General course objectives
The rapid advancement and increasing variety of high-throughput genomic tools, now offer opportunities to explore and apply them in natural and farmed populations. The aim of the course is to provide an array of theoretical and practical competences on genomics and bioinformatics with focus on animal breeding and conservation. Through theoretical, individual and group exercises, the students will learn how to handle, analyze and interpret a selected range of high-throughput genomics data in relation with genomic improvement and selection, resource management and traceability strategies of domesticated and wild animals, particularly fish and shellfish species.
Basic principles of conservation/population genetics, biodiversity breeding and genomic selection, high-throughput sequencing and genotyping platforms, hands-on bioinformatics pipelines to analyze a variety of genome and transcriptome-based data types. Discussions of current challenges in relation to application of genomic methods through confrontation with specific problems presented by selected guest speakers.
A student who has met the objectives of the course will be able to:
- Utilize the most important international databases to retrieve information on the genomic resources available for different species
- Utilize the Unix and R environment to handle genomic and transcriptomic data.
- Apply the most updated bioinformatics tools to analyze and interpret high throughput genomic and transcriptomic data with different available genomic information.
- Describe methods for DNA-based barcoding
- Describe and apply concepts and tools of genomics related with conservation and biodiversity (e.g. population-based inferences, population splits and mixtures, genome wide differentiation).
- Explain and utilize concepts and tools of genomics related with genetic improvement (e.g. signatures of selection, QTL, Genome Wide Association Studies, and genomic selection)
- Adopt critical approaches to evaluate and apply high-throughput genomic tools for problem-solving in practical cases of selection and conservation of animal species.
- Develop large-scale data projects and present results