Ecogenomics

Course manual 2023/2024

Course content

The field of ecogenomics strives to uncover the genetic and molecular mechanisms influencing the response and adaptation of organisms to their environment. Achieving this requires a good understanding of what are important phenotypes and needs plant 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), while many organisms that are the focus of ecological and agricultural research only have limited genomic resources.

In this course, you will learn how ecogenomics unites genomic and ecological approaches by exploring the natural variation in model or crop species and their relatives. We will explore the underlying principles of genomics and how they are being applied in ecogenomics. We will focus on ecogenomic studies of abiotic and biotic stress responses . Specific approaches that will be discussed include: adaptation to abiotic and biotic stress, phenotyping (including expression analysis, transcriptomics; metabolomics; microbiome analysis), genetic, QTL and GWAS, mapping, gene regulation, gene candidate verification, the use of ecogenomics in breeding and ecology, etc. Hands-on training will include: a practical on mapping in tomato, data analysis and statistics, the use of genomic databases and tools, quantitative trait loci (QTL) analysis and genome-wide association mapping.

Study materials

Literature

• Several textbooks will be used by the lecturers, including "Molecular Biology of the Cell" by Alberts et al, "Evolutionary Analysis" by Freeman & Herron, "A Primer of Genome Science" by Gibson and Muse. Other reading materials are provided on Canvas.

Syllabus

• A practical manual will be provided through Canvas at the start of the course

Software

• Software tools for GWAS data and other analyses will be provided

Other

• Selected reviews and primary literature are available on Canvas

Objectives

• Explain the strategy of Ecogenomics in answering biological questions
• Explain the principles of and difference between association mapping (GWAS) and mapping in biparental populations (QTL mapping)
• Explain the principle of genomics, transcriptomics, metabolomics, microbiome analysis
• Discuss the principles of how organisms can adapt or respond to their environment
• Translate knowledge on genetics and omics into ecological insight or breeding strategies
• Use online genomics resources
• Carry out an ecogenomics research project
• Analyse the results of a Genome Wide Association Study
• Interpret and present the experimental results

Teaching methods

• Lecture
• Computer lab session/practical training
• Presentation/symposium
• Self-study
• Working independently on e.g. a project or thesis
• Supervision/feedback meeting

Learning activities

Attendance

Programme's requirements concerning attendance (OER-B):

• Participation in all practical (computer) sessions, field work and seminars in the curriculum is in principle obligatory. Any additional requirements are described per section in the course manual. Also the possible consequences of not fulfilling this obligation are described.
  

Additional requirements for this course:

Attendance at lectures is highly recommended. Attendance during practical components is mandatory. The latter also applies to all (computer) practicals and tutorials. 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.

Assessment

The final grade is composed of the exam (0.6) and the practical performance, attitude and presentations (0.4). A student has passed the course when the exam scores 5.0 or higher and the weighted final grade is 5.5 or higher.

Inspection of assessed work

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).

Assignments

Two oral presentations about practical results and GWAS analysis, in groups

Fraud and plagiarism

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

Course structure

Timetable

The schedule for this course is published on DataNose.

Contact information

Coordinator

• prof. dr. ir. Harro Bouwmeester

h.j.bouwmeester@uva.nl

Staff

• dr. Thomas Blankers
• dr. P.M. Bleeker
• dr. L. Dong
• dr. rer. nat. Anna Heintz Buschart
• S.W. Alves Aflitos-Hoogstrate MSc
• dr. M. Kant
• prof. dr. ir. R.C. Schuurink