SASK16003U  Quantitative Genomics and Breeding

Volume 2017/2018
Education

MSc Programme in Animal Science - Semi-compulsory/Restricted electives

Content

The course content is structured in four modules. Module 1 focuses on quantitative genetics, module 2 focuses on linear models in animal breeding and module 3 focuses on breeding planning. Module 4 is a student project which brings together elements from each of the three first modules. The student project report is an essential part of the basis for the discussion at the final examination.

Quantitative Genetics

In this module the students are introduced to the basic modelling of the inheritance of quantitative traits, i.e. continuous traits which are influenced both by many genes as well as the environment. Both models with single genes and models assuming an infinite number of genes are used. Topics include genetic variation, inbreeding, heterosis, selection, selection response as well as the nature of molecular variation underlying quantitative genetic variation.

Linear Models in Animal Breeding

Selection of animals for genetic improvement is based on estimated breeding values that are derived from statistical models; mostly these are linear models. This module of the course focuses on these models and on how they are used in practical modern animal breeding. Genetic evaluation aims at assigning a breeding value to each animal with the goal of ranking animals and select animals with the best breeding values. Also model validation and comparison of models in terms of accuracy and bias is a part of this module.

Statistical models are used to separate genetic and environmental effects. Models that include information from both relatives and molecular information will be introduced. The course will cover selection index theory, setting up the additive relationship matrix A and its inverse, BLUP, and various models for single and multiple traits. Genomic  BLUPand estimation of variance components. Software that implements these methods will be introduced.

Breeding planning

Important topics in breeding planning are to compare genetic progress with the increase in inbreeding, and to explain and compare risks and consequences of different breeding schemes using simulation tools. Topics to be covered in this module include formulation of breeding goals, modeling and simulation, use of molecular information, reproductive technologies, selection strategies and mating strategies.

Learning Outcome

Knowledge:

Quantitative Genetics

  • Summarize the main principles in models for quantitative genetic variation, including the infinitesimal model and the finite locus model.
  • Explain how shared environments and shared genes contribute to the similarities among relatives.
  • Explain the consequences of selection on quantitative traits, including selection response, changes of variance, correlated response, inbreeding and molecular consequences of selection.

 

Linear Models in Animal Breeding

  • Compare and discuss strengths and weaknesses and of different methods for genetic evaluation.
  • Compare and discuss methods for incorporating DNA information in genetic evaluation.
  • Explain how breeding value estimation is used in the genetic improvement of modern livestock production.

 

Breeding planning

  • Explain the elements required to set up a successful breeding scheme.
  • Compare principles underlying the definition of breeding objectives and methods for their derivation.
  • Explain the effects of reproductive and genomic technologies.
  • Explain methods for maintaining genetic diversity in the presence of selection.
  • Discuss optimization of breeding plans in the presence of genotype-environment interactions and breeding plans utilizing cross breeding.
  • Describe examples of biological consequences of selection.

 

Skills:

The course enables the students analyze and interpret biological problems with concepts and methods from quantitative genetics.

The students should be able to apply software for breeding value estimation to a prepared example, interpret the output from breeding value estimation and undertake optimal choices from a set of breeding candidates.

The student should be able to use deterministic and stochastic methods to evaluate alternative breeding schemes.


Competencies:

After completing the course the students should be able to use tools of quantitative genetics and animal breeding to analyze and solve simple problems arising in animal breeding and other biological disciplines where problems of a quantitative genetic nature arise.

The students should be able to choose among different methods for breeding value prediction, interpret breeding values and make breeding decisions based on predicted breeding values.

Finally the students should be able to design breeding plans for simple situations.

  • Falconer, D.S. & Mackay, T. “Introduction to Quantitative Genetics”, 4th edn., Pearson Education Limited
  • Mrode, R.A. “Linear Models for the Prediction of Animal Breeding Values”, 3rd edn., CABI Publishing
  • Scientific papers
  • Course notes
NMAB14002U Statistical Data Analysis 2
NPLB14001U Genetik
SASA10142U Avl og Reproduktionsstyring
Lectures, theoretical exercises, practical computer exercises, projects and self-study. The first 6 weeks of the course are composed of a mixture of lectures and exercises, while the last two weeks are the project period.

Evaluation Model: Survey based model.
Oral
Collective
Credit
15 ECTS
Type of assessment
Oral examination, 40 minutes
The oral exam (40 minutes) will in equal parts be based on a discussion of the content of the student’s project report and on a randomly selected exam topic.
Exam registration requirements
  • A project report has to be prepared and submitted before the end of the project period.
Aid
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Internal examiner
Criteria for exam assesment

To achieve the maximum grade of 12, the student shall be abel to demonstrate the following in:

Knowledge:

Quantitative Genetics

  • Summarize the main principles in models for quantitative genetic variation, including the infinitesimal model and the finite locus model.
  • Explain how shared environments and shared genes contribute to the similarities among relatives.
  • Explain the consequences of selection on quantitative traits, including selection response, changes of variance, correlated response, inbreeding and molecular consequences of selection.

 

Linear models

  • Compare and discuss strengths and weaknesses and of various methods for genetic evaluation.
  • Compare and discuss methods for incorporating DNA information in genetic evaluation.
  • Explain how breeding value estimation is used in the genetic improvement of modern livestock production.

 

 Breeding planning

  • Explain the elements required to set up a successful breeding scheme.
  • Compare principles underlying the definition of breeding objectives and methods for their derivation.
  • Explain the effects of reproductive and genomic technologies.
  • Explain methods for maintaining genetic diversity in the presence of selection.
  • Discuss optimization of breeding plans in the presence of genotype-environment interactions and breeding plans utilizing cross breeding.
  • Describe examples of biological consequences of selection.

 

Skills:

The course enables the students analyze and interpret biological problems with concepts and methods from quantitative genetics.

The students should be able to apply software for breeding value estimation to a prepared example, interpret the output from breeding value estimation and undertake optimal choices from a set of breeding candidates.

The student should be able to use deterministic and stochastic methods to evaluate alternative breeding schemes.

Competencies:

After completing the course the students should be able to use tools of quantitative genetics and animal breeding to analyze and solve simple problems arising in animal breeding and other biological disciplines where problems of a quantitative genetic nature arise.

The students should be able to explain the merit of different methods for breeding value prediction, interpret breeding values and make breeding decisions based on predicted breeding values.

Finally the students should be able to design breeding plans for simple situations.

  • Category
  • Hours
  • Lectures
  • 56
  • Practical exercises
  • 48
  • Preparation
  • 188
  • Exam
  • 1
  • Colloquia
  • 8
  • Project work
  • 111
  • Total
  • 412