysis and molecular technologies. D2 - APPLYING KNOWLEDGE AND UNDERSTANDING¿ At the end of the training the student will be able to:¿ - Assess diagnosis and prevention of genetic diseases as well as for the evaluation of molecular-genetic traits of interest in animal populations; - perform genetic-molecular evaluation of characters of interest in animal populations; D3 - MAKING JUDGMENT¿ At the end of the training the student will be able to: - read the results of any genetic-molecular test performed by another laboratory or competent facility; D4 - COMMUNICATION¿ At the end of the training the student will be able to: - ¿organize, prepare and exhibit, to an audience made up of people of equal level of preparation, a presentation on genetic differences between animal populations, and on molecular diagnostics of hereditary diseases with their own evaluations supported by appropriate arguments, - ¿support an adversarial process with people of equal preparation and experts in different issues, scientific, procedural and / or technological nature; - - demonstrate language properties, as well as the ability to use terminology that is sufficiently appropriate for a correct approach to the profession, which is also important for job interviews. D5 - LIFELONG LEARNING SKILLS¿ At the end of the training the student will be able to:¿ - consult and understand scientific texts, even innovative ones, bibliographic updates, so as to employ them in contexts not only usual for the profession, including research; - manage a sufficiently broad mastery of the subject to guarantee an acceptable basis for continuing professional updating through ongoing lifelong learning. EAEVE Day One Competences: 2.5 The aetiology, pathogenesis, clinical signs, diagnosis and treatment of the common diseases and disorders that occur in all common domestic species. Only for genetically based diseases and for their molecular diagnosis
Teaching methods	The course include 18 hours of theoretical lectures on all scheduled topics and 8 hours of practical classes imparted as molecular biology laboratory exercises and as computer room exercises. The practical lessons in the laboratory will involve a maximum of 15 students at same time that will participate provided of white coat. The practical classes in a computer room will involve a number of students equal to the stations available and in any case not more than 15.
Extended program	The gene and its organization in complex genomes: DNA manipulation, molecular markers. Methods for sequencing the genome: DNA sequencing, NGS technologies, assembly of contiguous DNA sequences, interpretation of genome sequences. Functional genomics: transcription and gene expression, mobile genetic elements, epigenetic signals. Genes that control hereditary diseases and their possible molecular diagnosis. Genetic predisposition to diseases, gene editing. Bioinformatic elements: nucleic acids and proteins databases, sequence alignments and primer disign.

VETERINARY GENETICS

Code	85004203
CFU	3
Teacher	Maurizio Silvestrelli
Teachers	Maurizio Silvestrelli
Hours	30 ore - Maurizio Silvestrelli
Learning activities	Affine/integrativa
Area	Attività formative affini o integrative
Academic discipline	AGR/17
Type of study-unit	Obbligatorio (Required)
Language of instruction	Italian language
Contents	Mutation. Gene and genotype frequencies. Interspecific hybridization. Abnormal karyotypes. Freemartins. Classification of intersex. Genotype and phenotype. Coat colour, pathology and selection in dog, cat and horse. Inherited defects. The Hardy-Weinberg law. Extentions of the Hardy-Weinberg law. Summary and practical implications.
Reference texts	The suggested book is "Genetica animale applicata" ("Applied animal genetics") by G. Pagnacco
Educational objectives	This teaching is the only test that the student faces about inherited defects within the degree program that is proposed as a main target to provide the basic knowledge of the relation genotype/phenotype for pahtologic and veterinary aspects. The main skills that students will acquire are: - knowledge of dog, cat and horse breeds; - knowledge of abnormal karyotype in animals; -Mendelian genetic diseases in animals. The main skills that allow to apply the acquired knowledge will be: -identification of mode of inheritance (dominant/resessive) of Mendelian genetic deseases in animals; -evaluation of phenotype linked to pathology; -use of genotipe in practical animal breeding
Teaching methods	The course is organized as follows: -lectures on all subjects of the course; -exercise at the microscope lab to see chromosome aberrations in cattle. Students will be divided into groups (maximum 20 students per group) and there will be 1 tutorial of 2 hours
Learning verification modality	The final exam is an oral test. It consists of a discussion, lasting about 45 minutes, aimed at ascertaining the level of knowledge and ability reached by the student on the theoretical and methodological contents indicated in the program of the three modules: veterinary genetics, molecular genetics applied to animals, and genetic evaluation of animals. The oral exam also verifies the ability to contextualize knowledge for a correct use, the ability to communicate with language properties, and the autonomous organization in the exposition of the topics. For each of the three modules two open stimuli with open answers are proposed. In the evaluation of each module, up to 10 points are awarded for the level of knowledge achieved, up to 8 points for the demonstrated skills, up to 6 points for the ability to contextualize knowledge, up to 4 points for the correct use of technical terminology, and up to 4 points for exhibition autonomy. The exam is passed with at least 18 points in each of the three modules: the final grade is the rounded down average, weighted by the CFU, of the score awarded for each module. In the event that a score of 31 is reached in all three modules, the student is given the praise. Self-assessment material is available in UniStudium.
Extended program	Introduction. Dog, cat and horse breeds. Single genes in population, genetics and animal breeding. Mutation. Gene and genotype frequencies. Evolution of karyotypes. Interspecific hybridization. Abnormal karyotypes: abnormal autosomal chromosome number (translocation, monosomy and trisomy). Abnormal chromosome structure: deletion, duplication and inversion. Abnormal sex chromosome number. Freemartins. Classification of intersex. Genotype and phenotype. Coat colour and pathology in dog, cat and horse. Inherited defects: autosomal dominant, autosomal recessive, X-linked dominant, X-linked recessive. The Hardy-Weinberg law. Extentions of the Hardy-Weinberg law. Summary and practical implications

