Hubert Pausch: Catalogue data in Autumn Semester 2024 |
| Name | Prof. Dr. Hubert Pausch |
| Field | Animal Genomics |
| Address | Professur für Tiergenomik ETH Zürich, LFW B 58.2 Universitätstrasse 2 8092 Zürich SWITZERLAND |
| Telephone | +41 44 633 66 81 |
| hubert.pausch@usys.ethz.ch | |
| URL | http://www.ag.ethz.ch |
| Department | Environmental Systems Science |
| Relationship | Associate Professor |
| Number | Title | ECTS | Hours | Lecturers | ||||||||||||||||||||||||||||||||||||||||||||
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| 751-0441-00L | Scientific Analysis and Presentation of Data | 2 credits | 2G | H. Pausch, N. K. Kadri, A. Leonard | ||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Students will get an introduction to the scientific work with data covering all steps from data import from Excel via statistical analyses to producing correct scientific graphical output. Exercises with the software R/RStudio will provide hands-on opportunities to get acquainted with data analysis and presentation in adequate graphs. | |||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | This lecture with exercises gives an introduction to the scientific work with data, starting with data acquisition and ending with statistical analyses as they are often required for a bachelor thesis (descriptive statistics, linear regression, simple analyses of variance etc.). Using open-source R/RStudio software will be the primary focus via a hands-on approach. An imporant aspect will be to learn which graphical representation of data are best suited for the task (how can data be presented clearly and still scientifically correct?) | |||||||||||||||||||||||||||||||||||||||||||||||
| Content | Tentative Programme: - Introduction - Introduction to 'R' - Data import and graphical presentation - Correct and problematic graphical data displays - Statistical distribution and confidence intervals - Statistical tests - Repetition and hands-on applications - Correlation analysis - Linear regressions - Analysis of Variance Last week of semester: examination (Leistungskontrolle) | |||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | German and English | |||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Theoretical background in ensemble statistics from the mandatory course in the 4th semester; students should have cleared the examination of that fundamental course to be able to follow | |||||||||||||||||||||||||||||||||||||||||||||||
Competencies |
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| 751-6003-00L | Training Course in Research Groups (Large)  | 6 credits | 13P | S. M. Bernal Ulloa, S. Neuenschwander, M. Niu, H. Pausch, M. Saenz de Juano Ribes, S. E. Ulbrich | ||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The students will learn the conceptual and methodological background of research in the animal science groups of the Institute of Plant, Animal and Agroecosystem Science. In addition to teaching the theoretical background, the major aim of the course is to integrate the students into the research groups (on job training) and, hence, to focus on the practical application of the knowledge. | |||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | - Introduction into the conceptual and methodological basis of research - Integration of the students into the research groups (on job training) - Application of the gained knowledge | |||||||||||||||||||||||||||||||||||||||||||||||
| Content | The students will be integrated into the research groups’ day-to-day work and will thus deal with all aspects of scientific work. This comprises the planning (conceptually and logistically), execution (data collection, laboratory analyses) and evaluation (statistics, data presentation) of experiments as well as the basics of scientific writing (aim: later publication, Master thesis). The research topics and the range of methodologies vary between the animal science research groups in the Institute of Plant, Animal and Agroecosystem Sciences. | |||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | None | |||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Specific readings after enlisting in a particular research group. | |||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The number of training slots in the various groups is limited. It is therefore highly recommended to contact the group leaders early enough (first come first serve). The full integration in a research group often means to work on weekends. The total time budget is equivalent to about 180 hours. Active participation in group meetings (discussion, presentation) and short written reports about the work conducted are required for the 6 credit points. There are no grades, it is only pass or fail. | |||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 751-6003-01L | Training Course in Research Groups (Small) | 3 credits | 6P | S. M. Bernal Ulloa, S. Neuenschwander, M. Niu, H. Pausch, M. Saenz de Juano Ribes, S. E. Ulbrich | ||||||||||||||||||||||||||||||||||||||||||||
| Abstract | The students will learn the conceptual and methodological background of research in the animal science groups of the Institute of Plant, Animal and Agroecosystem Science. In addition to teaching the theoretical background, the major aim of the course is to integrate the students into the research groups (on job training) and, hence, to focus on the practical application of the knowledge. | |||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | - Introduction into the conceptual and methodological basis of research - Integration of the students into the research groups (on job training) - Application of the gained knowledge | |||||||||||||||||||||||||||||||||||||||||||||||
| Content | The students will be integrated into the research groups’ day-to-day work and will thus deal with all aspects of scientific work. This comprises the planning (conceptually and logistically), execution (data collection, laboratory analyses) and evaluation (statistics, data presentation) of experiments as well as the basics of scientific writing (aim: later publication, Master thesis). The research topics and the range of methodologies vary between the animal science research groups in the Institute of Plant, Animal and Agroecosystem Sciences. | |||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | None | |||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Specific readings after enlisting in a particular research group. | |||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | The number of training slots in the various groups is limited. It is therefore highly recommended to contact the group leaders early enough (first come first serve). The full integration in a research group often means to work on weekends. The total time budget is equivalent to about 90 hours. Active participation in group meetings (discussion, presentation) and