260045 Quantitative Genetics, Genomics and Breeding

Responsible DepartmentDepartment of Basic Animal and Veterinary Sciences

Earliest Possible YearMSc. 1 year
DurationOne block
Credits15 (ECTS)
Level of CourseMSc
ExaminationFinal Examination

oral examination

Some Aid allowed
All aids allowed for preparation. Some aids allowed during examination: - Project, presentation and own notes

Description of Examination: The oral examination is at the end of the course and consists of two parts. Firstly, students will be asked questions on one of the problem sets (random draw). Secondly, students draw a specific topic to present followed by discussion. The possible topics for part 2 are known to the students in advance. The oral examination can last up to 40 minutes (total for both parts). Students get 45 minutes to prepare the oral exam

Weight: The two parts of the oral examination are weighted equally.

7-point scale, internal examiner
Organisation of TeachingLectures, theoretical exercises, practical computer exercises, journal club and self study
Block PlacementBlock 2
Week Structure: A

Block 2
Week Structure: B
Language of InstructionEnglish
Optional Prerequisites210006 Statistical Data Analysis 2
210012 Mathematics and Models
260038 Breeding and Reproduction
Course Content
The goal of this course is to teach advanced topics and engage students in practical aspects of quantitative genetics, genome analyses and animal breeding. While the course is targeting Animal Science MSc students, it is also relevant for MSc and PhD students specializing in human and plant genetics as well as biotechnology and bioinformatics. It is expected to provide a strong foundation for students to either pursue PhD degrees and/or to provide essential qualifications and skills that are highly demanded in the animal breeding industry as well as in the agri-biotech, bio-statistical and bio-medical industries. Initially, the quantitative genetic theory will be introduced for single and multiple loci including mutation, migration, selection, linkage equilibrium, genetic parameters, and response to selection. Different inheritance modes, such as additive, dominance and epistasis are also considered. Principles of estimation of heritability and prediction of breeding values of animals from various information sources such as phenotypic information, pedigree and molecular genetic markers will be covered extensively. Genetic markers include both single markers such as microsatellites and genome-wide markers such as single nucleotide polymorphisms (ie. SNPs). The key issues in designing a breeding program and the basic theory for definition of breeding goals are presented. This includes different selection and mating strategies. Methods for investigating genetic consequences of different breeding strategies and methods for balancing genetic gain and inbreeding will be covered. Basic principles of linkage mapping, Quantitative Trait Loci (QTL) analysis and candidate gene analyses will be covered. Genome-wide association studies (GWAS) using SNP genetic markers will be introduced, with some hands-on experience using livestock and/or companion animal genome datasets. Principles of genomic breeding values and genomic selection will be introduced. Basic principles of microarray transcriptomic data and other -omic data analyses to discover causal and regulatory genes and biomarkers for common diseases and traits will be covered, with example experimental datasets. Concepts of integrated systems-genetics approaches will be covered. Students will be introduced to some statistical genetics and bioinformatic software to do these genome analyses. Current hot topics will be discussed in journal clubs, where also classical keynote publications are treated. Students will use one or more of the presented methodologies to analyze three to four research problem sets to gain working experience in this field.
Teaching and learning Methods
Lectures, theoretical exercises, practical computer exercises, genomic data analysis, self study, journal club and project work. In connection with journal club, lectures and exercises, the students are expected to participate actively in mutual discussions. The lectures will be supported by both theoretical and hands-on computer exercises such as real genomic datasets, different simulation methods, analysis software etc. The students are expected to analyse and draw conclusions from simple examples and later more realistic animal data sets. In connection with journal clubs each student is expected to present and chair the discussion of a selected scientific paper.
Learning Outcome
After completing the course students should be able to participate in designing breeding plans, infer breeding values and predict the expected genetic progress of a given breeding scheme. Students should also have some basic knowledge and skills to perform genomic analyses using large volumes of multiple data types in animals, humans and plants. More specifically, they should:

- have a comprehensive understanding of the animal breeding theory which forms the basis for inferring breeding values with or without DNA markers and designing breeding plans.
- have a basic understanding of statistical genetic and bioinformatics approaches involved in detecting genes and biomarkers with large (causal and regulatory) effects on complex diseases and various traits

- be able to estimate economic values of different traits and propose a sustainable breeding goal
- be able to apply methods to predict breeding values and estimate effects of genetic markers
- be able to predict expected genetic response and inbreeding level using deterministic and stochastic simulation
- be able to write own computer programs or use readily available software packages to perform relevant analyses
- be able to design high throughput genomic and transcriptomic experiments, analyse data and interpret results related to gene and biomarker discovery for complex diseases and traits in animals and other species

- be able to critically evaluate designs and methods used in animal breeding and published results
- design and manage all aspects of a breeding scheme for a given breed and animal species
- be able to design/contribute to gene and biomarker discovery experiments in animals, humans and other organisms
- be able to specify relevant research problems in animal genomics and analyze them
- be able to critically discuss research results and compare with literature findings
Course Literature
- Falconer D.S. & Mackay T.F.C. (1996) Introduction to quantitative genetics, 4th ed, Longman, England.
- R.A. Mrode. (2005). Linear models for the prediction of animal breeding values, 2nd ed, CABI Publishing.
- Various handouts (e.g. notes on genomic-wide association tests, genomic selection, gene expression data and systems genetics analyses) and scientific papers
Course Coordinator
Haja Kadarmideen, hajak@life.ku.dk, Department of Basic Animal and Veterinary Sciences/Genetics & Bioinformatics, Phone: 353-33577
Study Board
Study Committee V
Work Load
project work131