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Geraerts M, Vangestel C, Artois T, Fernandes JMDO, Jorissen MWP, Chocha Manda A, Danadu Mizani C, Smeets K, Snoeks J, Sonet G, Tingbao Y, Van Steenberge M, Vreven E, Lunkayilakio Wamuini S, Vanhove MPM, Huyse T. Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources. Mol Ecol 2022; 31:3304-3322. [PMID: 35460297 DOI: 10.1111/mec.16479] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/04/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.
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Affiliation(s)
- Mare Geraerts
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Carl Vangestel
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Terrestrial Ecology Unit, Ghent University, Ghent, Belgium
| | - Tom Artois
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Michiel W P Jorissen
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Auguste Chocha Manda
- Unité de recherche en Biodiversité et Exploitation durable des Zones Humides (BEZHU), Faculté des Sciences Agronomiques, Université de Lubumbashi, Lubumbashi, Democratic Republic of the Congo
| | - Célestin Danadu Mizani
- Département d'Ecologie et Biodiversité des Ressources Aquatique, Centre de Surveillance de la Biodiversité (CSB), Université de Kisangani, Kisangani, Democratic Republic of the Congo
| | - Karen Smeets
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Jos Snoeks
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Gontran Sonet
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Yang Tingbao
- Institute of Aquatic Economic Animals and Key Laboratory for Improved Variety Reproduction of Aquatic Economic Animals, Zhongshan University, Ghangzhou, China
| | - Maarten Van Steenberge
- OD Taxonomy and Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Emmanuel Vreven
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
| | - Soleil Lunkayilakio Wamuini
- Département de Biologie, I.S.P. Mbanza-Ngungu, Mbanza-Ngungu, Democratic Republic of the Congo.,Functional and Evolutionary Morphology Laboratory, University of Liège, Liège, Belgium
| | - Maarten P M Vanhove
- Research Group Zoology: Biodiversity and Toxicology, Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium.,Zoology Unit, Finnish Museum of Natural History, University of Helsinki, Helsinki, Finland.,Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tine Huyse
- Department of Biology, Royal Museum for Central Africa, Tervuren, Belgium.,Laboratory of Biodiversity and Evolutionary Genomics, KU Leuven, Leuven, Belgium
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Segev-Hadar A, Slosman T, Rozen A, Sherman A, Cnaani A, Biran J. Genome Editing Using the CRISPR-Cas9 System to Generate a Solid-Red Germline of Nile Tilapia ( Oreochromis niloticus). CRISPR J 2021; 4:583-594. [PMID: 34406049 DOI: 10.1089/crispr.2020.0115] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
In recent years, there has been increasing demand for red tilapia, which are commercial strains of hybrids of different tilapiine species or red variants of highly inbred Nile tilapia. However, red tilapia phenotypes are genetically unstable and affected by environmental factors, resulting in nonuniform coloration with black or dark-red color blotches that reduce their market value. Solute carrier family 45 member 2 (SLC45A2) is a membrane transporter that mediates melanin biosynthesis and is evolutionarily conserved from fish to humans. In the present study, we describe the generation of a stable and heritable red tilapia phenotype by inducing loss-of-function mutations in the slc45a2 gene. For this purpose, we identified the slc45a2 gene in Nile tilapia and designed highly specific guide RNAs (gRNA) for its genomic sequence. Multiplex microinjection of slc45a2-specific ribonucleoproteins to Nile tilapia zygotes induced up to 97-99% albinism, including loss of melanin in the eye. Next-generation sequencing of the injected zygotes demonstrated that all injected fish carried mutant alleles with variable mutagenesis efficiencies. Sanger sequencing of the genomic target region in the slc45a2 gene from fin clips, sperm, and F1 offspring of a highly mutant male identified various genomic indels and germline transmission of the sperm-identified indels. Overall, this work demonstrates the generation of somatic and germline slc45a2 mutant alleles, which leads to complete albinism in Nile tilapia.
