Unit ANIMAL BREEDING AND GENETICS

MOLECULAR GENETICS APPLIED TO DOMESTIC ANIMALS

Code	85104202
CFU	2
Teacher	Maurizio Silvestrelli
Teachers	Katia Cappelli (Codocenza)
Hours	26 ore (Codocenza) - 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. PROGRAM: THEORETICAL LESSONS: The gene and its organization in complex genomes (3 hours). Functional genomics: transcription and gene expression, mobile genetic elements, epigenetic signals (3 hours). DNA manipulation, genome mapping, molecular markers (4,5 hours). Methods for sequencing the genome: DNA sequencing, NGS technologies (1,5 hours). Assembly of contiguous DNA sequences, interpretation of genome sequences (1,5 hours). Genes that control hereditary diseases and their possible molecular diagnosis (3 hours). Bioinformatic elements: nucleic acids and proteins databases, sequence alignments (1,5 hours). PRACTICAL LESSONS PCR_RFLP to genotyp locus E of horse (2 hours). Databases of nucleic acids and proteins, access to molecular biology databases. (2 hours). Alignments of nucleotide and amino acid sequences, primer design (2 hours). Preparation of PCR-RFLP in silico test for molecular diagnosis of heritability disease (2 hours).
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 livestocksThe student is exptected to obtain knowlegde and independence in interpreting and planning molecular tests for diseases as well as aquiring information on unknonw disease through the emplyment of data analysis and molecular technologies.The achievement of these objectives is essential  for  the diagnosis  and prevention of genetic diseases as well as for the evaluation of molecular-genetic traits of interest in animal populations and for the reading of  results obtained from a possible molecular test performed by another laboratory or competent structure.
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 20.
Extended program	The gene and its organization in complex genomes: DNA manipulation, genome mapping, 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. 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	42 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 and pathology in dog, cat and horse. Inherited defects. The Hardy-Weinberg law. Extentions of the Hardy-Weinberg law. Summary and practical implications 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.
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	Per informazioni sui servizi di supporto agli studenti con disabilità e/o DSA visita la pagina http://www.unipg.it/disabilita-e-dsa
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	Maurizio Silvestrelli
Teachers	Camillo Pieramati (Codocenza)
Hours	50 ore (Codocenza) - 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 recessive genes. The animal productions and the additive model. Relationships and inbreeding. The liability to diseases. Genetic index, marker assisted selection and genomic index. === 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]
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; relationships and inbreeding; the additive infinitesimal model; heritability, repeatability and correlation of traits; estimation of breeding values; correlated traits; optimizing the genetic progress; QTL and MAS; genomic index. The practical and supervised activities do not match with lectures: they follow an independent path, 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.
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.
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]