SASK16003U Quantitative Genomics and Breeding

Volume 2016/2017
Education

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

Content

The goal of this course is to teach advanced topics and practical skills in quantitative genetics, population genetics, estimation of genetic (breeding) values and population genetic parameters using BLUP/REML methods, genomic prediction (GP), genomic selection (GS) and Genome-wide Association Studies (GWAS) using high-density single nucleotide polymorphisms (SNP) marker panels.  These topics are essential and core component of veterinary and animal sciences. Research, innovation and development in modern agricultural, biological-biotechnological, health and medical sciences are virtually impossible without quantitative- or statistical- or computational- genomics methods. While the course is targeting veterinary and animal science MSc students, it is also highly relevant for PhD students specializing in this area. Due to the nature of the course, it is suitable for students specializing in bio-statistics and biology-biotechnology, study programs. The course 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, genomics biotechnology and genomic science, bio-statistical, and bio-medical industries. Initially, the quantitative- and population genetics theory will be introduced including mutation, migration, selection, linkage (dis)equilibrium, inbreeding, genetic values, and response to selection. Principles of estimation of heritability and prediction of breeding values of animals from various information sources such as phenotypic information, pedigree, herd and management information and SNPs will be covered. Advanced methods in Quantitative Trait Loci (QTL) analysis, GWAS, single- and multiple-trait breeding value estimation, total merit selection index, genomic breeding value estimation, genomic selection, integrative systems genetics and experimental genomics will be introduced with some hands-on experience. Course may involve excursions to cattle and pig industries and breeding / genomic companies. Students will be trained in animal breeding, statistical- and computational genetics and bioinformatics software to do 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 research problem sets to gain working experience in this field.

Learning Outcome

Knowledge:


- have a comprehensive understanding of the quantitative- and population genetics theory and practical applications, genetic diversity, animal breeding theory, estimation of breeding values, selection index, heritability and other genetic parameters, gene mapping, GWAS, genomic prediction or genomic selection and designing breeding plans.

- have a basic understanding of integrative systems genetics  and experimental genomics approaches involved in detecting genes and biomarkers with large (causal and regulatory) effects on complex diseases and various traits of economic importance

 

Skills:


- be able to work in animal breeding and genomics/genetics industries and programs (including farm, companion and wild animals)

- be able to use advanced statistical / BLUP methods in estimating breeding values and genetic parameters in animal populations

- be able to conduct GWAS using genomic, phenotypic and pedigree datasets in animals and human

- be able to use and apply various methods to predict genomic breeding values and conduct genomic selection in animals

 - be able to write own computer programs or use readily available software packages to perform relevant analyses above

- be able to design systems genomics experiments, analyze data and interpret results related to gene and biomarker discovery for complex diseases and traits in animals and other species


Competencies:


- be able to transfer knowledge and skills gained during the course  to solve new issues or challenges posed by the research and innovation community including animal breeding, quantitative genomics, systems genetics and genomics experiments and be able publish results
- be able to design/contribute to genetic/genomic evaluation of farm animals and to breeding program designs, gene and biomarker discovery experiments in animals, humans and other organisms

- be able to specify relevant research problems in animal breeding and  genomics and analyze them

- be able to critically discuss research results and compare with literature findings

- Own course compendium from the group of Animal Breeding, Quantitative Genetics and Systems Biology

- Falconer D.S. & Mackay T.F.C. (1996) Introduction to quantitative genetics, 4th ed, Longman, England.

- R.A. Mrode. (2014). Linear models for the Prediction of Animal Breeding Values, 3rd ed, CABI Publishing.

- Various handouts (e.g. notes on genomic-wide association tests, genomic selection, bioinformatics and systems genetics analyses) and scientific journal papers

None
NMAB14002U Statistical Data Analysis 2
NPLB14001U Genetik
Lectures, theoretical exercises, practical computer exercises, mini-project, journal club, excursions and self study.
  • Category
  • Hours
  • Colloquia
  • 20
  • Exam
  • 1
  • Lectures
  • 50
  • Practical exercises
  • 110
  • Preparation
  • 100
  • Project work
  • 131
  • Total
  • 412
Credit
15 ECTS
Type of assessment
Oral examination, 40 minutes
The oral examination is at the end of the course, consists of two parts (equal weights) and can last up to 40 minutes. Students must have i) completed some selected exercises during the course and ii) either presented a chosen journal paper or have done a mini-project to quality for the final exam. The possible journal papers or mini project are known to the students well in advance.

In the oral exam, firstly, students will be asked questions on any one of the topics covered during the entire course (random draw). Secondly, students will be asked questions from theoretical or computer exercises or a journal paper presented during the course or a mini project they have done during the course. Students get 45 minutes to prepare the oral exam
Exam registration requirements
  • Must have passed selected assignments and computer exercises during the course
  • Must have presented a specific journal paper or done a mini-project
Aid
Only certain aids allowed

All aids allowed for preparation
Some aid allowed during examination:
- Project, journal papers, presentation and own notes

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:

Knowlegde: Student demonstrates comprehensive understanding of the quantitative- and population genetics theory, estimation of single- and multi-trait breeding values of animals, principles of selection index theory, concepts of heritability, principles of gene mapping/GWAS, key concepts of genomic prediction or genomic selection and designing breeding plans, and show a basic understanding of integrative or systems genomics

Skills: Student demonstrates skills to be able to work in animal breeding and genomics/genetics industries including ability to use advanced statistical / BLUP methods in estimating breeding values and genetic parameters in animal populations. Skills in GWAS and predicting genomic breeding values and conducting genomic selection in animals, skills in writing own computer programs or use readily available software packages

Competencies: Student demonstartes competenacies to be able to transfer knowledge and skills gained during the course to solve new issues or challenges posed by animal breeding, quantitative genomics and systems genetics. dmomonstrate to be able to design/contribute to genetic/genomic evaluation of farm animals and to breeding program designs.

 

For the first part of the oral exam, students should be able to answer questions regarding key concepts (both theoretical and experimental aspects of the entire course) and demonstrate good knowledge and understanding of the learned subject areas.

For the second part of the oral exam, students, via their oral presentation, should demonstrate thorough understanding of the specific topic or a mini-project presented and be able to answer questions regarding the specific topic or mini-project.