Please use this identifier to cite or link to this item:
Full metadata record
DC FieldValueLanguage
dc.contributor.advisorMcAndrew, Brendan-
dc.contributor.advisorPenman, David-
dc.contributor.authorSyaifudin, Mochamad-
dc.description.abstractThe tilapias are a group of African and Middle Eastern cichlid fish that are widely cultured in developed and developing countries. With many different species and sub-species, and extensive use of interspecies hybrids, identification of tilapia species is of importance in aquaculture and in wild populations where introductions occur. This research set out to distinguish between tilapia species and sub-species by retrieving species-specific nuclear DNA markers (SNPs) using two approaches: (i) sequencing of the coding regions of the ADA gene; and (ii) next-generation sequencing, both standard RADseq and double-digest RADseq (ddRADseq). The mitochondrial DNA (mtDNA) marker cytochrome c oxidase subunit I (COI) was used to verify tilapia species status. ADA gene sequence analysis was partially successful, generating SNP markers that distinguished some species pairs. Most species could also be discriminated using the COI sequence. Reference based analysis (RBA: using only markers found in the O. niloticus genome sequence) of standard RADseq data identified 1,613 SNPs in 1,002 shared RAD loci among seven species. De novo based analysis (DBA: based on the entire data set) identified 1,358 SNPs in 825 loci and RBA detected 938 SNPs in 571 shared RAD loci from ddRADseq among 10 species. Phylogenetic trees based on shared SNP markers indicated similar patterns to most prior phylogenies based on other characteristics. The standard RADseq detected 677 species-specific SNP markers from the entire data set (seven species), while the ddRADseq retrieved 38 (among ten species). Furthermore, 37 such SNP markers were identified from ddRADseq data from a subset of four economically important species which are often involved in hybridization in aquaculture, and larger numbers of SNP markers distinguished between species pairs in this group. In summary, these SNPs are a valuable resource in further investigating hybridization and introgression in a range of captive and wild stocks of tilapias.en_GB
dc.publisherUniversity of Stirlingen_GB
dc.subjectDNA markersen_GB
dc.subjectSingle Nucleotide Polymorphism (SNP)en_GB
dc.subjectAdenosine deaminase (ADA) geneen_GB
dc.subjectTilapia speciesen_GB
dc.subjectRAD sequencingen_GB
dc.subject.lcshAdenosine deaminaseen_GB
dc.subject.lcshGene targetingen_GB
dc.subject.lcshMarine biotechnologyen_GB
dc.subject.lcshFishes Geneticsen_GB
dc.titleSpecies-specific DNA Markers for Improving the Genetic Management of Tilapiaen_GB
dc.typeThesis or Dissertationen_GB
dc.type.qualificationnameDoctor of Philosophyen_GB
dc.contributor.funder1. Director General of Higher Education, Ministry of Research, Technology and Higher Education (Kemenristek Dikti), Indonesia; 2. MASTS pooling initiative (The Marine Alliance for Science and Technology for Scotland). MASTS is funded by the Scottish Funding Council (grant reference HR09011).en_GB
Appears in Collections:Aquaculture eTheses

Files in This Item:
File Description SizeFormat 
Thesis_M_Syaifudin_final +DJPedits_noncolour.pdfPhDThesis_M.Syaifudin_September20155.57 MBAdobe PDFView/Open

This item is protected by original copyright

Items in the Repository are protected by copyright, with all rights reserved, unless otherwise indicated.

The metadata of the records in the Repository are available under the CC0 public domain dedication: No Rights Reserved

If you believe that any material held in STORRE infringes copyright, please contact providing details and we will remove the Work from public display in STORRE and investigate your claim.