Course description

The aim of the course is to provide genetic and molecular genetic knowledge (e.g. sampling, genetic identification, genetic control of parentage, genetic diseases, diversity evaluation, estimation of breeding value) necessary to solve the tasks encountered in the practice of future veterinarians.

This subject, putting a special emphasis on Mendelian, clinical (hereditary diseases), population and molecular genetics, furthermore biotechnology and preservation of genetic resources. The methods of breeding value evaluation, selection, herd improvement, breeding systems, and animal production with traceability are also synthesized, using the classical and up to date scientific knowledge of Mendelian, population and molecular genetics.

 

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Lectures theme

1.      Introduction. Domestication of species, evolutionary consequences.

2.      Domestication was/is a process, when man was taming, breeding, raising and transforming of wild animals for his own sake during many generations.

3.      Gradual, multigenerational procedure and directed genetic progress (artificial selection) + mutations (micro-evolution). Close relation to mankind and civilization development; Domestic animals – animals living near humans, with human care and breeding, which differ from their wild ancestors in their genetic, morphological and behavioral characteristics.

4.      Fundamentals of Mendelian, cyto- and molecular genetics.

5.      The history of heredity, theories of inheritance before Mendel, Mendel’s work, and outstanding personalities of genetics after Mendel. Illumination of the basic concepts of heredity through examples of the typical characteristics of domestic animal species. Basic concepts of cytogenetics (e.g. genotype, paratype, meiosis, mitosis), genome structure (karyotype), and chromosome abnormalities. Basic concepts of molecular genetics (gene, allele, locus, genomics, epigenetics, mutation).

6.      Mendelian exceptions (expressivity, penetrance, allelic polymorphism, immunogenetics, epigenetics and pleiotropy, recombination and lethal genes).

7.      Clinical genetics, hereditary abnormalities (mono/oligogenic, mutations, diagnosis, prevention, liability). Epigenetics.

8.      Mendelian exceptions (linkage, sex linked, XL, ZL, uniparental inheritance, major genes, epistasis).

9.      Biotechnology in animal breeding (AI, ET, MOET, EMT).

10.   The most important artificial reproduction techniques (ART) used in animal husbandry: history, purpose, important steps of artificial insemination; sperm treatment techniques (dilution, deep freezing, vitrification); embryo transfer in domestic and wild endangered animal species, embryo transfer steps; steps and application of in vitro embryo production (IVP). The importance of chimerism in different animal species.

11.   Biotechnology in animal breeding (cloning, GMO, transgenesis, genome editing).

12.   Qualitative population genetics: polymorphism, gene and genotype frequencies, haplotype.

13.   “Characterization and definition of Mendelian traits. Conditions for genetic balance can be checked using the Hardy-Weinberg rule. The importance of gene and genotype frequency calculation for different traits in domestic animal species.

14.   Applying the Chi2 test to check Hardy-Weinberg ratios. Statistics of genetic diversity (number of samples, observed number of alleles, effective number of alleles) and methods for complete description of the stock.

15.   Quantitative population genetics: valuable traits, heritability, repeatability, correlation, regression.

16.   Quantitative population genetics characterizes the polygenic traits of stocks based on phenotypic values and genomic values. It examines the environmental factors affecting quantitative properties and shows changes over time. The primary valueable traits are the abilities taken into account for the specific utilization, the secondary ones are any other abilities that helps the realization of the primary ability regardless of the direction of utilization.

17.   Terms of breeding value and its estimation.

18.   Breeding value of an animal – is the deviation of the individual genetic merit from the mean genetic merit of a reference population. The individual breeding value is of altering degree, and changes according to the value (genetic merit) of the reference population or of mating partners. Genome-wide information makes the breeders accurately to determine a direct genomic estimated breeding value (dGV). If genomic information is available within the system, the official breeding value of an animal is the combined breeding value (gBV) from the classic breeding value (BV) based on own and / or relatives’ performance and the direct genomic value (dGV).

19.   Selection (methods, types, forms, selection index, MAS, efficiency).

20.   During artificial selection, humans purposefully leave breeding animals, and by mating them, they change the genetic composition (productivity, appearance, reproduction, adaptability) of the producing offspring generation. Index selection is the most effective kind of selection for several traits at the same time. Selection made according to a single index value formed from several properties results in the greatest economic benefit.

21.   Mating methods and breeding systems: pure breeding, crossbreeding, heterosis.

22.   Based on the mating plan, male and female individuals breed with each other according to one of the mating methods. In accordance with the breeding goal (increasing or decreasing homozygosity), we apply various breeding methods based on the degree of genetic relationship between paired individuals.

23.   Preservation and conservation of genetic diversity and resources, endangered breeds.

24.   The animal population designated for the preservation of genetic resources is kept in isolation, free from human intervention that causes genetic changes. Preservation is in vivo, when it comes to living animals in a traditional environment, and preservation is in vitro, when the sample is stored, for example, in a deep freezer. The in vivo version is realized by outbreeding, by pairing more distant than average relatives with each other. The goal is to preserve the original properties and genetic diversity, as well as adaptation to the environment.

