General course objectives
The aim is to provide students with knowledge and practical laboratory based experience of the application of modern DNA based methods in aquaculture. Students will learn about classical breeding methods and how genetic and genomic tools can lead a more efficient attainment of breeding goals. The course encompasses the newest developments in mediating large scale genome rearrangements such as manipulation of chromosome number, sex and gene transfer from other species and organisms (GMO). The main focus is on the application of genetic markers for multiple purposes including a) identification of suitable wild broodstock b) identification of individuals and families c) avoidance of inbreeding and loss of genetic diversity d) genomic mapping and marker assisted selection (MAS) of traits important for e.g. production, quality and fish welfare e) traceability of fish and fish products back to producer. In addition functional genomic tools such as RNA microarrays and their application for studying gene expression will be presented. Further, an introduction to the multitude of web-based genomic resources and how to access them will be provided. Finally, potential interactions between wild and domesticated fish and how to monitor them will be discussed in order to assure sustainable and biodiversity friendly aquaculture.
The course is based on cases illustrating application of modern DNA based methods in aquaculture and on hands on laboratory work using state of the art methods. The course reviews the importance and relative success of aquaculture activities encompassing a selective breeding program. Common goals for aquaculture breeding, such as productivity, disease resistance, flesh quality and fish welfare are presented.
Basic concepts of population and quantitative genetics relevant for aquaculture are introduced. Important terms such as selection, inbreeding and heritability are defined, followed by application of large scale genome rearrangements, i.e. manipulation of sex and chromosome number, and production of GMO (Genetically Modified Organism) fish using gene transfer among species.
This is followed by specific applications of DNA based methods in aquaculture, including laboratory exercises A major topic is the use of DNA methods for identification of a) suitable broodstock, b) individuals c) families and for d) tracing fish products back to the producer in a forensic context. A second major application is for locating sites in the genome – mapping – that influence the trait of interest for selective improvement, so-called QTL (Quantitative Trait Loci) mapping, including how this information can provide faster and more efficient selection through MAS (Marker Assisted Selection) and WGS (Whole Genome Selection).
The course includes group work on a practical aquaculture breeding case study defined and developed by the students in association with the course responsible/teachers. The final part of the course will be a discussion on interactions between wild fish and fish in aquaculture. The ultimate goal will be to design a strategy for avoiding and monitoring potential genetic threats to natural biodiversity, thus assuring sustainable future aquaculture.
A student who has met the objectives of the course will be able to:
- Demonstrate broad knowledge on DNA based genetic and genomic analyses and their application in aquaculture.
- Demonstrate knowledge of fundamental population genetic/genomic and quantitative genetic terms such as inbreeding, selection, heritability and adaptation.
- Explain how selection works in order to change traits of interest for aquaculture.
- Demonstrate knowledge on methods for chromosome number and sex manipulation as well as gene transfer and GMO production.
- Explain basic differences among various types of genetic markers and evaluate their usefulness for different applications.
- Understand and analyse genetic marker data for identification of individuals, families and broodstocks including application for traceability.
- Understand and explain basic principles of QTL (Quantitative Trait Loci) mapping and its application to MAS (Marker Assisted Selection).
- Explain the principles of gene expression analysis and evaluate relevant applications for aquaculture.
- Find, access and use web-based genomic resources of relevance to aquaculture.
- Demonstrate knowledge of end-to-end design, development and evaluation of a breeding programme for new species in aquaculture.
- Evaluate genetic and demographic consequences of interactions between wild and aquaculture organisms and discuss how potential negative effects can be monitored and alleviated.