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300319 UE Plant Chromosome Structure and Evolution: theory and practice (2019W)

Chromosome analysis in flowering plants

5.00 ECTS (3.00 SWS), SPL 30 - Biologie
Continuous assessment of course work



max. 8 participants
Language: English


Classes (iCal) - next class is marked with N

VB: 01.10.2019 at 11:00; first lecture (in total 4 lectures): 08.10.2019 11:00.
Practical course will be blocked in December: 02-06.12.2019
Due to the fact that the practical work will be done in in the cytogenetic laboratory (work in pairs, each group has own set of species to analyze) the number of participating students is limited to 8 per course.

Tuesday 01.10. 11:00 - 12:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 08.10. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 15.10. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 22.10. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 29.10. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 05.11. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 12.11. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG
Tuesday 19.11. 11:00 - 13:00 Übungsraum 3 (Fakultätszentrum für Biodiversität) Rennweg 1.OG


Aims, contents and method of the course

The purpose of the course is two-fold. First, it offers an overview of plant cytogenetic techniques: from traditional chromosome counting to more recently established techniques of chromosome painting (in situ hybridization) and immunocytochemistry. Second, it presents detailed and up-to-date information about plant chromosome structure (centromere, telomere etc.) and main types of DNA sequences used for cytogenetic analyses. The newest methods developed recently to analyse genome composition and to characterize different types of repetitive DNA is plant genomes (high-throughput sequencing) will also be introduced. The course introduces also types and consequences of chromosome rearrangements including polyploidy, in the context of chromosome evolution. The use of cytogenetic data (obtained from both classical and molecular cytogenetic studies) in inferring plant taxa relationships and in evolutionary studies of different plant groups will be discussed. The course will give the up-to-date overview of the state-of-art in the analyses of plant chromosomes.
The practical part of the course will include chromosome preparation in selected groups of plants, as well as classical and molecular chromosome staining methods. The students learn to perform DNA:DNA in-situ hybridization (FISH), in particular to prepare and label some of the DNA probes (e.g., species-specific repetitive DNA, rDNAs, telomeric sequences), to detect of the hybridization sites (fluorescence) and to analyse the obtained data. The students will acquire practical skills in chromosome handling and learn to analyse and interpret chromosomal data in evolutionary context.

Assessment and permitted materials

Written exam - theory from course material before practical starts 30% (15 points max)
Active participation in experiment planning and results analyses 40% (20 points max)
Written report summarizing results (in form of scientific manuscript) 30% (15 points max)

Min 50% for positive grade

50-46 points - 1
45-39 points - 2
38-31 points - 3
30-25 points - 4
24.75 and below - 5 (below 50%)

Minimum requirements and assessment criteria

- To present and discuss in details the structure, types and function of chromosomes, and to emphasize their role in evolutionary processes.
- To present most relevant case studies.
- To introduce most important cytogenetic and genomic techniques, including state of the art next generation sequencing, and to discuss their application for evolutionary cytogenetics of plants.
- To introduce modern techniques used nowadays to study the structure and function of plant genomes and to emphasize the importance of such analyses as complementary approach for phylogenetic, evolutionary, or populational studies.
- To introduce methods for in situ-hybridization probe preparation and labelling, chromosome preparation and quality checks, and finally in situ hybridization (FISH).
Students will apply gathered knowledge to analyze and to interpret obtained results (light and fluorescent microscopy).

Examination topics

- Lectures
- Planning of the experiments; material pre-treatment and fixation; preparation of chromosome spreads using classical methods; documentation.
- Enzymatic chromosome preparations; DNA probe preparation and labelling (PCR labelling, nick translation); preparation of buffers and solutions for FISH.
- Checking of the quality of DNA probe labelling; FISH (fluorescent in situ hybridization); pretreatments, and hybridization.
- FISH: washing, detection and amplification.
- Analysis of FISH data (microscopy)

Reading list

Maluszynska J. (ed.) 1998. Plant cytogenetics. Silesian University, Katowice, Poland.
Fukui K., and Nakamya S. (1996). Plant chromosomes. Laboratory methods. CRC Press, Boca Raton.
Weiss-Schneeweiss H., and Schneeweiss G.M. 2012. Karyotype Evolution in Angiosperms. Springer
Levin D. A. (2002) The role of chromosomal change in plant evolution. Oxford University Press, New York, USA.
Puertas M.J. & Naranjo T. (eds.) 2005. Plant cytogenetics. Karger, Basel.
Schwarzacher T., and Heslop-Harrison P. (2000) Practical in situ hybridization. 2nd ed. BIOS, Oxford UK.
Singh R.J. (2003) Plant cytogenetics. CRC Press, Boca Raton.
Stebbins G. L. (1971) Chromosomal evolution in higher plants. Edward Arnold, London.
Puertas M.J. & Naranjo T. (eds.) 2008. Plant cytogenetics. Karger, Basel.
Birchler J. & Pires C. (eds) 2010. Advances in Plant Cytogenetics. Karger, Basel.
Plant Genome Diversity (book; 2 volumes; 2012 and 2013; Springer)

Association in the course directory


Last modified: Mo 07.09.2020 15:22