Practical lessons theme

1.      Life career, lifetime and age estimation.

2.      The lives of domestic animals are characterized by life stages (growth, development), special dates (maturation, breeding maturity, first calving, introduction into use), and lifespan according to the specialized main directions of utilization and the task of the individual (breeding animal, producing animal). Productive and reproductive capacity changes with age. Teething, as a genetically determined feature, as well as age-related changes in the teeth can be used to estimate age.

3.      Individual markings, herd booking, identification, traceability.

4.      The topic covers the following areas: organization of domestic animals (breeding organizations, herd book registration, production recording, data register), individual marking in domestic animals (mandatory, optional, permanent and temporary). Furthermore, the importance of individual identification (based on biological signs, genetic markers and artificial numberings) and traceability in the safety of the food chain. National Animal Breeding Database: a database operated by the National Food Chain Safety Office for the registration of data related to animal breeding, breeders, keepers and owners. Farm Information System and Uniform Registration Systems of Species.

5.      Taking biological samples, parentage and identity control, DNA-polymorphisms (microsatellites, SNP).

6.      Considerations during the collection of biological samples, sample collection methods, packaging, and storage of samples. Sample types suitable for different DNA tests, and properties of the genetic regions to be tested. Steps of genetic testing methods to verify paternity and identity on an individual level (e.g. with restriction endonucleases). Detection of DNA polymorphisms (microsatellites and SNPs) by PCR, electrophoresis, and sequencing techniques.

7.      Molecular diagnosis of hereditary disorders.

8.      Autosomal and X-linked inheritance in practical animal breeding.

9.      Forensic animal genetics.

10.   Involvement of animals in criminal cases: human aspects (animal attacks, economic damage), animal rights (animal abuse), silent witnesses, environmental crimes (wildlife damage), international cooperation. Conditions for on-site investigations and forensic DNA testing. Genetic markers for DNA profiling and identification at the species level (“DNA barcoding”). Genetic methods for tracing the origin of animal product composition.

11.   Practical biotechnology: artificial insemination (AI) and embryo manipulations (EMT) and cloning

12.   Using artificial reproduction techniques (ART), the efficiency of production of breeding and production animals can be increased, and additional advantages of the methods are also presented, such as the avoidance of infections and injuries, as well as the possibility of sperm testing. Presentation of the basic observations (e.g. estrus), tools and methods (e.g. ultrasound, detectors and biosensors, tests), and the basic steps required for successful application on different animal species.

13.   Transgenesis, gene editing, gene-mapping, QTL analysis, application of genomial information.

14.   Calculation of gene and genotype frequencies.

15.   Practical examples of gene and genotype frequency calculation in equilibrium and non-equilibrium situations, in the case of intermediate or dominant-recessive inheritance linked to auto- and sex chromosomes in different animal species. Application of the Hardy-Weinberg rule and statistics with the Chi-square test to examine the difference between the expected and observed frequencies, as well as to characterize the genetic balance of the herds. The results obtained can be used to estimate the proportion of carriers of the mutant allele and, among other things, to check the changes occurring in the herds.

16.   Bioinformatics, genomics, proteomics.

17.   Calculation of breeding value.

18.   It deals with the practical approach and methods of determining breeding value, touching on the following topics: pre-correction, correction (for several effects at the same time, with iteration: repeating a mathematical or calculation procedure based on the results of a previous run, typically as a means of obtaining successive approximations aimed at solving the problem), heritability , degree of genetic relationship and genetic trend. Emphasizes the use of the mathematical method in direct (breeding work) and indirect (other research) aspects.

19.   Calculation of genetic improvement (response to selection).

20.   Response to selection (R, “gain”, advance or progress) is the difference between the mean genetic value of progeny of selected parents and the mean genetic value of original population The selection differential and the generation interval are used in its calculation.

21.   Pedigree analysis, calculation of genetic relationship and inbreeding coefficients.

22.   Pedigree examination is an important part of getting to know the breed’s past kinship structure, and at the same time it provides an indispensable reference point for achieving future goals. In this context, the degree of kinship, the inbreeding coefficient in the classical sense (Write’s coefficient) and F-statistics are determined, as well as more modern population parameters, such as the real number of founders (f) and the effective numbers of founder genomes or founder genome equivalents (fg), then also, molecular homozygosity (including ROH).

23.   Taking body measurements on living animal and pictures (VAM), geometric morphometry.

Exam information

In the regular exam period, the exam consists of two parts (practical and theoretical). At first, students are controlled by a questionnaire on computer (called as GAT-test) according to their rapid answers to basic figures, definitions, associations and calculations as a threshold to enter into the theoretical part. The performance of GAT-test is successful from 60%. Then, a theory test in computer (Moodle test) too is taken. In case of failure, the practical exam (GAT test) with a score of better than 80% is not required to be repeated. The questions of the GAT test can be practiced online in advance.  Time span between the exam failed and its re-take should exceed 5 days.

The GAT result contributes 10% to the final grade, the Moodle result contributes 90%