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Affiliation(s)
- Adi Segev-Hadar
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel; and Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Tatiana Slosman
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel; and Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Ada Rozen
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Amir Sherman
- Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Avner Cnaani
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel; and Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
| | - Jakob Biran
- Department of Poultry and Aquaculture, Institute of Animal Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel; and Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon Lezion, Israel
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3
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Yáñez JM, Joshi R, Yoshida GM. Genomics to accelerate genetic improvement in tilapia. Anim Genet 2020; 51:658-674. [PMID: 32761644 DOI: 10.1111/age.12989] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 12/13/2022]
Abstract
Selective breeding of tilapia populations started in the early 1990s and over the past three decades tilapia has become one of the most important farmed freshwater species, being produced in more than 125 countries around the globe. Although genome assemblies have been available since 2011, most of the tilapia industry still depends on classical selection techniques using mass spawning or pedigree information to select for growth traits with reported genetic gains of up to 20% per generation. The involvement of international breeding companies and research institutions has resulted in the rapid development and application of genomic resources in the last few years. GWAS and genomic selection are expected to contribute to uncovering the genetic variants involved in economically relevant traits and increasing the genetic gain in selective breeding programs, respectively. Developments over the next few years will probably focus on achieving a deep understanding of genetic architecture of complex traits, as well as accelerating genetic progress in the selection for growth-, quality- and robustness-related traits. Novel phenotyping technologies (i.e. phenomics), lower-cost whole-genome sequencing approaches, functional genomics and gene editing tools will be crucial in future developments for the improvement of tilapia aquaculture.
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Affiliation(s)
- J M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago, 8820808, Chile.,Núcleo Milenio INVASAL, Casilla 160-C, Concepción, Chile
| | - R Joshi
- GenoMar Genetics AS, Bolette Brygge 1, Oslo, 0252, Norway
| | - G M Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Av Santa Rosa 11735, La Pintana, Santiago, 8820808, Chile
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Kim JE, Goo IB, Hwang JA, Kim HS, Choi HS, Lee JH. Genetic variability comparison of cultured Israeli carp (Cyprinus carpio) from Korea using microsatellites. Genes Genomics 2018; 40:635-642. [PMID: 29892945 DOI: 10.1007/s13258-018-0663-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/25/2018] [Indexed: 10/18/2022]
Abstract
In aquaculture, cultured fish often undergo continuous cross-fertilization without any inflow of new broodstock. This lowers genetic diversity, leading to increased disease rates and decreased survival rates. To improve the mass production and easy culture of Israeli carp, it is essential to investigate the population structure and genetic diversity of these fish. However, such a survey has not yet been performed on Korean Israeli carp. In this study, we used seven microsatellite markers to analyze the genetic diversity and association of cultured Israeli carp from Korea and China. The average numbers of alleles per locus (N A ) for two Korean (KorA and KorB) and two Chinese (ChA and ChB) populations were as follows: KorA (10.42), KorB (14.43), ChA (20.57) and ChB (20.71). The expected heterozygosity (H e ) ranged from 0.672 to 0.897 and from 0.827 to 0.938 in the Korean sample and Chinese sample respectively. The genetic diversity of the Korean Israeli carp was about half that of the Chinese carp. The diversity of the Korean Israeli carp was very low, suggesting that the immunity of this population could be weak, and that diversity-recovery studies are urgently needed. Therefore, our results may therefore form the foundation for future research efforts towards genetic monitoring and selective breeding, continuous research needs to be conducted in order to recover the genetic diversity of the Korean Israeli carp.
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Affiliation(s)
- Jung Eun Kim
- Inland Aquaculture Research Center, National Institute of Fisheries Science (NIFS), Changwon, 51688, South Korea
| | - In Bon Goo
- Inland Aquaculture Research Center, National Institute of Fisheries Science (NIFS), Changwon, 51688, South Korea
| | - Ju-Ae Hwang
- Inland Aquaculture Research Center, National Institute of Fisheries Science (NIFS), Changwon, 51688, South Korea
| | - Hyeong Su Kim
- Inland Aquaculture Research Center, National Institute of Fisheries Science (NIFS), Changwon, 51688, South Korea
| | - Hye-Sung Choi
- Southwest Sea Fisheries Research Institute, National Institute of Fisheries Science (NIFS), Yeosu, 59780, South Korea
| | - Jeong-Ho Lee
- Inland Aquaculture Research Center, National Institute of Fisheries Science (NIFS), Changwon, 51688, South Korea.
