SASA10149U Quantitative Genetics, Genomics and Breeding
Volume 2013/2014
Education
MSc Programme in Animal
Science - semi-compulsory
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.
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:
Knowledge:
- 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
Skills:
- 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
Competencies:
- 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
Knowledge:
- 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
Skills:
- 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
Competencies:
- 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
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
- 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
Academic qualifications
SMAF10070U Statistik
dataanalyse 2
SMAF10074U Matematik og modeller
SASA10142U Avl og reproduktionsstyring
SMAF10074U Matematik og modeller
SASA10142U Avl og reproduktionsstyring
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.
Workload
- Category
- Hours
- Colloquia
- 20
- Exam
- 1
- Lectures
- 50
- Practical exercises
- 110
- Preparation
- 100
- Project work
- 131
- Total
- 412
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Exam
- Credit
- 15 ECTS
- Type of assessment
- Oral examination, 40 minutesThe 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.
Weigh: The two parts of the oral examination are weighted equally.
Following are criteria for grading on a 7-point scale.
12: Over 90% correct answers in Oral exam
10: Over 80% correct answers in Oral exam
7: Over 70% correct answers in Oral exam
4: Over 60% are correct answers in Oral exam
02: Over 50% are correct answers in Oral exam
00: Over 30% are correct answers in Oral Exam
-3: Under 30% are correct answers in Oral exam - Aid
- Only certain aids allowed
All aids allowed for preparation. Some aids allowed during examination: project, presentation and own notes
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
More than one internal examiner
Criteria for exam assesment
See learning outcome
Course information
- Language
- English
- Course code
- SASA10149U
- Credit
- 15 ECTS
- Level
- Full Degree Master
- Duration
- 1 block
- Placement
- Block 2
- Schedule
- A And B
- Course capacity
- No limit
- Continuing and further education
- Study board
- Study Board of Biology and Animal Science
Contracting department
- Department of Veterinary Clinical and Animal Sciences
Course responsibles
- Haja Kadarmideen
Saved on the
28-08-2013