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How Genomics is Boosting Spain's Aquaculture Breeding Programmes

06 October 2016

SPAIN - Spain has a long history of aquaculture, with the earliest shellfish and fish rearing facilities in the country traced back to Roman times. By the Middle Ages, trout and carp were reared for the first time in Europe in the grounds of Spanish monasteries and abbeys. In 1870 the first trout farm was created – and supported by the Spanish Government in response to dwindling conditions of freshwater lakes. Today Spain has a well-developed aquaculture industry, supplying a variety of fish and shellfish to meet both domestic and international demands for seafood.

Far from standing still, the Spanish aquaculture industry is ever-evolving. In a recently published paper in the journal Aquaculture, Professor Paulino Martínez (Universidad de Santiago de Compostela) explains how genomics has – and will continue to be – vital for improving Spain’s aquaculture breeding programmes.

Given that Spain is the largest producer of farmed turbot (Scopthalmus maximus) in Europe, it is somewhat unsurprising that Spain’s first experience with aquaculture genomics began with the flatfish.

Turbot genetic breeding programmes started in the early 1990s and focused on managing parentage to avoid inbreeding issues. Early work used available genealogical information but as technology and techniques improved, microsatellite traceability tools were introduced.

These tools allowed turbot broodstock to be organised according to relatedness, and check the ‘goodness’ of families in the breeding programmes, both to avoid interbreeding, and aid in selective breeding.

Proving successful, such molecular tools were later expanded to breeding programmes for other species, including sea bass (Dicentrarchus labrax) where the tools have been vital in estimating the heritability of undesirable traits, such as those that produce deformities. Molecular tools have also been used in mollusc breeding programs, including aiding in the assessment of grooved carpet shell clam (Ruditapes decussatus) management practices.

Disease is one of the major challenges faced by fish farmers. Understanding how and why species are susceptible to a variety of different pathogens is essential to improving overall disease resistance in farmed fish, and potentially developing vaccines to prevent disease in the first place.

Thanks to funding from the Spanish and Regional Governments in 2004, and later the European Commission, genomic tools produced a genetic map of turbot – and eventually full genome sequencing of turbot. Alongside gene expression analysis, the wealth of genetic data derived from these studies has aided the selection of disease resistance and other desirable traits, such as faster growth.

Other uses of genome mapping and sequencing include assisting the development of all-female populations of turbot for the industry. Female turbots are more desirable for aquaculture because they have faster growth rates than males, shortening the time needed for the turbot to reach a marketable size.

Transcriptome databases of Senegalese sole (Solea senegalensis) and turbot – including those for larval and adult tissues under various experimental conditions, were created to understand the mechanisms behind a variety of traits desired by the industry in these species.

These same databases have also been used to analyse gene expression relating to gonad development, disease resistance, and to understand effects – and therefore suitability - of different diets on farmed individuals.

With the technology proving successful, similar databases and studies were also applied to sea bass, sea bream (Sparus aurata), Manila clams (Ruditapes philippinarum), and European flat oysters (Ostrea edulis). Most recently, the whole turbot genome is being used as reference in the latest genotyping (RAD-seq) and gene expression (RNA-seq) techniques.

Genomics hasn’t just helped improve current aquaculture breeding programmes - it is helping assess the feasibility of breeding novel species. A number of mollusc species are being assessed for their disease resistance abilities to see how they will perform in intensive aquaculture settings.

Genomics is also helping with the development of breeding programmes for Mediterranean mussels (Mytillus galloprovincialis) - the dominant aquaculture species in Spain. Focusing on a number of areas essential to successful breeding, current research includes evaluating the mussel’s immune responses to a variety of pathogens, and the genetic mechanisms behind toxin accumulation in the species.

With continuing research programmes both within Spain and in collaboration with the European Commission, genomics looks to continue to offer the aquaculture industry the answer to many of its most difficult challenges, and potentially help improve aquaculture’s sustainability.

Sam Andrews

Sam Andrews
Freelance journalist

Samantha is a marine conservation biologist/ecologist. She holds an MSc in Marine Environmental Management, an Advanced Graduate Diploma (3/4 of a Masters) in Fisheries Management, and is currently undertaking a PhD focusing on marine spatial management for conservation and sustainable ocean use. She has worked closely alongside Government, NGOs, and the fishing industry to help improve the ways in which we interact with the ocean. When she is not doing science, she works as a marine science communicator.

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