Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato

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dc.contributor.authorMarand, Alexandre P.en
dc.contributor.authorJansky, Shelley H.en
dc.contributor.authorZhao, Hainanen
dc.contributor.authorLeisner, Courtney P.en
dc.contributor.authorZhu, Xiaobiaoen
dc.contributor.authorZeng, Zixianen
dc.contributor.authorCrisovan, Emilyen
dc.contributor.authorNewton, Linseyen
dc.contributor.authorHamernik, Andy J.en
dc.contributor.authorVeilleux, Richard E.en
dc.contributor.authorBuell, C. Robinen
dc.contributor.authorJiang, Jimingen
dc.contributor.departmentFralin Life Sciences Instituteen
dc.contributor.departmentSchool of Plant and Environmental Sciencesen
dc.date.accessioned2018-01-05T18:57:10Zen
dc.date.available2018-01-05T18:57:10Zen
dc.date.issued2017-10-30en
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
dc.description.versionPublished versionen
dc.format.extent16 pagesen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1186/s13059-017-1326-8en
dc.identifier.issn1474-760Xen
dc.identifier.urihttp://hdl.handle.net/10919/81547en
dc.identifier.volume18en
dc.language.isoenen
dc.publisherBiomed Centralen
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
dc.rightsCreative Commons Attribution 4.0 Internationalen
dc.rights.holderThe Author(s)en
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/en
dc.subjectBiotechnology & Applied Microbiologyen
dc.subjectGenetics & Heredityen
dc.subjectRECOMBINATION RATE VARIATIONen
dc.subjectHUMAN GENOMEen
dc.subjectHOT-SPOTSen
dc.subjectSACCHAROMYCES-CEREVISIAEen
dc.subjectANALYSIS TOOLKITen
dc.subjectHOTSPOTSen
dc.subjectARABIDOPSISen
dc.subjectGENEen
dc.subjectDROSOPHILAen
dc.subjectELEMENTSen
dc.titleMeiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potatoen
dc.title.serialGenome Biologyen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
pubs.organisational-group/Virginia Techen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciencesen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/CALS T&R Facultyen
pubs.organisational-group/Virginia Tech/Agriculture & Life Sciences/Horticultureen
pubs.organisational-group/Virginia Tech/All T&R Facultyen
pubs.organisational-group/Virginia Tech/University Research Institutesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciencesen
pubs.organisational-group/Virginia Tech/University Research Institutes/Fralin Life Sciences/Fralin Affiliated Facultyen

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