Syllabus
1. molecular markers - characteristics of molecular data, an overview of techniques, differences among marker types2. molecular markers - the use of markers for various applications and problem solutions3. isozymes - electrophoresis, enzyme types, methods of evaluations of isozyme gels, codominant data and their evaluation, basics of population genetics, genetic diversity, population variability and structure, F statistics, use of isozymes in systematics, relationships between plant traits and isozyme diversity4. DNA, dominant markers (RAPD, ISSRs, AFLP) - genetic information, genome structure, approaches to study of DNA, PCR principle, RAPD, ISSRs, AFLP - principles, (diss)advantages, evaluation of dominant marker data, use in determining of clonal structure, genetic variability distribution, phylogenetics of closely related species, population studies, statistical techniques and software overview for evaluation of variability and detection of the structure in the data5. restriction techniques (RFLP, PCR-RFLP), chloroplast DNA - principle and use of restriction endonucleases, RFLP (Southern blotting), PCR-RFLP (use of universal primers for study of variable genome regions), specificity of cpDNA (non-recombinant, haploid, uniparental inheritance, conservative) and its use in hybridisation and seed dispersal studies, pollen/seed ratio in total gene flow, phylogeography - postglacial migrations6. microsatellites - types and variability of simple sequence repeats, nuclear and chloroplast microsatellites, isolation of microsatellite regions and primer design, evaluation of the data (codominance, high variability), mutational models, specific statistics and software, parentage analysis, population and systematics studies7. classical sequencing - the principle of dideoxy sequencing, use of automated sequencer, sequencing of chloroplast DNA (rbcL, trnL-F, non-coding regions), DNA evolutionary models, tree-building approaches molecular clocks, saturation, gene banks8. sequencing 2 - sequencing of nuclear DNA (ITS, rDNA genes, low-copy genes), advantage and use of different genes and intergenic regions9. next-generation sequencing (NGS) - overview and principle of the basic technologies, approaches, data evaluation, application overview10. Hyb-Seq and phylogenomics - principle of the methods, application examples, phylogenomic data evaluations, gene tree vs. species tree11. RADseq and population genomics - different RADseq modifications (original RAD, 2bRAD, GBS, ddRAD, ezRAD), RADseq data properties and evaluation, applications - phylogenetics, phylogenomics (selection, adaptation, diversification, hybridization)Each lecture consists of two following parts:1. presentation and discussion of two papers related to the topic of the previous lesson (with emphasis on both, systematics and population biology)2. explaining the molecular technique, showing examples of the data and methods of their evaluation, examples of the use of the technique for solving diverse problems The course is taught with the support of the project reg. number CZ.02.2.69/0.0/0.0/16_015/0002362
Annotation
The lecture is taught in English. Study literature and tutorials are given in English. The lecture comprises traditional as well as modern methods of molecular markers (incl. NGS) and their use for various applications in plant systematics and population biology. The important parts are discussions of scientific papers.
Due to the current restrictions, the lecture is partly organized via Google Meet, see https://meet.google.com/uqo-wovw-pgm, partly by individual consultations.