GEN-30306 Genetic Analysis Trends and Concepts

Course

Credits 6.00

Teaching methodContact hours
Lecture12
Tutorial17
Practical77
Course coordinator(s)dr. ir. AJM Debets
Lecturer(s)prof. dr. JAGM de Visser
dr. ir. TG Wijnker
dr. ir. E Bastiaans
dr. ir. AJM Debets
Examiner(s)dr. ir. AJM Debets

Language of instruction:

English

Assumed knowledge on:

GEN-11806 Fundamentals of Genetics and Molecular Biology, GEN-21306 Introduction to Genetic Analysis or BIC-20306 Cell physiology and Genetics

Continuation courses:

GEN-30806 Population and Quantitative Genetics

Contents:

Note: This course can not be combined in an individual programme with PBR-31803 Genetics.

This advanced course explains the most important genetic concepts to unravel and understand complex biological phenomena. We in detail explain the genetic processes underlying variation and its inheritance and their relevance with respect to evolution. We center our course around three main themes: Mutation, recombination and (epi-)genetic transmission. All three themes are both cause and consequence of evolution.
We expect students to gain a thorough understanding of the concept of a separation between soma and germline and its genetic and evolutionary consequences: Cells in the soma differentiate and change phenotypically because of epigenetic but also genetic processes like for example polyploidization, mitotic recombination and cytoplasmic segregation. Similar processes affect the germline through meiotic recombination, mutation, segregation, ploidy changes and epigenetics. We expect students to integrate this knowledge into a larger understanding of how such mechanisms affect selection (that act on the soma as well as on gametes) and trade-offs in reproduction strategies. Mutations that favor the germline might adversely affect the soma and vice versa. Antagonistic pleiotropy, mutation accumulation are important concepts in this respect.
We illustrate these fundamental concepts in a series of both classical and state-of-the-art experiments, using a wide variety of model- (and well-studied) organisms like Arabidopsis, Aspergillus, Drosophila, Human and E. coli. In addition we discuss a number of classical research papers (like Mendels' original paper) and current research highlights in contemporary reviews (on topics like mutation, recombination and genetic transmission).

Learning outcomes:

After successful completion of this course students are expected to be able to:
- explain the consequences of the soma-germline differentiation;
- calculate the mutation rate, explain how it can be induced, and can evolve;
- calculate the recombination rate, and explain how it can evolve;
- do linkage mapping of genes and centromeres, by meiotic recombination (including tetrad analysis) and mitotic recombination;
- use and explain genetic- and epigenetic concepts like: polyteny, X-chromosome inactivation, (endo-)polyploidy, aneuploidy;
- use and explain evolutionary-genetics concepts like: mutation accumulation, antagonistic pleiotropy, experimental evolution, epistasis, QTLs, complementation, genetic parasites;
- explain why each individual is a mutant and a recombinant.

Activities:

- lectures for theoretical background and introduction to the experiments;
- literature reading and discussion for further theoretical background;
- students will carry out many lab-experiments on (evolutionary) genetic analysis of microorganisms (bacteria and fungi), insects, plants and human buccal cells;
- at the end of each experiment students hand in a provisional report (generally less than 1 page) in which the main results are described and explained.
- each student prepares and discusses one final report of an experiment based on the combined data of all groups (from the provisional reports).

Examination:

- active participation/laboratory performance/reporting (10%);
- literature/experiment discussion (10%);
- written closed book test with open questions (80%).

Literature:

The theoretical background and a general overview of the background of the course is given in several chapters of the textbook of Griffiths (AJF Griffiths et al. An Introduction to Genetic Analysis, Freeman & Co, 11th ed.).
A specification of the theoretical and practical information is given in the guidelines of the course, which include references to the textbook, further readings, exercises and relevant websites. All lectures and lab class instructions include PowerPoint presentations, which are essential parts of the study material. These materials are uploaded on the MyPortal site of the course.
The literature (current reviews and seminal papers) to be discussed is included in the manual.

ProgrammePhaseSpecializationPeriod
Compulsory for: BBIBiologyBScA: Cell and Molecular Biology6WD
BPWPlant SciencesBScA: Plant Genomics and Health1AF, 6WD
Restricted Optional for: MBIBiologyMScB: Organismal Adaptation and Development1AF, 6WD
MBIBiologyMScA: Cell and Molecular Biology1AF, 6WD
MBTBiotechnologyMScA: Cellular/Molecular Biotechnology6WD
MMLMolecular Life SciencesMScA: Biomedical Research6WD
MMLMolecular Life SciencesMScB: Biological Chemistry6WD
MPSPlant SciencesMScD: Plant Breeding and Genetic Resources1AF, 6WD
MPBPlant BiotechnologyMScC: Molecular Plant Breeding and Pathology1AF, 6WD
MinorPeriod
Compulsory for: WUPBRBSc Minor Plant Breeding6WD
Restricted Optional for: WUPBTBSc Minor Plant Biotechnology1AF