Plant Genomics

Course content

This course is an advanced course in theoretical and applied genomics with a focus on plant technology and examples.

The key techniques used in molecular genetics and tools for analyzing data, from genomics to  phenotyping, will be presented and examples both from model and crop plants are included. Together with these techniques the basis for the development of markers and how markers are used in molecular breeding is central.  For an introduction a crash course in bioinformatics is included. The course will give information and give the students tools to describe and characterize genomes.

Following topics are covered:


Crash course, Bioinformatics and Crash course, Molecular genetics
Genomes: Model plants versus crops
Next-generation sequencing technologies
Gene expression
Transcription factors, focus on MYB family
Forward and reverse genetics
Genetic markers and Quantitative Trait Loci
Genotype – Phenotype

Map based cloning and QTL dissection
Functional Genomics
Metabolomics
Biomarkers and RNAi/siRNA

Genome engineering


There will be student workshop on four functional genomics assignments and the findings of the case study will be debated.


In practical exercises complementing the lectures, you will get familiar with some of the tools used, e.g. tracking of gene expression, both quantitatively as well as in plant tissue, analysis of quantitative trait loci, and genetic manipulation techniques.

Education

BSc Programme in Biology-Biotechnology
BSc Programme in Biology

Learning outcome

After successful completion of the course, the students will have gained:

Knowledge
- Describe basic principles for the study of major model plants and general plant evolution
- Identify and describe the key techniques used for molecular genetics and selected tools used to analyse genomic information, including map based cloning and QTLs.
- Explain genetic markers and their use for qualitative and quantitative traits
- Compare basic central experimental techniques used in plant genomics and molecular breeding and propose their application for novel challenges

Skills
- Complete with confidence an assessment of the techniques used to study complex biological processes in plant model systems
- Apply common bioinformatic tools to screen databases of model plant species and use genome browsers to analyse simple problems
- Practice molecular and genetic tools for plant improvement through molecular breeding of crops for food, fodder and production of high value crops for e.g. biomedicine, biofuel and green factories
- Conduct a simple transformation procedure

Competences
- Evaluate various forward and reverse genomics approaches for gene isolation and functional studies
- Relate gene differences with phenotype by means of genomics
- Explain advantages or disadvantages of model plants versus crops
- Communicate effectively with other students in a debate to justify conclusions on a given problem

Teaching includes a mix of lectures, laboratory and computer exercises complemented by cases for student groups. Laboratory work demonstrates selected key issues in plant genomics. Computer exercises demonstrate the potential of internet resources. Students are expected to work in groups for their exercises and the cases, and written and oral presentations of the results are a requirement for admission to the final exam.

Laboratory manuals and a dedicated Plant Genomics Compendium, consisting of all relevant chapters and papers discussed in class will be distributed in electronic form. Next to the compendium, no specific textbook will be required for this course. However, general botany and genetics textbooks may be consulted for the most basic concepts not covered within this course. The student should on his or her own initiative locate additional reading material that matches lecture material.

Further information will be available on Absalon.

Course in Molecular Genetics is recommended

ECTS
7,5 ECTS
Type of assessment
Oral examination
Oral examination (presentation and questions):
The students receive the assignment at 9.00 and submit an individual, short PowerPoint presentation at 12.00 the next day. The exact date is given in the beginning of the course. At the oral exam the student present the results of the assignment (5 min) followed by a short discussion of the course curriculum (15 min).
Aid
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
One internal examinator
Criteria for exam assessment

See learning outcome.

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 40
  • Theory exercises
  • 20
  • Practical exercises
  • 45
  • Exam
  • 4
  • Preparation
  • 97
  • English
  • 206