GENETIC EVALUATION OF LIVESTOK

Code	85004302
CFU	2
Teacher	Camillo Pieramati
Teachers	Camillo Pieramati
Hours	26 ore - Camillo Pieramati
Learning activities	Caratterizzante
Area	Discipline della zootecnica, allevamento e nutrizione animale
Academic discipline	AGR/17
Type of study-unit	Obbligatorio (Required)
Language of instruction	Italian
Contents	Selection against genetic diseases. The animal merit: the genetic index, the marker assisted selection, and the genomic evaluation.
Reference texts	R.M. Bourdon: 'Understanding Animal Breeding ', Pearson ed. Lecturer's notes, presentations, spreadsheets and datasets are available from the UniStudium website.
Educational objectives	A firm knowledge of the founding basis of genetic improvement of animals: genetic prophylaxis of Mendelian diseases and of liability to diseases; the additive infinitesimal model; the estimate of Breeding Value; use of genomic data. The practical and supervised activities are organized in order to help the student in understanding the toughest topics (e.g. the statistical and mathematical aspects). The main abilities and competences are: - calculating the risk in different mating, - analyzing the information on breeding animals; - helping the breeders in the genetic improvement. EAEVE Day One Competences: 2.3 (The structure, function and behaviour of animals and their physiological and welfare needs, including healthy common domestic animals, captive Wildlife and laboratory-housed animals) and 2.4 (A knowledge of the businesses related to animal breeding, production and keeping). LOGBOOK, 3rd paragraph "Animal production": Information technology and statistics - Use of a spreadsheet (students could already receive this certification during their 1st year)
Teaching methods	Lectures will deal with all the main topics of the course. Practical training will be in a PC lab, and the students divided into 4 rotating groups.
Learning verification modality	The final exam is on the whole "Animal Breeding and Genetics" course (three modules). Self-assessment test are available in the "UniStudium" website.
Extended program	LECTURES. - Introduction to the course. The aim, the programme, the schedule, the text and the other didactic stuff, the final exam. [0,5 h] - Genetic diseases. Positive and negative mutations, dominant and recessive mutations; chance of mutation's loss. [1,5] - Genetic disease: differences between pets and livestock; positive and negative lists. Recessive disease: understanding a genetic tree. Recessive disease in pets: calculating the risk and the use of the Bayes' theorem (practical examples); sensibility and specificity of a diagnostic test (practical examples with genetic tests); the genetic prophylaxis in dogs. [4 h] - The test mating: mating to females with different genotypes; mating to more than one kind of genotype; the allele frequency in the population: lethal recessive allele in natural selection and a comparison between natural selection and the discovery of carriers. [5 h] - Genetic prophylaxis in the Italian Holstein, Brown and Italian beef breeds. The Hal gene in swine. Scrapie and resistant haplotypes. The persistence of lethal genes: the selection-mutation equilibrium and the balanced polymorphism. [4 h] - Liability to diseases: heritability; multiple thresholds. [3 h] PRACTICAL AND SUPERVISED ACTIVITIES. - Marker Assisted Selection. Semi-quantitative genetics: the major gene. Pleiotropy and genetic linkage. MAS. Sax's experiment. Marker and QTL. The Daughter Design: the bases; finding the alleles origin; the effect of the frequency; the Gran-Daughter Design. PIC and effective alleles. [1 h] - Simulating a Daughter Design: minor genes, major gene and marker; pleiotropy and genetic linkage; the frequency of haplotypes and the recombination frequency; the effect of environment; genetic variance. Phenotypic variance component and the heritability: performance test and progeny test; repeatability: effect on culling and effect on generation interval; correlated traits: direct and indirect response, selecting for more than one trait; the covariance between loci and assortative mating; the covariance between genotype and environment and the preferential treatment. The linkage disequilibrium: cis and trans haplotypes; the effect of crossing over on "double cis" and "double trans"; population disequilibrium and family disequilibrium. ANOVA of a DD: the meaning of the interaction. Understanding the simulation of a DD: effect of the additive variance, the heritability, linkage disequilibrium and recombination frequency. [3 h] - The genetic index. The meaning of index. BLP selection index, BLUP index and Genomic index. GEBV (Genome Enhanced Breeding Value). A practical example of calculating a BLP selection index: estimating environmental effects by least squares method, correcting phonotypes for factors and covariates. [2 h] - The pedigree file; calculating additive relationships; inbreeding; genomic relationships; the properties of the index; calculating the weights, the index, the accuracies, the genetic progress; optimizing the response. [2 h]