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dc.contributor.authorMarand, Alexandre P.en_US
dc.contributor.authorJansky, Shelley H.en_US
dc.contributor.authorZhao, Hainanen_US
dc.contributor.authorLeisner, Courtney P.en_US
dc.contributor.authorZhu, Xiaobiaoen_US
dc.contributor.authorZeng, Zixianen_US
dc.contributor.authorCrisovan, Emilyen_US
dc.contributor.authorNewton, Linseyen_US
dc.contributor.authorHamernik, Andy J.en_US
dc.contributor.authorVeilleux, Richard E.en_US
dc.contributor.authorBuell, C. Robinen_US
dc.contributor.authorJiang, Jimingen_US
dc.date.accessioned2018-01-05T18:57:10Z
dc.date.available2018-01-05T18:57:10Z
dc.date.issued2017-10-30en_US
dc.identifier.issn1474-760Xen_US
dc.identifier.urihttp://hdl.handle.net/10919/81547
dc.description.abstractBackground: Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers. Results: Using a whole genome sequencing-based approach, we developed two high-density reference-based haplotype maps using diploid potato clones as parents. The vast majority (81%) of meiotic crossovers were mapped to less than 5 kb. The fine-scale accuracy of crossover detection was validated by Sanger sequencing for a subset of ten crossover events. We demonstrate that crossovers reside in genomic regions of “open chromatin”, which were identified based on hypersensitivity to DNase I digestion and association with H3K4me3-modified nucleosomes. The genomic regions spanning crossovers were significantly enriched with the Stowaway family of miniature inverted-repeat transposable elements (MITEs). The occupancy of Stowaway elements in gene promoters is concomitant with an increase in recombination rate. A generalized linear model identified the presence of Stowaway elements as the third most important genomic or chromatin feature behind genes and open chromatin for predicting crossover formation over 10-kb windows. Conclusions: Collectively, our results suggest that meiotic crossovers in potato are largely determined by the local chromatin status, marked by accessible chromatin, H3K4me3-modified nucleosomes, and the presence of Stowaway transposons.en_US
dc.format.extent? - ? (16) page(s)en_US
dc.languageEnglishen_US
dc.publisherBiomed Central Ltden_US
dc.relation.urihttp://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000413970000001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=930d57c9ac61a043676db62af60056c1en_US
dc.rightsCreative Commons Attribution 4.0 International (CC BY 4.0)*
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectBiotechnology & Applied Microbiologyen_US
dc.subjectGenetics & Heredityen_US
dc.subjectRECOMBINATION RATE VARIATIONen_US
dc.subjectHUMAN GENOMEen_US
dc.subjectHOT-SPOTSen_US
dc.subjectSACCHAROMYCES-CEREVISIAEen_US
dc.subjectANALYSIS TOOLKITen_US
dc.subjectHOTSPOTSen_US
dc.subjectARABIDOPSISen_US
dc.subjectGENEen_US
dc.subjectDROSOPHILAen_US
dc.subjectELEMENTSen_US
dc.titleMeiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potatoen_US
dc.typeArticle - Refereed
dc.description.versionPublished (Publication status)en_US
dc.rights.holderThe Author(s).
dc.title.serialGENOME BIOLOGYen_US
dc.identifier.doihttps://doi.org/10.1186/s13059-017-1326-8
dc.identifier.volume18en_US
pubs.organisational-group/Virginia Tech
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Faculty
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Horticulture
pubs.organisational-group/Virginia Tech/All T&R Faculty
pubs.organisational-group/Virginia Tech/University Research Institutes
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Fralin Affiliated Faculty


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Creative Commons Attribution 4.0 International (CC BY 4.0)
License: Creative Commons Attribution 4.0 International (CC BY 4.0)