Please use this identifier to cite or link to this item: http://hdl.handle.net/1893/34812
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dc.contributor.authorBoschiero, Clarissaen_UK
dc.contributor.authorGheyas, Almas Aen_UK
dc.contributor.authorRalph, Hannah Ken_UK
dc.contributor.authorEory, Lelen_UK
dc.contributor.authorPaton, Boben_UK
dc.contributor.authorKuo, Richarden_UK
dc.contributor.authorFulton, Janeten_UK
dc.contributor.authorPreisinger, Rudolfen_UK
dc.contributor.authorKaiser, Peteen_UK
dc.contributor.authorBurt, David Wen_UK
dc.date.accessioned2023-02-10T01:00:20Z-
dc.date.available2023-02-10T01:00:20Z-
dc.date.issued2015-12en_UK
dc.identifier.other562en_UK
dc.identifier.urihttp://hdl.handle.net/1893/34812-
dc.description.abstractBackground Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of several modern layer chicken lines from diverse breeds. Results To reduce the error rates seen in InDel detection, this study used the consensus set from two InDel-calling packages: SAMtools and Dindel, as well as stringent post-filtering criteria. By analysing sequence data from 163 chickens from 11 commercial and 5 experimental layer lines, this study detected about 883 K high quality consensus InDels with 93 % validation rate and an average density of 0.78 InDels/kb over the genome. Certain chromosomes, viz, GGAZ, 16, 22 and 25 showed very low densities of InDels whereas the highest rate was observed on GGA6. In spite of the higher recombination rates on microchromosomes, the InDel density on these chromosomes was generally lower relative to macrochromosomes possibly due to their higher gene density. About 43–87 % of the InDels were found to be fixed within each line. The majority of detected InDels (86 %) were 1–5 bases and about 63 % were non-repetitive in nature while the rest were tandem repeats of various motif types. Functional annotation identified 613 frameshift, 465 non-frameshift and 10 stop-gain/loss InDels. Apart from the frameshift and stopgain/loss InDels that are expected to affect the translation of protein sequences and their biological activity, 33 % of the non-frameshift were predicted as evolutionary intolerant with potential impact on protein functions. Moreover, about 2.5 % of the InDels coincided with the most-conserved elements previously mapped on the chicken genome and are likely to define functional elements. InDels potentially affecting protein function were found to be enriched for certain gene-classes e.g. those associated with cell proliferation, chromosome and Golgi organization, spermatogenesis, and muscle contraction. Conclusions The large catalogue of InDels presented in this study along with their associated information such as functional annotation, estimated allele frequency, etc. are expected to serve as a rich resource for application in future research and breeding in the chicken.en_UK
dc.language.isoenen_UK
dc.publisherSpringer Science and Business Media LLCen_UK
dc.relationBoschiero C, Gheyas AA, Ralph HK, Eory L, Paton B, Kuo R, Fulton J, Preisinger R, Kaiser P & Burt DW (2015) Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes. <i>BMC Genomics</i>, 16, Art. No.: 562. https://doi.org/10.1186/s12864-015-1711-1en_UK
dc.rightsThis 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 use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.en_UK
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en_UK
dc.subjectDindelen_UK
dc.subjectSAMtoolsen_UK
dc.subjectFalse discovery rateen_UK
dc.subjectInDelen_UK
dc.subjectLayer chickenen_UK
dc.subjectLoss-of-function mutationen_UK
dc.subjectNext generation sequencingen_UK
dc.titleDetection and characterization of small insertion and deletion genetic variants in modern layer chicken genomesen_UK
dc.typeJournal Articleen_UK
dc.identifier.doi10.1186/s12864-015-1711-1en_UK
dc.identifier.pmid26227840en_UK
dc.citation.jtitleBMC Genomicsen_UK
dc.citation.issn1471-2164en_UK
dc.citation.volume16en_UK
dc.citation.publicationstatusPublisheden_UK
dc.citation.peerreviewedRefereeden_UK
dc.type.statusVoR - Version of Recorden_UK
dc.contributor.funderBiotechnology and Biological Sciences Research Councilen_UK
dc.contributor.funderDepartment for Environment Food & Rural Affairsen_UK
dc.author.emailalmas.gheyas@stir.ac.uken_UK
dc.citation.date31/07/2015en_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.affiliationHy-Lineen_UK
dc.contributor.affiliationLohmann Tierzucht GmbHen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.contributor.affiliationRoslin Instituteen_UK
dc.identifier.isiWOS:000358760400001en_UK
dc.identifier.scopusid2-s2.0-84938067109en_UK
dc.identifier.wtid1831202en_UK
dc.contributor.orcid0000-0002-7682-4394en_UK
dc.date.accepted2015-06-22en_UK
dcterms.dateAccepted2015-06-22en_UK
dc.date.filedepositdate2023-02-08en_UK
rioxxterms.apcnot requireden_UK
rioxxterms.typeJournal Article/Reviewen_UK
rioxxterms.versionVoRen_UK
local.rioxx.authorBoschiero, Clarissa|en_UK
local.rioxx.authorGheyas, Almas A|0000-0002-7682-4394en_UK
local.rioxx.authorRalph, Hannah K|en_UK
local.rioxx.authorEory, Lel|en_UK
local.rioxx.authorPaton, Bob|en_UK
local.rioxx.authorKuo, Richard|en_UK
local.rioxx.authorFulton, Janet|en_UK
local.rioxx.authorPreisinger, Rudolf|en_UK
local.rioxx.authorKaiser, Pete|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.filenames12864-015-1711-1.pdfen_UK
local.rioxx.filecount1en_UK
local.rioxx.source1471-2164en_UK
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