Genomic boost to disease resistance in rohu carp
A collaborative project between Norway and India has discovered markers for genes that control resistance against the bacterial disease Aeromoniasis in rohu carp. Aeromoniasis is a devastating disease that affects aquaculture of this and many other carp species throughout the world.
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How genetic markers are useful:
One can use conventional selective breeding methods when improving traits such as growth rate. However, traits like disease resistance are more difficult to improve through selective breeding. This is because it is not possible to directly test the performance (eg. hours of survival) of individuals in the breeding population without killing or infecting the potential broodstock and thereby making them unable to breed.
The marker tests for genes affecting disease resistance that have been developed by Nofima and CIFA will allow the genetic merit of individuals in the breeding population to be assessed without exposing these valuable broodstock to disease. The markers will also allow more rapid improvement of the trait.
Breeding programmes can make use of these new markers to select rohu carp broodstock (Labeo rohita) with genetic variants that make them more resistant to disease. This would develop a breed of fish that survives and thrives even in the presence of the disease. The small rural communities in India that farm this fish would benefit as production and profitability per pond would be substantially improved.
The research has been funded by the Norwegian Research Council and the Department of Biotechnology of India, and carried out by Nofima (the Norwegian Institute of Food, Fisheries and Aquaculture research) and CIFA (Central Institute of Freshwater Aquaculture, India).
The fish and the disease
Rohu is farmed in India, Bangladesh, Burma and Thailand. Carp are the world’s most important group of aquaculture species accounting for more than half of total global fish production from aquaculture. Over 1.2 million tonnes of rohu is farmed in India per year.
Aeromoniasis disease caused by the bacteria Aeromonas hydrophila, is a major problem for the aquaculture of this species in India, and also for other carp species around the world. It is a bacteria that causes haemorrhaging and ulceration when fish are stressed. It is widespread and difficult to control and treat. Previous work by Nofima and CIFA showed that some fish inherit genes that give them higher resistance to the disease (ie. that there is genetic variation affecting disease resistance). These fish have an immune system that is better able to prevent and fight infection by the disease.
We know that the immune system of fish is complex and that the reaction to bacterial infections is likely to be controlled by many different genes, most with small effects on the animal’s ability to resist the outbreak of disease.
In the search for the markers, the genetic code (DNA sequence) of the genes present in different individuals was analysed. The inheritance of genetic code variants in over 3,000 genes was compared in large families that had been challenged with exposure to the disease. The study looked for associations between the number of hours individual rohu survived after infection with the disease and the genetic code of the genes that were inherited. In this way, several gene markers associated with disease resistance were identified. Some of the markers either occurred in, or mapped closely to, genes with known roles of immune function in fish.
High throughput sequencing and genotyping technologies were used to read the genetic code of the 3000 genes which were mapped to positions on the 25 chromosome pairs present in rohu.
Gene that causes bacterial destruction
One of the genes identified by the scientists in Norway was the pore forming protein, perforin, which is produced by T-cells and natural killer-cells, and thought to be inserted into the membrane of invading cells such as bacteria, allowing enzymes to enter and destroy these foreign cells. Animals inheriting a particular perforin variant survive 2-3 hours longer on average than other animals challenged with the disease. The scientists in India found that expression of this gene in the spleen of rohu was increased twenty-fold around 12 hours after Aeromonas hydrophila infection. Greater expression of this gene was also found in gill tissue after infection.
The project has produced many other interesting leads about genes affecting immunity in fish which the scientists in Norway and India are keen to pursue in future projects.
Two decades of carp collaboration between India and Norway
Nofima’s work in India began in 1992 with a project funded by Norad (Norwegian Agency for Development) to assist the Central Institute of Freshwater Aquaculture (CIFA) in Orissa to establish a breeding program for rohu carp. Rohu is farmed in clay ponds by relatively poor rural communities in India. The initial focus of the breeding program was to improve the growth rate of the fish. Strong genetic improvement (17% per generation on average during the initial years of the breeding program) was achieved with the selective breeding for growth rate in rohu.
The latest project has run a number of workshops in India to exchange knowledge about genomics, animal health and breeding. The series of projects that Nofima has had in collaboration with CIFA, and other institutes in India, have been of great success and have greatly benefitted aquaculture in India.
CIFA distributes the genetically improved rohu to farmers throughout India. The genetically improved fish is called “Jayanti” rohu (Jayanti meaning “victorious” in the Hindi language). If these latest discoveries can be effectively applied with selective breeding to improve the resistance of farmed rohu carp, survival and overall performance of the fish will be improved, greater production per pond area will be possible and farmers and consumers in India will benefit.
Therefore, effective application of the technologies developed by this project should result in farmed Jayanti rohu acquiring the immune defence needed to achieve “victory” in the fight against this disease, a “victory” also for the farmers and consumers in India!