Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/34813
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dc.contributor.authorGheyas, Almas Aen_UK
dc.contributor.authorBoschiero, Clarissaen_UK
dc.contributor.authorEory, Lelen_UK
dc.contributor.authorRalph, Hannahen_UK
dc.contributor.authorKuo, Richarden_UK
dc.contributor.authorWoolliams, John Aen_UK
dc.contributor.authorBurt, David Wen_UK
dc.date.accessioned2023-02-10T01:00:39Z-
dc.date.available2023-02-10T01:00:39Z-
dc.date.issued2015-06en_UK
dc.identifier.urihttp://hdl.handle.net/1893/34813-
dc.description.abstractNext-generation sequencing has prompted a surge of discovery of millions of genetic variants from vertebrate genomes. Besides applications in genetic association and linkage studies, a fraction of these variants will have functional consequences. This study describes detection and characterization of 15 million SNPs from chicken genome with the goal to predict variants with potential functional implications (pfVars) from both coding and non-coding regions. The study reports: 183K amino acid-altering SNPs of which 48% predicted as evolutionary intolerant, 13K splicing variants, 51K likely to alter RNA secondary structures, 500K within most conserved elements and 3K from non-coding RNAs. Regions of local fixation within commercial broiler and layer lines were investigated as potential selective sweeps using genome-wide SNP data. Relationships with phenotypes, if any, of the pfVars were explored by overlaying the sweep regions with known QTLs. Based on this, the candidate genes and/or causal mutations for a number of important traits are discussed. Although the fixed variants within sweep regions were enriched with non-coding SNPs, some non-synonymous-intolerant mutations reached fixation, suggesting their possible adaptive advantage. The results presented in this study are expected to have important implications for future genomic research to identify candidate causal mutations and in poultry breeding.en_UK
dc.language.isoenen_UK
dc.publisherOxford University Press (OUP)en_UK
dc.relationGheyas AA, Boschiero C, Eory L, Ralph H, Kuo R, Woolliams JA & Burt DW (2015) Functional classification of 15 million SNPs detected from diverse chicken populations. <i>DNA Research</i>, 22 (3), pp. 205-217. https://doi.org/10.1093/dnares/dsv005en_UK
dc.rights© The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.en_UK
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_UK
dc.subjectSNPen_UK
dc.subjectnext-generation sequencingen_UK
dc.subjectchickenen_UK
dc.subjectselection signatureen_UK
dc.subjectfunctional variantsen_UK
dc.titleFunctional classification of 15 million SNPs detected from diverse chicken populationsen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1093/dnares/dsv005en_UK
dc.identifier.pmid25926514en_UK
dc.citation.jtitleDNA Researchen_UK
dc.citation.issn1756-1663en_UK
dc.citation.issn1340-2838en_UK
dc.citation.volume22en_UK
dc.citation.issue3en_UK
dc.citation.spage205en_UK
dc.citation.epage217en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderDepartment for Environment Food & Rural Affairsen_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.author.emailalmas.gheyas@stir.ac.uken_UK
dc.citation.date29/04/2015en_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.identifier.isiWOS:000356658900003en_UK
dc.identifier.scopusid2-s2.0-84931064883en_UK
dc.identifier.wtid1831194en_UK
dc.contributor.orcid0000-0002-7682-4394en_UK
dc.date.accepted2015-03-20en_UK
dcterms.dateAccepted2015-03-20en_UK
dc.date.filedepositdate2023-02-08en_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
rioxxterms.versionVoRen_UK
local.rioxx.authorGheyas, Almas A|0000-0002-7682-4394en_UK
local.rioxx.authorBoschiero, Clarissa|en_UK
local.rioxx.authorEory, Lel|en_UK
local.rioxx.authorRalph, Hannah|en_UK
local.rioxx.authorKuo, Richard|en_UK
local.rioxx.authorWoolliams, John A|en_UK
local.rioxx.authorBurt, David W|en_UK
local.rioxx.projectProject ID unknown|Biotechnology and Biological Sciences Research Council|http://dx.doi.org/10.13039/501100000268en_UK
local.rioxx.projectProject ID unknown|Department for Environment Food & Rural Affairs|en_UK
local.rioxx.freetoreaddate2023-02-08en_UK
local.rioxx.licencehttp://creativecommons.org/licenses/by/4.0/|2023-02-08|en_UK
local.rioxx.filenamedsv005.pdfen_UK
local.rioxx.filecount1en_UK
local.rioxx.source1756-1663en_UK
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