Species-Specific Marker Discovery in Tilapia

Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site a...

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Autores principales:	Mochamad Syaifudin, Michaël Bekaert, John B. Taggart, Kerry L. Bartie, Stefanie Wehner, Christos Palaiokostas, M. G. Q. Khan, Sarah-Louise C. Selly, Gideon Hulata, Helena D’Cotta, Jean-Francois Baroiller, Brendan J. McAndrew, David J. Penman
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2019
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6a5d9a9175b040aaa41063eed2a4d5a1
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spelling	oai:doaj.org-article:6a5d9a9175b040aaa41063eed2a4d5a12021-12-02T15:08:10ZSpecies-Specific Marker Discovery in Tilapia10.1038/s41598-019-48339-22045-2322https://doaj.org/article/6a5d9a9175b040aaa41063eed2a4d5a12019-09-01T00:00:00Zhttps://doi.org/10.1038/s41598-019-48339-2https://doaj.org/toc/2045-2322Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.Mochamad SyaifudinMichaël BekaertJohn B. TaggartKerry L. BartieStefanie WehnerChristos PalaiokostasM. G. Q. KhanSarah-Louise C. SellyGideon HulataHelena D’CottaJean-Francois BaroillerBrendan J. McAndrewDavid J. PenmanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 9, Iss 1, Pp 1-11 (2019)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Mochamad Syaifudin Michaël Bekaert John B. Taggart Kerry L. Bartie Stefanie Wehner Christos Palaiokostas M. G. Q. Khan Sarah-Louise C. Selly Gideon Hulata Helena D’Cotta Jean-Francois Baroiller Brendan J. McAndrew David J. Penman Species-Specific Marker Discovery in Tilapia
description	Abstract Tilapias (family Cichlidae) are of importance in aquaculture and fisheries. Hybridisation and introgression are common within tilapia genera but are difficult to analyse due to limited numbers of species-specific genetic markers. We tested the potential of double digested restriction-site associated DNA (ddRAD) sequencing for discovering single nucleotide polymorphism (SNP) markers to distinguish between 10 tilapia species. Analysis of ddRAD data revealed 1,371 shared SNPs in the de novo-based analysis and 1,204 SNPs in the reference-based analysis. Phylogenetic trees based on these two analyses were very similar. A total of 57 species-specific SNP markers were found among the samples analysed of the 10 tilapia species. Another set of 62 species-specific SNP markers was identified from a subset of four species which have often been involved in hybridisation in aquaculture: 13 for Oreochromis niloticus, 23 for O. aureus, 12 for O. mossambicus and 14 for O. u. hornorum. A panel of 24 SNPs was selected to distinguish among these four species and validated using 91 individuals. Larger numbers of SNP markers were found that could distinguish between the pairs of species within this subset. This technique offers potential for the investigation of hybridisation and introgression among tilapia species in aquaculture and in wild populations.
format	article
author	Mochamad Syaifudin Michaël Bekaert John B. Taggart Kerry L. Bartie Stefanie Wehner Christos Palaiokostas M. G. Q. Khan Sarah-Louise C. Selly Gideon Hulata Helena D’Cotta Jean-Francois Baroiller Brendan J. McAndrew David J. Penman
author_facet	Mochamad Syaifudin Michaël Bekaert John B. Taggart Kerry L. Bartie Stefanie Wehner Christos Palaiokostas M. G. Q. Khan Sarah-Louise C. Selly Gideon Hulata Helena D’Cotta Jean-Francois Baroiller Brendan J. McAndrew David J. Penman
author_sort	Mochamad Syaifudin
title	Species-Specific Marker Discovery in Tilapia
title_short	Species-Specific Marker Discovery in Tilapia
title_full	Species-Specific Marker Discovery in Tilapia
title_fullStr	Species-Specific Marker Discovery in Tilapia
title_full_unstemmed	Species-Specific Marker Discovery in Tilapia
title_sort	species-specific marker discovery in tilapia
publisher	Nature Portfolio
publishDate	2019
url	https://doaj.org/article/6a5d9a9175b040aaa41063eed2a4d5a1
work_keys_str_mv	AT mochamadsyaifudin speciesspecificmarkerdiscoveryintilapia AT michaelbekaert speciesspecificmarkerdiscoveryintilapia AT johnbtaggart speciesspecificmarkerdiscoveryintilapia AT kerrylbartie speciesspecificmarkerdiscoveryintilapia AT stefaniewehner speciesspecificmarkerdiscoveryintilapia AT christospalaiokostas speciesspecificmarkerdiscoveryintilapia AT mgqkhan speciesspecificmarkerdiscoveryintilapia AT sarahlouisecselly speciesspecificmarkerdiscoveryintilapia AT gideonhulata speciesspecificmarkerdiscoveryintilapia AT helenadcotta speciesspecificmarkerdiscoveryintilapia AT jeanfrancoisbaroiller speciesspecificmarkerdiscoveryintilapia AT brendanjmcandrew speciesspecificmarkerdiscoveryintilapia AT davidjpenman speciesspecificmarkerdiscoveryintilapia
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Species-Specific Marker Discovery in Tilapia

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