A reference genome assembly and adaptive trait analysis of Castanea mollissima 'Vanuxem,' a source of resistance to chestnut blight in restoration breeding

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dc.contributor.authorStaton, Margareten
dc.contributor.authorAddo-Quaye, Charlesen
dc.contributor.authorCannon, Nathanielen
dc.contributor.authorYu, Jialien
dc.contributor.authorZhebentyayeva, Tetyanaen
dc.contributor.authorHuff, Matthewen
dc.contributor.authorIslam-Faridi, Nurulen
dc.contributor.authorFan, Shenghuaen
dc.contributor.authorGeorgi, Laura L.en
dc.contributor.authorNelson, C. Danaen
dc.contributor.authorBellis, Emilyen
dc.contributor.authorFitzsimmons, Saraen
dc.contributor.authorHenry, Nathanen
dc.contributor.authorDrautz-Moses, Danielaen
dc.contributor.authorNoorai, Rooksana E.en
dc.contributor.authorFicklin, Stephenen
dc.contributor.authorSaski, Christopheren
dc.contributor.authorMandal, Mihir Kumaren
dc.contributor.authorWagner, Tyler K.en
dc.contributor.authorZembower, Nicoleen
dc.contributor.authorBodenes, Catherineen
dc.contributor.authorHolliday, Jason A.en
dc.contributor.authorWestbrook, Jared W.en
dc.contributor.authorLasky, Jesseen
dc.contributor.authorHebard, Frederick, Ven
dc.contributor.authorSchuster, Stephan C.en
dc.contributor.authorAbbott, Albert G.en
dc.contributor.authorCarlson, John E.en
dc.contributor.departmentForest Resources and Environmental Conservationen
dc.date.accessioned2021-03-16T12:13:39Zen
dc.date.available2021-03-16T12:13:39Zen
dc.date.issued2020-07-23en
dc.description.abstractForest tree species are increasingly subject to severe mortalities from exotic pests, pathogens, and invasive organisms, accelerated by climate change. Such forest health issues are threatening multiple species and ecosystem sustainability globally. One of the most extreme examples of forest ecosystem disruption is the extirpation of the American chestnut (Castanea dentata) caused by the introduction of chestnut blight and root rot pathogens from Asia. Asian species of chestnut are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of a reference genome for Chinese chestnut (C. mollissima) "Vanuxem," one of the donors of disease resistance for American chestnut restoration. From the de novo assembly of the complete genome (725.2 Mb in 14,110 contigs), over half of the sequences have been anchored to the 12 genetic linkage groups. The anchoring is validated by genetic maps and in situ hybridization to chromosomes. We demonstrate the value of the genome as a platform for research and species restoration, including signatures of selection differentiating American chestnut from Chinese chestnut to identify important candidate genes for disease resistance, comparisons of genome organization with other woody species, and a genome-wide examination of progress in backcross breeding for blight resistance. This reference assembly should prove of great value in the understanding, improvement, and restoration of chestnut species.en
dc.description.adminPublic domain – authored by a U.S. government employeeen
dc.description.notesThis project was funded by the Forest Health Initiative (https://foresthealthinitiative.org/) through grant #137RFP#2008-011 to JEC. Support was also provided by the United States Department of Agriculture (USDA) National Institute of Food and Agriculture grant 2016-67013-24581 to The American Chestnut Foundation. Additional support was provided through several grants-inaid to JEC fromThe American Chestnut Foundation and to JEC andMES through the USDA National Institute of Food and Agriculture Federal Appropriations under Project PEN04532 (Accession number 1000326) and NE-1833, respectively. Construction of saturated genetic maps and root RNAseq dataset was partially supported by the Foundation for the Carolinas. Bioinformatics was supported by National Science Foundation (NSF) Award #1444573, "Standards and Cyberinfrastructure that Enable 'Big-Data' Driven Discovery for Tree Crop Research" (MES; PI Main). Emily Bellis was supported by NSF Postdoctoral Research Fellowships in Biology Grant No. 1711950. Rooksana Noorai was supported by an Institutional Development Award (IDeA) from the National Institute of GeneralMedical Sciences of the National Institutes of Health under grant number P20GM109094.en
dc.description.sponsorshipForest Health Initiative [137RFP, 2008-011]; United States Department of Agriculture (USDA) National Institute of Food and AgricultureUnited States Department of Agriculture (USDA) [2016-67013-24581]; USDA National Institute of Food and Agriculture Federal Appropriations [PEN04532, 1000326, NE-1833]; Foundation for the Carolinas; National Science Foundation (NSF)National Science Foundation (NSF) [1444573]; NSF Postdoctoral Research Fellowships in Biology Grant [1711950]; Institutional Development Award (IDeA) from the National Institute of GeneralMedical Sciences of the National Institutes of HealthUnited States Department of Health & Human ServicesNational Institutes of Health (NIH) - USA [P20GM109094]; American Chestnut Foundationen
dc.format.mimetypeapplication/pdfen
dc.identifier.doihttps://doi.org/10.1007/s11295-020-01454-yen
dc.identifier.eissn1614-2950en
dc.identifier.issn1614-2942en
dc.identifier.issue4en
dc.identifier.other57en
dc.identifier.urihttp://hdl.handle.net/10919/102723en
dc.identifier.volume16en
dc.language.isoenen
dc.rightsPublic Domainen
dc.rights.urihttp://creativecommons.org/publicdomain/mark/1.0/en
dc.subjectChestnuten
dc.subjectGenomeen
dc.subjectIn situ hybridizationen
dc.subjectDisease resistanceen
dc.subjectChestnut blighten
dc.subjectPhytophthora root roten
dc.titleA reference genome assembly and adaptive trait analysis of Castanea mollissima 'Vanuxem,' a source of resistance to chestnut blight in restoration breedingen
dc.title.serialTree Genetics & Genomesen
dc.typeArticle - Refereeden
dc.type.dcmitypeTexten
dc.type.dcmitypeStillImageen

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