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Bilaga 1/Appendix 1

Preliminär kursplan/Preliminary course syllabus

Bilaga till ansökan om medel för doktorandkurser vid LTV-fakulteten / Appendix to


application for funding of PhD courses at the LTV Faculty

Course name: Field-omics and remote sensing - analysis of ‘-omics’ and phenotypic data in
field trials and controlled environments (3 ECTS),

Pre-requisites: PhD students interested in handling, interpreting and visualizing ‘-omics’


data in the context of relatively uncontrolled environments, e.g. field trials. Some experience
of handling large datasets in R, cytoscape or similar application is advantageous but not
necessary.

Number of credits: 3 ECTS

Purpose: The last years’ rapid technological advancements have enabled genome-scale
capturing of biological processes. Gene expression analysis by microarrays as well as protein
and metabolite identification by mass spectrometry are today common techniques used in
many laboratories. However, combining different types of data and making biological sense
out of large datasets remains challenging. The generation of such large datasets - often
referred to as ‘-omics’ data - demands partly new considerations for experimental set-ups,
sampling, data analysis and visualization. Simultaneously, rapid advancement is undergone
within remote sensing enabling new ways to phenotype plants.

This course will provide theoretical and practical aspects when designing experiments for the
generation of ‘-omics’ as well as remote sensing data and how to go from sampling to
interpreting the results and finding biologically relevant conclusions. Strategies both in field
trials and in controlled environments will be covered. Suitable statistical methods to deal with
the variation in this type of data will be presented.

The overall goal is to point out the possibilities in using ‘-omics’ techniques, but also to
highlight possible pitfalls. The potential in using ‘-omics’ data in future plant breeding efforts
will also be discussed.

Intended Learning outcomes:

After the completion of the course, the student is expected to be able to:

• Explain how to design field trials suitable for representative sampling of plant
material for subsequent ‘-omics’ and/or remote sensing data generation.
• Describe at least 10 detection techniques of ‘-omics’ data and critically evaluate the
suitability and feasibility in selection of appropriate -omics technique(s) for a given
biological problem
• Apply various data analysis pipelines and statistics to analyze the omics data sets
• Demonstrate the integration of phenotyping and ‘-omics’ data through Cytoscape.
• Discuss challenges and future possibilities in this emerging field

Content: Experimental design for field trials and in controlled environments. Methods to
record climate data and soil properties. Remote sensing. Phenotyping and scoring plant
material. Sampling of plant material. Pooling strategies. Survey of available ‘-omics’
techniques and their suitability for different experimental set-ups and in field trials. Statistical
methods for analysis of ‘-omics’ data. Integration of different types of data. Incorporating
genotype information with systems biology. Interpretation and visualization of data by e.g.
pathway and gene set enrichment analysis. Biomarker discovery. Using sequence information
and inferring cross-species information for functional annotation. The use of ‘-omics’ data for
plant breeding.

Pedagogical approach: Lectures, demonstrations, laboratory and field exercise and


computer practical. The students will receive scientific publications to read latest two weeks
in advance, including the articles for the journal club that should be prepared beforehand.

What is required to pass: Active participation during lectures and computer practical, field
and biotron experiment as well as approved presentation of subject-related article in journal
club both orally and in text. Every missed lesson by the student has to be compensated a
written summary addressing the subject area and answering one key question based on the
lecture slides and related assigned reading (minimum half an A4 page).

Technical requirements: Own laptop.

Course organizers: Erik Alexandersson and Aakash Chawade