6 EC
Semester 1, period 2
5042ECOG6Y
The field of ecological genomics strives to uncover the genetic and molecular mechanisms influencing responses and adaptations of organisms to their environment. Achieving this aim requires insight in evolution and selection pressure and how that results in natural variation. Using this natural variation to study mechanisms requires a good understanding of both ecologically important phenotypes and species with a well-developed genomic tool-kit. Molecular biological and genomic tools have primarily been developed for model organisms (such as yeast and Arabidopsis) representing a narrow spectrum of phenotypes, whereas many organisms that are the focus of ecological research have had limited genomic resources devoted to them.
In this course, we will focus on the ways in which ecogenomics unites genomic and ecological approaches, which are: (1) to explore the natural variation found within model or crop species, (2) to analyze close relatives with a broader range of phenotypes (e.g. comparative genomics ), and (3) to generate new genomic resources for the species of interest . We will explore the underlying principles of genomics and how they are being applied for each of these three approaches. We will specifically focus on ecogenomics studies of abiotic stress responses. Specific approaches that will be discussed and demonstrated include: genetic mapping, expression analysis (transcriptomics), phenotyping (metabolomics, microbiome analysis, etc.), gene candidate verification. Analysis tools that will be studied “hands-on” will include: the use of genomic databases and tools, quantitative trait loci (QTL) analysis, physiological experiments and genome-wide association studies.
Selected reviews and primary literature will be placed on Canvas
Practical manual will be available via Canvas
|
Activity |
Hours |
|
|
Hoorcollege |
26 |
|
|
Practicum |
36 |
|
|
Presentatie |
4 |
|
|
Tentamen |
3 |
|
|
Labtopcollege |
20 |
|
|
Self study |
77 |
|
|
Total |
168 |
(6 EC x 28 uur) |
Additional requirements for this course:
Attendance at lectures is highly recommended. Attendance for the (computer) practical and tutorials (werkcollege, WC) sessions is mandatory linking to the course objectives 5-9. If you are unable to participate due to personal circumstances (such as illness or special family circumstances), please contact the course coordinator by e-mail. The course coordinator will then discuss with you whether there are options to participate/contribute in an alternative way (e.g. online) or compensate your absence later. If you are not able to follow education for a long time (longer than 1 week), please also contact the study advisor.
| Item and weight | Details | Remarks |
|
Final grade | The weighted final grade is 5.5 or higher | |
|
0.6 (60%) Tentamen | Must be ≥ 5, Mandatory | |
|
0.2 (20%) presentation practical results | Mandatory | |
|
0.1 (10%) QTL tutorial | Mandatory | |
|
0.1 (10%) GWAS tutorial | Mandatory |
The final grade is composed of the exam (0.6), the practical (presentation, performance)(0.2), and the tutorials (0.2). A student has passed the course when the exam scores 5.0 or higher and the weighted final grade is 5.5 or higher.
For at least twenty working days after the announcement of the results of a written examination, the student can, on request, inspect his/her assessed work, the questions and assignments set, as well as the standards applied for marking. The place and time will be announced via Canvas (from Teaching and Examination Regulations).
Two assignments based on QTL and GWAS will be given and graded.
The practical work will be carried out in groups, and the presentations will be assessed.
The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl
| Weeknummer | Onderwerpen | Studiestof |
|
1 |
Intro, adaptation, phenotyping, gene regulation, GWAS tutorial |
See Canvas |
|
2 |
QTL mapping, use of ecogenomics for breeding and ecology, metagenomics and metabolomics |
See Canvas |
|
3 |
Practical introgression mapping |
See Canvas |
|
4 |
Practical introgression mapping, data analysis |
See Canvas |
This is a 4-week fulltime course in period 2a (November).
Participation in all practical (computer) sessions and workshops is mandatory.
The course has a Canvas site; the course will be taught in English.