Genomic approaches to identification and preservation of wild tilapia genetic resources for aquaculture

Lead Research Organisation: Bangor University
Department Name: Sch of Biological Sciences

Abstract

Most of the world's fisheries are over-exploited and it seems inevitable that fish-farming will largely replace fishing, just as livestock arming has replaced hunting as the main source of food from land animals. Unfortunately, many farmed fish, such as salmon, are themselves predators and need to be fed on fish meal. Tilapia are tropical freshwater fish that can be grown largely on vegetable matter and agricultural waste and so promise much for future sustainable production. Global tilapia production grew 280 percent over the 10 years to 2012, with a harvest of ~4.5 million tonnes, more than 5 times greater than the entire UK fishery and aquaculture industry. Tilapia is now a $7.6 billion dollar industry. Most tilapia production is based on a handful of strains, but there are more than 50 wild species throughout Africa which could harbour valuable genes for growth, disease resistance, temperature & salt tolerance etc. Many tilapia will hybridize readily, so that the natural genetic traits could easily be bred into farmed strains without the need for GM technology. However, this feature also renders them vulnerable to genetic swamping by stocking with alien farmed strains into natural water bodies, a practice now widespread in Africa. At present, little is known of the status of wild tilapia strains, and international agencies seem to be largely unaware that widespread stocking is in progress, and there is little appreciation of its possible consequences. We propose to survey the natural tilapia diversity of Tanzania, a particular hotspot for wild tilapia strains. We will assess the effects of stocking at the molecular genetic level through sequencing the genomes of native and stocked forms. We will locate pure stocks of native forms and make recommendations for their conservation in-situ and ex-situ (e.g. in pond culture or sperm banks). We will estimate the growth rates of pure and hybrid forms in their natural habitats using scale rings and relate these to particular genetic traits, making predictions of the likely genetic consequences of stocking. We will also investigate the ecological niches of pure and hybrid strains from stable isotope ratios. It is possible that genetic material from native strains is actually helping hybrid forms to establish themselves, or indeed that the stocked forms may be failing to get established, perhaps in some habitats, if not supplemented by regular stocking programmes. We will develop quick molecular diagnostic tests of hybridization for the benefit of fishery managers in other locations, and use these to calibrate simple visual methods to identify hybrids in the field. The genome sequence information of all of these tilapia strains will be deposited in online public databases, where it will provide a major resource for future studies in tilapia strain development and conservation. We will also advise the government of Tanzanian and international agencies such as WorldFish about remaining pure populations of native strains to prioritise their conservation. This be backed up by depositing tissue/sperm samples for long-term deep-freeze storage, so that these unique and endangered genetic resources might be available to breeders seeking to improve tilapia strains in the future.

Technical Summary

We aim to survey the wild genetic resources for one of the world's most significant aquaculture species (tilapias of the genus Oreochromis) in a particular hotspot of diversity (Tanzania), where native stocks are being heavily impacted by widespread introduction of exotic Nile Tilapia strains, and contaminants such as spotted tilapia (Oreochromis leucostictus). We will (i) assess the extent and predictability of hybridization following introduction from genomic data; (ii) estimate the nature of genomic introgression, including testing whether particular genomic regions or types of genes more likely to introgress into native and exotic phenotypes; (iii) estimate the relative growth and ecological niche of pure and alien genotypes in hybridizing systems from scales stable isotopes and relate this to phenotype; (iv) develop a quick economical diagnostic test of the extent of introgression; and (v) enhance the genomic resources for global strain improvement through bioinformatics (sequences of all species), tissue banking and identification of candidate stocks for in-situ conservation.

Planned Impact

Threatened native tilapia genome resources will be identified and preserved for the benefit of the aquaculture industry globally and in Tanzania in particular, disseminated through workshops organised with our partners in the Tanzanian Fisheries Research Institute (TAFIRI) and the University of Dar-es-Salaam. This will take the form of identifying native strains endangered by introduction of exotics and recommending their in-situ conservation, pond culture and restocking. This will be backed up by depositing tissue and sperm samples with WorldFish for cryopreservation and the depositing of genome sequence information in public databases, so that desirable traits can be identified for crossing into cultured strains. We will enhance capacity in research and identification of strains of tilapia within Tanzania, through participation of local staff and research students in our fieldwork and workshops and through preparation of a field guide to the tilapias of Tanzania. This will lead to improved research and monitoring and ultimately to enhancement of the aquaculture industry. We believe that this research will be of great interest to students and the general public in the UK and internationally and we will carry out a variety of dissemination activities through a range of media. Furthermore, the genome sequence information will be publicly available to future researchers, benefiting the wider academic community interested in research themes as diverse as fish health and evolutionary biology.
 
