Characterization & exploitation of copy number variation in Atlantic salmon

Atlantic salmon aquaculture is worth more than 1 billion pounds sterling annually to the UK economy and represents a rapidly expanding global industry facing major challenges to ensure sustainable growth. There is currently a major opportunity to develop genetic tools that allow the breeding and production of salmon with favourable traits, including high resistance to disease and parasites and the capacity to convert environmentally sustainable diets into fast-growing and nutritionally-valuable flesh. The objective of this studentship is to characterize an unstudied aspect of genetic variation in Atlantic salmon called copy number variation (CNV) and to exploit this knowledge in aquaculture, focussing on improved flesh growth and quality characteristics.

CNVs are duplicated or deleted regions of chromosomal DNA and one of the main forms of genomic variation distinguishing individuals within animal species. They are widely associated with functional genes and much scientific data links them to a range of diseases or other important biological variation in humans and other species. However, despite their recognised importance, CNVs have never been researched or applied in farmed finfish species. This represents a major untapped resource considering the large potential gains that might be made using CNVs as markers for valuable aquaculture traits. Our project will exploit deep DNA sequencing technology and the latest computational methods to detect CNVs in Atlantic salmon from many genetic backgrounds, including fish showing large variation in fillet yield (the percentage of edible flesh), flesh gaping (damage to the flesh arising during production) and flesh texture (the firmness of edible flesh). These traits are strongly linked to the profitability of aquaculture, impacting many parts of the production chain that ultimately leads to the consumer at the supermarket shelf.

Thus, we will characterize salmon CNVs spanning the genome, determining those affecting protein-coding genes. We will use independent technologies to thoroughly validate the CNVs and to establish their effects on gene expression - an important measure of functional importance for the animal. The final step of our project will involve using statistical methods to associate a characterized panel of CNVs with trait data taken from a much larger group of salmon. The objective here will be to identify specific CNV markers for flesh traits which have high economic value.

The project will be led by the University of Aberdeen (UoA) with Xelect Ltd - a BBSRC supported company - as its industrial partner. Xelect will provide a range of salmon populations, expertise in genetics and trait identification, plus access to a growing database of trait variation. The main business of Xelect is to develop genetic markers for use in the salmon industry: the company currently licenses markers to salmon egg producers across the world. Therefore, the project is likely to lead to the development and licensing of CNV markers globally, both for the traits mentioned already, and potentially many others in the future. The UoA will benefit from a major advancement in understanding of the Atlantic salmon genome, which, in addition to having applied value, has strong relevance in many other academic research contexts. The UoA may also benefit from a contractual agreement with Xelect to share a portion of financial royalties coming from licensing of CNV markers. Finally, as CNVs are very poorly characterized in fish generally, the project will provide proof-of-concept on the feasibility of CNV detection and exploitation, which can be applied in other species of societal importance.