New bioinformatics tool spots hybrid fish that threaten the survival of natural tilapia populations in aquaculture


A new genomic marker tool has been shown to be able to accurately identify tilapia species and distinguish their hybrids, providing a new resource to help develop aquaculture and strengthen conservation in Tanzania, Africa.

Basically, the new tool offers a cheaper alternative to full genome data analysis – the current approach to monitoring local biodiversity.

Led by the Earlham Institute, alongside the Tanzania Fisheries Research Institute, University of Roehampton, Bangor University, University of Bristol and University of East Anglia in the UK, the new genomic marker tool enables identification of tilapia species and identifies hybridization between invasive and native tilapia species.

Production from tropical inland aquaculture has grown rapidly over the past decades to reach 47 million tonnes in 2018. Tilapia, a genus-dominated group of cichlids Oreochromis and from Africa and the Middle East, played a key role in this expansion, accounting for 5.5 million tonnes of the world total. The continued expansion of inland aquaculture is particularly important in Africa, where climate change and population growth are straining vulnerable food production systems.

Due to the gradual increase in inland water temperature due to climate change, African fisheries are suffering from the physical and chemical changes associated with the aquatic environment. This, coupled with continued population growth expected to reach 9 billion people in sub-Saharan Africa and Asia by 2100, raises additional food security concerns.

Tilapia is endemic to Africa and East Africa, including Tanzania, is a hotspot of natural diversity for tilapia species. At least eight entirely endemic Oreochrome are found in Tanzania and 12 other species endemic to watersheds shared with neighboring countries. Several of these species are adapted to unique environmental conditions, such as high temperatures, salinity and pH and could be of interest for future aquaculture developments.

Lead author Dr Adam Ciezarek, postdoctoral researcher with the Haerty Group at the Earlham Institute, said: “One of the main challenges in tilapia aquaculture is species discrimination. currently on morphological traits, which are particularly difficult to identify in females and juveniles, which can lead to accidental contamination of stocks. O. niloticus) are known to be widely distributed across Africa and to hybridize with Oreochromis species.

“In response to the need to accurately distinguish between species but also to identify potential hybrids that can be made cost-effectively and more quickly, an optimized design based on 96 single nucleotide polymorphism (SNP) biomarkers was developed. This design has also been shown to be more accurate than microsatellite or morphological identification of interspecific hybrids.

“Tilapia is an extremely important group of fish for aquaculture. Farmed strains have been introduced into many water bodies as non-native species, creating a problem in areas where the species of Native tilapia are prone to hybridization. Hybrid tilapia survive less well and grow more slowly. , which threatens the survival of natural populations.

“It also threatens the survival of tilapia farms, as stocks are often taken from the wild. If they store what they believe to be pure species, suitable for breeding, but in fact store slow-growing hybrids, the farm may fail.

“It is important to be able to spot these hybrids, but it is unreliable to separate them from pure tilapia species by physical characteristics alone. We have shown that it is possible to identify them using whole genome data. a greatly reduced set of 96 SNPs can perform just as well, with greater efficiency and accuracy, and at much lower cost. »

Co-lead author Professor George Turner, School of Natural Sciences, Bangor University, said: “Case studies point to several places where introduced aquaculture species have become established in the wild, threatening native species. Oreochromis species in Tanzania. Currently, native Oreochrome the species are poorly characterized and their conservation could benefit from the identification of purebred populations to protect.

“Such safeguarding of wild relatives of farmed species would also protect unique genetic resources that could be used to improve the traits of farmed species. Oreochrome cichlid strains.”

Dr Ciezarek added: “The new SNP markers represent an important resource for assessing the purity of broodstock in fisheries hatcheries, helping to conserve unique endemic biodiversity. We hope this more affordable and practical tool will be used to accurately assess potential farmed stocks, as well as survey natural water bodies for evidence of hybridization between tilapia. »

The article “Whole Genome Resequencing Data Enables Targeted SNP Panel for Conservation and Aquaculture of Oreochromis cichlid fish is published in Aquaculture.

This study was funded by the UKRI Biotechnology and Biological Sciences Council, the Royal Society and the Leverhulme Trust.

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