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Wang WL, Chen WH, Tian HY, Liu Y. Detection of Frozen-Thawed Cycles for Frozen Tilapia (Oreochromis) Fillets Using Near Infrared Spectroscopy. JOURNAL OF AQUATIC FOOD PRODUCT TECHNOLOGY 2018. [DOI: 10.1080/10498850.2018.1461156] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Wen-Li Wang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijng, PR China
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Wei-Hua Chen
- College of Food Science and Technology, Shanghai Ocean University, Shanghai, PR China
| | - Hong-Yu Tian
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology & Business University (BTBU), Beijng, PR China
| | - Yuan Liu
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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6
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Dias MAD, de Freitas RTF, Arranz SE, Villanova GV, Hilsdorf AWS. Evaluation of the genetic diversity of microsatellite markers among four strains of Oreochromis niloticus. Anim Genet 2016; 47:345-53. [PMID: 26932188 DOI: 10.1111/age.12423] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2016] [Indexed: 11/26/2022]
Abstract
Different strains of Nile tilapia can be found worldwide. To successfully use them in breeding programs, they must be genetically characterized. In this study, four strains of Nile tilapia - UFLA, GIFT, Chitralada and Red-Stirling - were genetically characterized using 10 noncoding microsatellite loci and two microsatellites located in the promoter and first intron of the growth hormone gene (GH). The two microsatellites in the GH gene were identified at positions -693 to -679 in the promoter [motif (ATTCT)8 ] and in intron 1 at positions +140 to +168 [motif (CTGT)7 ]. Genetic diversity was measured as mean numbers of alleles and expected heterozygosity, which were 4 and 0.60 (GIFT), 3.5 and 0.71 (UFLA), 4.5 and 0.57 (Chitralada) and 2.5 and 0.42 (Red-Stirling) respectively. Genetic differentiation was estimated both separately and in combination for noncoding and GH microsatellites markers using Jost's DEST index. The UFLA and GIFT strains were the least genetically divergent (DEST = 0.10), and Chitralada and Red-Stirling were the most (DEST = 0.58). The UFLA strain was genetically characterized for the first time and, because of its unique origin and genetic distinctness, may prove to be an important resource for genetic improvement of Nile tilapia. This study shows that polymorphisms found in coding gene regions might be useful for assessing genetic differentiation among strains.
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Affiliation(s)
- M A D Dias
- Depto. de Zootecnia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - R T F de Freitas
- Depto. de Zootecnia, Universidade Federal de Lavras, Lavras, Minas Gerais, Brazil
| | - S E Arranz
- Facultad de Ciencias Bioquímicas y Farmaceuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Area Biología, Universidad Nacional de Rosario, Rosario, Argentina
| | - G V Villanova
- Facultad de Ciencias Bioquímicas y Farmaceuticas, Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Area Biología, Universidad Nacional de Rosario, Rosario, Argentina
| | - A W S Hilsdorf
- Núcleo Integrado de Biotecnologia, Universidade de Mogi das Cruzes, Mogi das Cruzes, São Paulo, Brazil
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7
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Genetic diversity of invasive Oreochromis spp. (tilapia) populations in Guangdong province of China using microsatellite markers. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.03.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Mu X, Hu Y, Wang X, Song H, Yang Y, Luo J. Genetic Variability in Cultured Stocks of Scleropages formosus in Mainland China Revealed by Microsatellite Markers. ACTA ACUST UNITED AC 2011. [DOI: 10.3923/javaa.2011.555.561] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Granevitze Z, Hillel J, Chen GH, Cuc NTK, Feldman M, Eding H, Weigend S. Genetic diversity within chicken populations from different continents and management histories. Anim Genet 2007; 38:576-83. [DOI: 10.1111/j.1365-2052.2007.01650.x] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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