short written reports about the work conducted are required for the 3 credit points. There are no grades, it is only pass or fail. | |||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 751-6243-00L | Breeding and Conservation of Animal Genetic Resources | 2 credits | 2V | H. Pausch, C. Flury, H. Signer-Hasler | ||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Animal genetic resources refer to the genetic and species diversity of livestock. Only a few production breeds have been further developed through breeding, while local breeds have no longer been able to survive in this competition. Without the support of endangered breeds and the sustainable breeding of productive breeds, many regionally typical breeds are threatened with extinction. | |||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Learning Objectives: Part 1: At the end of the course, students are able to assess the importance and problems of small ruminant breeding and husbandry in Switzerland and neighbouring countries. They know the most important breeding objectives and are able to assess them in terms of production and sustainable development in small ruminants and cattle. Learning objectives part 2: The second part gives an overview of the distribution, endangerment and conservation of breed diversity of farm animals in Switzerland and internationally. The theory is illustrated with numerous examples and the knowledge is deepened in exercises. The students: - have an overview of the national and international distribution of animal genetic resources and are familiar with the database DAD-IS (Domestic Animal Diversity Information System). - can name the national and international efforts to conserve agricultural livestock breeds. - know how to describe genetic diversity. - can point out what is important in the management of small populations. - can describe different conservation measures, especially in situ and ex situ conservation. - can describe current national and international conservation programmes for different livestock breeds. | |||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | Examination: Examination Part 1: Graded written examination (1 hour) on the material covered. Examination Part 2: Graded semester performance completed during the block course. Parts 1 and 2 contribute equally to the final grade. | |||||||||||||||||||||||||||||||||||||||||||||||
| 751-6301-AAL | Animal Breeding Enrolment ONLY for MSc students with a decree declaring this course unit as an additional admission requirement. Any other students (e.g. incoming exchange students, doctoral students) CANNOT enrol for this course unit. | 2 credits | 4R | H. Pausch | ||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Introduction to basics of animal breeding. Importance of animal production. Species of livestock and their products, performance recording, functional traits, genetic diversity, breeding goals. Qualitative and quantitative traits. Basic knowledge of breeding methods: genetic and environmental variation, heritability, genetic correlation, estimation of breeding values, selection, mating systems. | |||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | Show the importance of animal production for Swiss and international agriculture. Name the livestock species, their products, systematic classification and breeding and production goals. Describe methods to measure animal performance (performance recording) and functional traits. Define the most important parameters and methods in animal breeding. | |||||||||||||||||||||||||||||||||||||||||||||||
| Content | Domestication, history of animal breeding. Definition, models of animal production, species of livestock, numbers, distribution. Genetic polymorphisms and their applications in animal breeding. Genetic diversity, breeds, production and breeding goals. Traits: performance, fucntional. Performance recording. herd replacement. Qualitative (monogenic) and quantitative (polygenic) traits, Mendelian genetics, quantitative genetics. Genetic and environmantal variation, heritability, genetic correlation, selection, selection response. | |||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Transparencies and single chapters of textbook are made available on homepage. | |||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Tierzucht (Willam/Simianer) UTB 3526 (2011) Additional literature to be announced in the lecture. | |||||||||||||||||||||||||||||||||||||||||||||||
| Competencies |
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| 751-8003-00L | Genetics in Agricultural Sciences | 2 credits | 2G | H. Pausch, B. Studer | ||||||||||||||||||||||||||||||||||||||||||||
| Abstract | Important concepts from population, quantitative and molecular genetics are introduced and applied to plant and animal populations. | |||||||||||||||||||||||||||||||||||||||||||||||
| Learning objective | After the course, the students will be able to - work with genetic polymorphisms and explain mechanisms underlying allele frequency changes in natural and experimental populations; - determine factors affecting the selection intensity - explain the difference between genotypic and phenotypic values - quantify the expected genetic gain per time unit - explain important molecular methods to determine genetic polymorphisms; - map traits in plant and animal populations using molecular marker information; - integrate different concepts from population, molecular and quantitative genetics and explain their importance for applications in genetics in agricultural sciences. | |||||||||||||||||||||||||||||||||||||||||||||||
| Content | Molecular genetics (15%) - DNA sequence variation - Marker & genotyping techologies (SSRs, AFLPs, SNPs, KASP, GBS, RADseq, AmpSeq, Chip Technologies) Population genetics (30%) - Allele- and genotype frequencies in populations - Hardy-Weinberg equilibrium - Genetic drift, differentiation of populations - Fitness, selection - Inbreeding, relationship, effective population size Quantitative genetics (40%) - Recombination, crossing over, linkage analysis, genetic mapping - QTL mapping - Forms of selection and selection differential - Heritability - Quantification of expected genetic gain - genotypic value, allele substitution effect, breeding value Integrative genetics (15%) - Genome-wide association mapping - Estimation of genomic breeding values | |||||||||||||||||||||||||||||||||||||||||||||||
| Lecture notes | Slides and exercises will be provided in advance of each class via Moodle | |||||||||||||||||||||||||||||||||||||||||||||||
| Literature | Further reading: Falconer & Mackay: Introduction to Quantitative Genetics Lübberstedt & Varshney: Diagnostics in Plant Breeding | |||||||||||||||||||||||||||||||||||||||||||||||
| Prerequisites / Notice | German | |||||||||||||||||||||||||||||||||||||||||||||||
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