Description We have discovered that exotic tilapia strains have been widely stocked into natural water bodies across Tanzania. In many cases, these seem to be replacing unique native strains of tilapias. In some cases, the exotics have hybridised with the natives, leading to genetic swamping. These hybrids can be hard to identify other than using molecular genetic methods. Where the exotics have replaced the natives, are many of the genes of the native strains still 'hidden' in the genome of the invasive species? We are still trying to test this. We have also found that a lot of strains being reared for fish farming (and used to stock natural waters) are not the fast-growing Nile Tilapia that the farmers think, but are actually 'contaminated' with 2 other species that grow to smaller sizes. Also native strains have sometimes gained access to the breeding ponds from inflowing streams, and have hybridised with the exotics, which have then been stocked in completely different parts of the country, which have different native strains. Unique native tilapia strains may hold precious genes for disease resistance or environmental tolerances valuable for future generation of fish farmers. These are being threated by poor stocking and fish farming practice, which are not even bringing superior strains to local farmers. We have brought this to the attention of government, academic and private sector stakeholders in Tanzania and are helping to develop policies to improve breeding and stocking practices and to conserve remaining native strains.
Exploitation Route We have brought our results to the attention of government, academic and private sector stakeholders in Tanzania and are helping to develop policies to improve breeding and stocking practices and to conserve remaining native strains. Our methods and results could be used more widely within Africa, where native tilapia strains are still found in the wild. We have now obtained further funding from BBSRC for additional development of bioinformatic and genomic tools for tilapia and a charity grant (JRS Biodiuversity Foundation) to further develop the smartphone App, increase stakeholder engagement with data collection and deposit our data in the public domain. The latter project has expanded our geographic coverage to Kenya, in collaboration with the National Museums of Kenya (NMK).
Sectors Agriculture, Food and Drink,Environment

 
Description Our findings have been discussed at a number of meetings in Tanzania and Malawi. The importance of zoned aquaculture and screening of farmed strains has been agreed at a high-level meeting of stakeholders in Tanzania in Zanzibar in September 2016. The Malawi Government obtained funding from the World Bank to undertake a survey of the Lake Malawi catchment (including the Tanzanian sector) to check for establishment of exotic species, reinforcing its commitment to excluding exotic species from its waters. We attended a workshop at the Sokoine University of Agriculture at Morogoro, Tanzania in January 2017 to discuss issues around stocking of exotic species and the use of mixed strains in aquaculture, as well as providing training in strain identification, attended by senior government officials, as well researchers, local fishery officers and private sector representatives. Representatives of a private sector fish farming company organised a follow-up workshop for over 120 fishfarmers in the Mbeya region at which it was resolved to promote the use of native strains in the lake Malawi catchment. The Tanzanian Fisheries Research Institute has instituted a programme of culturing native strains at Kyela, so they can be used to stock cages in the lake. In 2018, we participated in a workshop in Dar Es Salaam, attended by researchers and stakeholders including government officials and fish farmers which resulted in the production of a Policy Document in relation to zoned aquaculture. This was accepted by the Permanent Secretary for the Fisheries Sector at the Ministry of Livestock and Fisheries in an interview with national newspaper.
First Year Of Impact 2016
Sector Agriculture, Food and Drink,Environment
Impact Types Economic

 
Description Ensuring pedigree of aquaculture broodstock
Geographic Reach Local/Municipal/Regional 
Policy Influence Type Influenced training of practitioners or researchers
Impact Identification of commercial and governmental fish hatchery broodstock as mixed (hybrid) stocks rather than pure Nile tilapia (as currently marketed) resulted in: - Raising awareness of issues of biosecurity, importance of correct species identification - Practice change in separating fish farm stocks from local water bodies - Practice change in growing wild-caught stocks to maturity for species ID to ensure pure breeding lines
 
Description Species selection for fish farming (zonal aquaculture)
Geographic Reach National 
Policy Influence Type Influenced training of practitioners or researchers
Impact Ongoing engagement around biodiversity preservation led to policy change in the stocking of native rather than exotic species. Working with industry - local company Rofacol who organised a workshop emphasising benefits of farming native species for >120 farmers and stakeholders in Kyela.
 
