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dc.creatorHamilton, M.G.en_US
dc.creatorMekkawy, W.en_US
dc.creatorBenzie, J.en_US
dc.creatorKilian, A.en_US
dc.date.accessioned2019-06-28T07:10:06Z
dc.date.available2019-06-28T07:10:06Z
dc.date.issued2019
dc.identifier.citationMatthew Hamilton, Wagdy Mekkawy, John Benzie, Andrzej Kilian. (19/6/2019). Single Nucleotide Polymorphisms (SNPs) reveal sibship among founders of a Bangladeshi Rohu (Labeo rohita) breeding population. Frontiers in Genetics, Article 597(10).en_US
dc.identifier.issn1664-8021en_US
dc.identifier.urihttps://hdl.handle.net/20.500.12348/3634
dc.description.abstractRohu (Labeo rohita) is a significant freshwater aquaculture species with approximately 1.8 Mt produced annually. Fin clips obtained from the founders of a newly established Bangladesh-based breeding population (∼140 fish from each of the Halda, Jamuna, and Padma rivers) were used to identify 9157 SNPs and 14 411 silicoDArT markers using the Diversity Arrays Technology (DArT) genotyping-by-sequencing platform known as DArTseq. After quality control, 1985 SNPs were retained and used to examine population structure within and among river systems. Examination of genomic relationships revealed evidence of full- and half-sibling relationships among founders. Accordingly, sibship and dummy parents were assigned within each river population using a maximum likelihood approach with COLONY software. Founders that had no dummy parents in common were then identified for population genetic analyses. Only 40 unique dummy parents and 17 founders with no common dummy parents were identified from the Halda river, compared with 206 (96) from the Jamuna and 184 (83) from the Padma. Overall pairwise FST estimates among rivers were low (<0.005) and the optimum number of clusters using unsupervised K-means clustering was one, indicating little genetic divergence among the river populations in our SNPs. These results suggest that observed sibship among founders should be accounted for in future pedigree-based analyses and it cannot be assumed that fertilized spawn collections are representative samples of river populations.en_US
dc.languageenen_US
dc.publisherFrontiers Mediaen_US
dc.rightsCC-BY-4.0en_US
dc.sourceFrontiers in Genetics;Article 597,(2019)en_US
dc.subjectgenotyping-by-sequencingen_US
dc.subjectparentage assignmenten_US
dc.subjectgenomic relationshipen_US
dc.subjectadditive genetic relationshipen_US
dc.subjectsilicodart markeren_US
dc.subjectFishen_US
dc.titleSingle Nucleotide Polymorphisms (SNPs) reveal sibship among founders of a Bangladeshi Rohu (Labeo rohita) breeding populationen_US
dc.typeJournal Articleen_US
cg.contributor.crpFISHen_US
cg.contributor.funderUnited States Agency for International Developmenten_US
cg.coverage.countryBangladeshen_US
cg.coverage.regionSouthern Asiaen_US
cg.subject.agrovocsingle nucleotide polymorphismen_US
cg.subject.agrovoccarpen_US
cg.subject.agrovoccyprinidaeen_US
cg.contributor.affiliationWorldFishen_US
cg.contributor.affiliationDiversity Arrays Technology Pty Ltden_US
cg.identifier.statusOpen accessen_US
cg.identifier.ISIindexedISI indexeden_US
cg.contribution.worldfishauthorHamilton, M.G.en_US
cg.contribution.worldfishauthorMekkawy, W.en_US
cg.contribution.worldfishauthorBenzie, J.en_US
cg.description.themeSustainable aquacultureen_US
dc.identifier.doi10.3389/fgene.2019.00597en_US
cg.identifier.urlhttps://mel.cgiar.org/reporting/download/hash/147ff3ce4c8ef9a98ce4e4d3707a1dceen_US
cg.creator.idMatthew Gray Hamilton: 0000-0001-8098-8845en_US


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