Course: Molecular Methods in Plant Science

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Course title Molecular Methods in Plant Science
Course code KBO/309
Organizational form of instruction Lecture + Lesson
Level of course Master
Year of study not specified
Frequency of the course In each academic year, in the winter semester.
Semester Winter
Number of ECTS credits 5
Language of instruction Czech
Status of course Compulsory, Compulsory-optional
Form of instruction Face-to-face
Work placements This is not an internship
Recommended optional programme components None
Course availability The course is available to visiting students
Lecturer(s)
  • Koutecký Petr, Mgr. Ph.D.
  • Košnar Jiří, Mgr. Ph.D.
Course content
Lectures: Presentation of methods of molecular biology used to infer genetic variation of plants, especially at lower taxonomic levels (genus, species, populations); the main research objectives include population genetics, microevolutionary processes, phylogeography. For each method, we will illustrate (where appropriate): (i) technical background (technical principles, raw data structure), (ii) basics of the data analysis, (iii) applications in botany, (iv) examples of published studies. Methods included: 1. Sampling of the plant material (sampling strategy concerning the expected variation, mode of reproduction, etc.; preservation of the material before analyses), 2. Whole genome analysis, karyological methods (flow cytometry, FISH, GISH). 3. Allozymes; 4. DNA extraction from plant tissues, 5. PCR, optimisation; 6. Electrophoresis; 7. Multilocus fingerprinting (PCR-RFLP, AFLP, ISSR, T-RFLP, etc.), 8. Microsatellites (SSR), 9. Direct (Sanger) DNA sequencing, 10. Cloning, 11. Next-generation-sequncing and its application (RADseq, Hyb-seq, sequence capture, etc.). Practical part: Use of selected methods in the laboratory (flow cytometry, DNA isolation, electrophoresis, PCR and PCR-based methods, PCR-RFLP, cloning, preparing samples for sequencing and fragment analysis); if possible, own material of the students will be analysed.

Learning activities and teaching methods
Monologic (reading, lecture, briefing), Laboratory, E-learning, Case studies
  • Class attendance - 72 hours per semester
  • Preparation for exam - 30 hours per semester
  • Preparation for credit - 30 hours per semester
Learning outcomes
Presentation of methods of molecular biology used to infer genetic variation of plants, especially at lower taxonomic levels (genus, species, populations); the main research objectives include population genetics, microevolutionary processes, phylogeography. The methods already available (or planned in future) in the laboratory of the Department of Botany will be presented more in detail. In opposite, methodology of phylogeny reconstruction at higher taxonomic levels as well as methods used to study intra-cellular processes will be mentioned only briefly since other more specialized courses focussed on them are available at the faculty.
Understanding the principles of the most often used methods of molecular biology and their use in botany. Basics of work in a molecular biology laboratory.
Prerequisites
This is an introductory course to the topics of molecular methods, no specific knowledge exceeding the basic courses of the first year at Faculty of Sciences is required; basic understanding of scientific texts in English is necessary. However, especially for understanding the published papers used as examples of application of the methods, it is advisable for students to know the basics of statistical analysis of biological data (Biostatistics or similar subjects) and basics of genetics and related subjects.

Assessment methods and criteria
Combined exam, Development of laboratory protocols

Exam: understanding basics of the methods (ability to explain the technical principle), understanding basics of data analysis and use of the methods in botany (for which research questions the particular method is/is not suitable and why). Practical part: attendance at the practical part (at least 75%), completing laboratory protocols.
Recommended literature
  • Avise J. C. Molecular Markers, Natural History, and Evolution, ed. 2. Sinnauer Kluwer Academic Publishers, 2004.
  • Avise J. C. Phylogeography: the history and formation of species. Hardvard University Press, 2000.
  • Halliburton R. Introduction to population genetics. Pearson Prentice Hall, 2004.
  • Weising K. et al. DNA fingerprinting in plants: principles, methods, and applications. Taylor & Francis, 2005.
  • Zima J., et al. Genetické metody v zoologii. PřF UK, Praha, 2004.


Study plans that include the course
Faculty Study plan (Version) Category of Branch/Specialization Recommended year of study Recommended semester
Faculty: Faculty of Science Study plan (Version): Botany (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter
Faculty: Faculty of Science Study plan (Version): Botany (1) Category: Biology courses - Recommended year of study:-, Recommended semester: Winter