Description Zanzibar Declaration
Geographic Reach National 
Policy Influence Type Membership of a guideline committee
Impact International partners on the 'Zanzibar Declaration' as a policy briefing outcome from the AgriFose workshop, and commitment to the establishment of a National Aquaculture Development Centre (NADC) in Tanzania
 
Description ESRC Impact Acceleration Account (IAA) Bangor Impact Project Grant scheme
Amount £19,985 (GBP)
Organisation Economic and Social Research Council 
Sector Public
Country United Kingdom
Start 03/2016 
End 01/2017
 
Description GCRF Impact Acceleration Account
Amount £10,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 03/2017
 
Description Global Challenge Research Fund: Data and Resources
Amount £164,268 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 10/2016 
End 07/2017
 
Description International Travel Award Scheme
Amount £4,500 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2016 
End 11/2016
 
Description Junior Scientist Travel Grant
Amount £750 (GBP)
Organisation The Genetics Society 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2016 
End 07/2016
 
Description Mapping for Conservation of Native Tilapia Resources in East Africa
Amount $264,100 (USD)
Organisation JRS Biodiversity Foundation 
Start 10/2017 
End 09/2020
 
Description Travel grant
Amount £780 (GBP)
Organisation The Fisheries Society of the British Isles 
Sector Learned Society
Country Unknown
Start 05/2016 
End 07/2016
 
Title Genotyping array to distinguish exotic and native species of tilapia 
Description A novel SNP panel generated from whole genome sequence data to accurately delimit native and introduced tilapia species in Tanzania 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact Verification of heredity/purity of fish farm and hatchery broodstock (results awaited) 
 
Description AgriFose partnership 
Organisation Swedish University of Agricultural Sciences
Country Sweden 
Sector Academic/University 
PI Contribution Participation in and presentation at Stakeholders workshop organised by AgriFose project team
Collaborator Contribution Involvement in Stakeholders workshop Knowledge transfer Support of future grant applications
Impact Workshop output
Start Year 2016
 
Description COSTECH partnership 
Organisation Commission for Science and Technology
Country Tanzania, United Republic of 
Sector Public 
PI Contribution Knowledge transfer
Collaborator Contribution Knowledge transfer
Impact Pending collaborative grant application to JRS Biodiversity Foundation
Start Year 2017
 
Description MALF partnership 
Organisation Ministry of Livestock and Fisheries Development
Country Tanzania, United Republic of 
Sector Public 
PI Contribution Knowledge exchange
Collaborator Contribution Knowledge exchange
Impact Support for pending grant applications Support for engagement and workshop activities
Start Year 2016
 
Description NARO collaboration 
Organisation National Agricultural Research Organisation
Country Uganda 
Sector Public 
PI Contribution Species identification Knowledge eschange Conference attendance
Collaborator Contribution Local knowledge exchange, surveys and sampling
Impact Preliminary species surveys and expanded geographical reach
Start Year 2015
 
Description NMK partnership 
Organisation National Museums of Kenya
Department Centre for Bee Biology and Pollination
Country Kenya 
Sector Public 
PI Contribution Knowledge sharing
Collaborator Contribution Knowledge sharing
Impact Pending collaborative grant application to JRS Biodiversity Foundation
Start Year 2017
 
Description SUA partnership 
Organisation Sokoine University of Agriculture
Country Tanzania, United Republic of 
Sector Academic/University 
PI Contribution Convening of training workshop, January 2017 Pending collaborative grant applications
Collaborator Contribution Logistical organisation for workshop, January 2017 Pending collaborative grant applications
Impact Collaborative grant application to JRS Biodiversity Foundation
Start Year 2016
 
Description Tilapia for sustainable fish production while maintaining Biodiversity 
Organisation Worldfish
Country Malaysia 
Sector Charity/Non Profit 
PI Contribution F. Di Palma is a research partner in the new CGIAR research program on fish agri-food systems.
Collaborator Contribution J. Benzie from WorldFish is a research partner on Earlham BBSRC Core Strategic programme "Genomics for Food Security" for the Natural diversity and adaptation in aquaculture research activities.
Impact Partnership yielded activities in Core strategic programmes and training workshops and further partnerships.I t is multidisciplinary including genomics, informatics, breeding expertise, Fisheries officers from tanzania, Ministry of aquaculture and Life stocks in Tanzania, further academic institutions in Tanzania Uk and Sweden, ecology, and environmental policy as well as disease resistance.
Start Year 2016
 
Description UDSM partnership 
Organisation University of Dar es Salaam
Country Tanzania, United Republic of 
Sector Academic/University 
PI Contribution Knowledge exchange, collaborative grant writing, supervision of postgraduate research students
Collaborator Contribution Knowledge exchange, collaborative grant writing
Impact New research projects and fieldwork to under-surveyed areas (Zanzibar and Pemba)
Start Year 2016
 
Description Aquaculture Stakeholders workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Involvement, session chairing and presentations given at "AgriFose Stakeholders' workshop on tilapia aquaculture in Tanzania and the way forward" workshop, Tanzania.
Discussions centred around opportunities and challenges for growing fisheries and aquaculture while preserving biodiversity.
Activity resulted in formation of an international consortium.
Year(s) Of Engagement Activity 2016
 
Description Aquaculture press release 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact Press release on aims of ongoing project.
Resulted in contact from: media outlets requesting further details; aquaculture stakeholders.
Year(s) Of Engagement Activity 2017
URL http://www.bbsrc.ac.uk/news/fundamental-bioscience/2017/170111-pr-double-fish-production-while-prese...
 
