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

Date:
December 9, 2021
Source:
Earlham Institute
Summary:
A new genomics marker tool has been shown to accurately identify
tilapia species and tell apart their hybrids, providing a novel
resource to help develop aquaculture and empower conservation in
Tanzania, Africa.

Crucially, the new tool offers a cheaper solution than full
genome data analysis -- the current approach to monitoring local
biodiversity.



FULL STORY ==========================================================================
A new genomics marker tool has been shown to accurately identify tilapia species and tell apart their hybrids, providing a novel resource to help develop aquaculture and empower conservation in Tanzania, Africa.


========================================================================== Crucially, the new tool offers a cheaper solution than full genome data analysis -- the current approach to monitoring local biodiversity.

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

Tropical inland aquaculture production has increased rapidly in recent
decades to 47m tonnes in 2018. Tilapia, a group of cichlid fish dominated
by the genus Oreochromis and native to Africa and the Middle East,have
been a key part of this expansion -- accounting for 5.5m tonnes of the
global total. Continued expansion of inland aquaculture is particularly important in Africa, where climate change and population growth are
putting vulnerable food production systems under added strain.

As a result of inland waters' temperature gradually rising due to climate change, African fisheries suffer from associated physical and chemical
changes to the aquatic environment. This coupled with the continuous
population growth that is estimated to reach 9 billion inhabitants in sub Saharan Africa and Asia by 2100, causes further concern for food security.

Tilapia are endemic to Africa, and East Africa including Tanzania
is a hotspot of natural diversity for tilapia species. At least eight fully-endemic Oreochromis species are found in Tanzania and an additional
12 species that are endemic to catchments shared with neighbouring countries.Several of these species are adapted to unique environmental conditions, such as elevated temperatures, salinity, and pH and could
be of interest for future aquaculture developments.



==========================================================================
Lead author Dr Adam Ciezarek, Postdoctoral Scientist in the Haerty
Group at the Earlham Institute, said: "One of the major difficulties
in tilapia aquaculture lies with the discrimination of species. This
currently relies on morphological traits, which are particularly a
problem to identify in females and juveniles.

This in turn can lead to accidental stock contamination. Furthermore,
non- native farmed tilapia populations (Nile tilapia,O. niloticus)
are known to be widely distributed across Africa and to hybridise with
native Oreochromis species.

"In response to the need to accurately distinguish species but also
identify potential hybrids that can be carried out cost-effectively and
faster, an optimised design based on 96 single nucleotide polymorphisms
(SNPs) biomarkers was developed. This design has also proven to be
more accurate than microsatellite or morphological identification of interspecific hybrids.

"Tilapia are a hugely important group of fish for aquaculture. Farmed
strains have been introduced to many water bodies as non-native species,
which creates a problem in areas where native tilapia species are prone
to hybridising.

Hybrid tilapia survive less well and grow slower, which threatens the
survival of natural populations.

"This also threatens the survival of tilapia farms, as stocks are often
taken from the wild. If they're stocking what they believe to be pure
species, suitable for farming, but are in fact stocking slowly growing
hybrids, the farm may fail.

"It's important to be able to spot these hybrids, yet it's unreliable
to separate them from pure tilapia species by physical characteristics
alone. We have shown that it is possible to identify them using
full-genome data.

Crucially, we have also demonstrated that a vastly reduced set of 96
SNPs can perform just as well -- with greater efficiency and precision,
and at a much lower cost." Lead co-author Prof George Turner, School
of Natural Sciences at Bangor University, said: "Case studies indicate
several locations where introduced aquaculture species have become
established in the wild, threatening native Oreochromis species in
Tanzania. At present, native Oreochromis species are poorly characterised,
and their conservation could benefit from the identification of purebred populations for protection.



========================================================================== "Such safeguarding of the wild relatives of farmed species would
also protect unique genetic resources that could be used to enhance
traits in cultured Oreochromiscichlid strains." Dr Ciezarek added:
"The novel SNP markers represent an important resource for assessing
broodstock purity in fishery hatcheries, helping to conserve unique
endemic biodiversity. We hope that this more affordable and convenient
tool will be used to accurately assess potential farm stocks, as well
as surveying natural water bodies for evidence of hybridisation between tilapia." The paper "Whole genome resequencing data enables a targeted
SNP panel for conservation and aquaculture of Oreochromis cichlid fishes"
is published in Aquaculture.

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

========================================================================== Story Source: Materials provided by Earlham_Institute. Note: Content
may be edited for style and length.


========================================================================== Journal Reference:
1. A. Ciezarek, Antonia G.P. Ford, Graham J. Etherington, Nasser
Kasozi,
Milan Malinsky, Tarang K. Mehta, Luca Penso-Dolfin, Benjamin
P. Ngatunga, Asilatu Shechonge, Rashid Tamatamah, Wilfried Haerty,
Federica Di Palma, Martin J. Genner, George F. Turner. Whole genome
resequencing data enables a targeted SNP panel for conservation
and aquaculture of Oreochromis cichlid fishes. Aquaculture, 2022;
548: 737637 DOI: 10.1016/ j.aquaculture.2021.737637 ==========================================================================

Link to news story: https://www.sciencedaily.com/releases/2021/12/211209124445.htm

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