NPLB13001U  Plant Genomics

Volume 2013/2014
Education
BSc Programme in Natural Sciences & IT
MSc Programme in Agriculture
Content
The Big Picture: Introduction and Overview
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
From microarrays to next-generation sequencing (RNA-seq)
Forward and reverse genetics
Genetic markers and Quantitative Trait Loci
Genotype – Phenotype; Map based cloning and QTL dissection
Two very different plant genomics models: rice and moss
Functional Genomics
Metabolomics
Biomarkers and RNAi/siRNA*
Student workshop on four functional genomics assignments
Functional genomics debate on the findings of the case study

Those contents marked with an asterisk will be offered as shared sessions between the Plant and Mammalian Genomics courses.

In four practical exercises complementing the lectures, you will get familiar with the generation of haploid plant cell cultures, tracking of gene expression, both quantitatively as well as in plant tissue, analysis of quantitative trait loci, and genetic manipulation techniques.
Learning Outcome
This intense course is an advanced course in theoretical and applied genomics with a focus on, but not limited to plant technology and examples. Upon completion, the student will be able to apply common bioinformatic tools to screen databases of model plant species and use genome browsers to analyse simple problems. The student should identify and describe the key techniques used for molecular genetics and selected tools used to analyse genomic information, including map based cloning and QTLs. The student will have sufficient knowledge of the relationship between phenotypic traits and genotypic variation to use the most recent information and resources on plant genomes to independently solve basic assignments. Thorough understanding of the concepts of forward and reverse genetics should be demonstrated by the student through the evaluation of examples given for both strategies. The students will be able to explain typical features and advantages or disadvantages of model plants versus crops. The student should understand the concept underlying next-generation-sequencing and the possibilities for their application. The students will become familiar with basic cell culture techniques through preparation of haploid cell cultures, and assessment of basic related statistics in the first lab exercise. The student will be able to define modes of regulation of gene expression and illustrate the concept by interpretation of transcript accumulation in the second lab exercise. Throughout a dedicated computer exercise, the students will define QTLs, describe their use in molecular breeding and demonstrate statistical distribution. The students will carry out genetic transformation of moss to apply the learned concepts and techniques and use the generated cell lines to evaluate different approaches used. Finally, through discussion in a group and application of the learned concepts, the student should analyse a novel problem based on functional genomics, develop a solution for the given challenge and justify their findings in a debate with the other groups. Passing the laboratory exercises requires completing written reports evaluating the outcomes of the experimental part.

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
- 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
- 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
- Manipulate cell cultures and 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
- Communicate effectively with other students in a debate to justify conclusions on a given problem

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.

Course in Molecular Genetics is recommended
50 % are covered by lectures and discussion classes, 50 % for practical exercises, reports and supervised case studies (student workshop). 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.
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.
Credit
7,5 ECTS
Type of assessment
Written assignment, 27 hours
Written take-home assignment
Duration 27 hours (Assignment issued at 9.00 and submitted at 12.00 the next day)
Exam registration requirements
Three passed lab reports (75 %) and participation in the oral presentation of case are a requirement
Aid
All aids allowed
Discussion with other students participating in the course allowed, but the assignment is not group work and individual reports have to be submitted.
Marking scale
7-point grading scale
Censorship form
No external censorship
Several internal examiners (internal examiner, who does NOT lecture on the course, plus the two course responsibles)
Re-exam
If 10 or fewer register for the reexamination the examination form will be oral.
Criteria for exam assesment
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  • Category
  • Hours
  • Lectures
  • 40
  • Theory exercises
  • 20
  • Practical exercises
  • 45
  • Exam
  • 4
  • Preparation
  • 97
  • Total
  • 206