Description Bangor Science Festival 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact As part of the 'Hidden Worlds' experience during Bangor Science festival, we hosted tours of our research aquarium explaining about the rare native cichlid fish species we have been studying and outlining the importance of native tilapia genetic resources and the threats posed by stocking of exotic farmed strains.
Year(s) Of Engagement Activity 2018
URL https://www.bangor.ac.uk/bangorsciencefestival/events/hidden-worlds-exhibition-11585
 
Description Conference poster: Examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other audiences
Results and Impact Poster presentation on work on examining genetic diversity and traits under selection in several aquaculture-relevant tilapia species at Genome Science conference, Nottingham, UK.
Year(s) Of Engagement Activity 2018
 
Description Finding ways to double tilapia production article 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Article detailing aims of project.
Year(s) Of Engagement Activity 2017
URL http://theconversation.com/finding-ways-to-double-tilapia-production-in-tanzania-without-doing-damag...
 
Description Looking to aquaculture blog article 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Blog article on aims of the project.
Contact received from readers in Tanzania and Uganda
Year(s) Of Engagement Activity 2016
URL http://www.earlham.ac.uk/looking-aquaculture
 
Description MolecoFish Workshops 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact MolecoFish workshop in Dar Es Salaam to advice on policy issues relating to tilapia aquaculture. Produced a policy document. Accepted by Permanent Secretary at the Ministry of Livestock and Fisheries. Publicised via National TV and newspapers.
Year(s) Of Engagement Activity 2018
 
Description Morogoro Training workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Training workshop "Biodiversity, species identification, and stocking of non-native tilapiines" held at Sokoine University of Agriculture, Morogoro, Tanzania.
Speakers included UK project team alongside local Tanzania collaborators. Participants included fisheries officers, goverment officials, research staff from Tanzania Fisheries Research Institute, and industry representatives.
Year(s) Of Engagement Activity 2017
 
Description Operation Wallacea 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Schools
Results and Impact We presented talks, practical work and fieldwork activities for visiting groups of students from UK, China and Portugal, along with local school children from Tanzania as part of an Operation Wallacea field season. We covered issues arising from the project, namely the uniqueness of native populations of the local fishes and threats posed by stocking with farmed tilapia strains.
Year(s) Of Engagement Activity 2017
URL https://www.youtube.com/watch?v=pWXQJeVQk3g
 
Description Press release: Breeding diversity into the future of aquaculture 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact Press release on breeding diversity into the future of aquaculture in a popular well-read aquaculture magazine.
Year(s) Of Engagement Activity 2018
URL https://issuu.com/international_aquafeed/docs/iaf1801_w1/20
 
Description Research conference 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Conference presentation to graduate students & researchers
Year(s) Of Engagement Activity 2015
URL https://www.uni-graz.at/~sefck/CichlidScience/home.htm
 
Description Research presentation - FSBI oral presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Research presentation on preliminary results from genomic analysis
Year(s) Of Engagement Activity 2016
 
Description Research presentation at Genome 10K conference - Norwich, UK 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Research talk at Genome10K meeting
Year(s) Of Engagement Activity 2017
URL http://www.earlham.ac.uk/genome-10k-and-genome-science-conference
 
Description Research presentation at Newton Workshop: Detection and Prevention of biological invasions: A major challenge for human societies and biodiversity conservation 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Funded participation at the Newton Links Researcher workshop Detection and Prevention of biological invasions: A major challenge for human societies and biodiversity conservation
Year(s) Of Engagement Activity 2017
URL https://www.britishcouncil.org/workshop-detection-and-prevention-biological-invasions
 
Description Research presentation at the African Great Lakes Conference 2017 - Entebbe, Uganda 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact Research presentation on the project, including the TilapiaMap app development. New collaborations discussed, including the use of the app in other regions and feasibility of extending to other species and areas.
Year(s) Of Engagement Activity 2017
URL https://afrialliance.org/event/african-great-lakes-conference-2017/
 
Description Talk: A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Around 30 people from age range 5-60 attended a talk on "A kaleidoscope of colours, shapes and sustainable plates: diving into cichlid fish diversity" at the Norwich Science Festival. This sparked widespread questions and discussion afterwards and reported an all-round interest in the work and research carried out at Earlham Institute.
Year(s) Of Engagement Activity 2018
URL https://norwichsciencefestival.co.uk/events/water-day-gallery-stage/
 
Description Training workshop in Nairobi 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Mentoring workshop on research and use of TilapiaMap phone app
Year(s) Of Engagement Activity 2019