NPLB13001U Plant Genomics
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.
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.
- Category
- Hours
- Exam
- 4
- Lectures
- 40
- Practical exercises
- 45
- Preparation
- 97
- Theory exercises
- 20
- Total
- 206
As
an exchange, guest and credit student - click here!
Continuing Education - click here!
- Credit
- 7,5 ECTS
- Type of assessment
- Oral examinationOral exam (presentation, questions):
The students receive an assignment at 9.00 and submit individually a short PowerPoint presentation at noon the next day; the precise day will be announced at the start of the course.
At the oral exam, the students will present the findings of their assignment (5 minutes) followed by a brief discussion (15 minutes) in context of the curriculum. - Exam registration requirements
- Three passed lab reports (75 %) and participation in the oral presentation of case are a requirement
- Aid
- All aids allowed
- 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
See learning outcome
Course information
- Language
- English
- Course code
- NPLB13001U
- Credit
- 7,5 ECTS
- Level
- Bachelor
- Duration
- 1 block
- Placement
- Block 4
- Schedule
- B (Mon 8-12 + Tues 13-17 + Fri 8-12)
- Course capacity
- No limitations
- Continuing and further education
- Study board
- Study Board of Natural Resources and Environment
Contracting department
- Department of Plant and Environmental Sciences
Course responsibles
- Björn Robert Hamberger (7-656d726875716b43736f6871316e7831676e)
- Søren Kjærsgaard Rasmussen (3-837b8250807c757e3e7b853e747b)