Subject description
Genetic molecular markers are heritable polymorphisms that are related to changes in DNA sequence and can be detected and measured in one or more populations of individuals. They are the tools of choice of modern genetics and enable the study of important questions in population genetics, ecological genetics, and evolution. Next generation sequencing (NGS) is about to revolutionize genetic analysis. Currently NGS techniques are mainly used to sequence individual genomes, but due to the high sequence coverage these data can be applied in the field of molecular markers as well. They are especially attractive for use in e.g. population analysis of non-model organisms.
The following topics will be included:
a) short overview of currently used NGS methods and their impact on genetic marker technology (comparison with tradicional molecular markers)
b) NGS molecular marker discovery and current genotyping methods (reduced representation sequencing, including reduced-representation libraries (RRLs) and complexity reduction of polymorphic sequences (CRoPS); Restriction site associated DNA markers or RAD-seq; and low coverage genotyping, including multiplexed shotgun genotyping (MSG) and genotyping by sequencing (GBS)).
c) Design of next generation marker discovery experiments (goals, availability of reference genome, expected degree of polymorphisms, choice of restriction enzymes, adapters, PCR amplification, sequencing, polling of individuals or multiplexing, challenges).
d) Data analysis challenges (methods, availability of program packages)
e) Future directions of the field.
f) Selected literature examples of the use.
The subject is taught in programs
Objectives and competences
The main educational aim of the course is to present methods and research activities, which are used in the field of next generation molecular markers with emphasis on non-model species.
Teaching and learning methods
Lectures, seminar and consultations.
Expected study results
Knowledge and understanding:
Acquisitions of knowledge related to design and use of molecular markers based on NGS use.
Students will get knowledge and competences which will allow them to solve research problems in the field of molecular markers.
Basic sources and literature
Izbrana poglavja iz sledečih knjg:
1) Molecular Markers in Plants. Robert J. Henry (Editor). ISBN: 978-1-118-47299-6. 216 pages.
September 2012, Wiley-Blackwell
2) Tag-based Next Generation Sequencing. Matthias Harbers (Editor), Guenter Kahl (Editor) ISBN: 978-3-527-32819-2. 608 pages. December 2011, Wiley-Blackwell
3) Relevantni članki (Relevant articles)
Revijalni članki s področja, tekoča periodika in druga učna gradiva.
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