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Highâ throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections
dc.contributor.authorKlein, Laura L.
dc.contributor.authorMiller, Allison J.
dc.contributor.authorCiotir, Claudia
dc.contributor.authorHyma, Katie
dc.contributor.authorUribe‐convers, Simon
dc.contributor.authorLondo, Jason
dc.date.accessioned2018-04-04T18:47:05Z
dc.date.available2019-04-01T15:01:10Zen
dc.date.issued2018-02
dc.identifier.citationKlein, Laura L.; Miller, Allison J.; Ciotir, Claudia; Hyma, Katie; Uribe‐convers, Simon ; Londo, Jason (2018). "Highâ throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections." American Journal of Botany 105(2): 215-226.
dc.identifier.issn0002-9122
dc.identifier.issn1537-2197
dc.identifier.urihttps://hdl.handle.net/2027.42/142889
dc.publisherCRC Press
dc.publisherWiley Periodicals, Inc.
dc.subject.otherVitaceae
dc.subject.othergenotypingâ byâ sequencing
dc.subject.othergermplasm
dc.subject.othergrapevine
dc.subject.otherphylogenomics
dc.subject.otherVitis
dc.titleHighâ throughput sequencing data clarify evolutionary relationships among North American Vitis species and improve identification in USDA Vitis germplasm collections
dc.typeArticleen_US
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelBiology
dc.subject.hlbsecondlevelBotany
dc.subject.hlbtoplevelScience
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/142889/1/ajb21033_am.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/142889/2/ajb21033.pdf
dc.identifier.doi10.1002/ajb2.1033
dc.identifier.sourceAmerican Journal of Botany
dc.identifier.citedreferencePetit, R. J., and A. Hampe. 2006. Some evolutionary consequences of being a tree. Annual Review of Ecology, Evolution, and Systematics 37 ( 1 ): 187 â 214.
dc.identifier.citedreferenceMoore, M.O., and J. Wen. 2016. Vitaceae. In Flora of North America Editioral Committee [eds.], Flora of North America North of Mexico, Vol. 12. Oxford University Press, New York, New York, USA.
dc.identifier.citedreferenceMullins, M. G., A. Bouquet, and L. E. Williams. 1992. The grapevine and its wild relatives. In M. G. Mullins, A. Bouquet, and L. E. Williams [eds.], Biology of the grapevine. Cambridge University Press, Cambridge, United Kingdom.
dc.identifier.citedreferenceMunson, T.V. 1909. Foundations of American Grape Culture. Orange Judd Company.
dc.identifier.citedreferenceMyles, S., A. R. Boyko, C. L. Owens, P. J. Brown, F. Grassi, M. K. Aradhya, B. Prins, et al. 2011. Genetic structure and domestication history of the grape. Proceedings of the National Academy of Sciences 108 ( 9 ): 3530 â 3535.
dc.identifier.citedreferenceNational Research Council. 1991. US Committee on Managing Global Genetic Resources: Agricultural Imperatives. Managing Global Genetic Resources: The U.S. National Plant Germplasm System. Washington (DC): National Academies Press, USA. Available from: https://www.ncbi.nlm.nih.gov/books/NBK235638/.
dc.identifier.citedreferenceOllitrault, P., A. Garciaâ Lor, J. Terol, F. Curk, F. Ollitrault, M. Talon, and L. Navarro. 2015. Comparative values of SSRs, SNPs and InDels for citrus genetic diversity analysis. Acta Horticulturae, 1065: 457 â 466.
dc.identifier.citedreferencePéros, J. P., G. Berger, A. Portemont, J. M. Boursiquot, and T. Lacombe. 2011. Genetic variation and biogeography of the disjunct Vitis subg. Vitis (Vitaceae). Journal of Biogeography 38 ( 3 ): 471 â 486.
dc.identifier.citedreferencePoland, J. A., and T. W. Rife. 2012. Genotypingâ byâ sequencing for plant breeding and genetics. The Plant Genome 5 ( 3 ): 92 â 102.
dc.identifier.citedreferencePurcell, S., B. Neale, K. Toddâ Brown, L. Thomas, M. A. R. Ferreira, D. Bender, J. Maller, et al. 2007. PLINK: a toolset for wholeâ genome association and populationâ based linkage analysis. American Journal of Human Genetics 81: 559 â 575.
dc.identifier.citedreferenceR Core Team ( 2013 ) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. Website: http://www.R-project.org/.
dc.identifier.citedreferenceRen, H., and J. Wen. 2007. Vitis. In Z. Y. Wu, P. H. Raven, and D. Y. Hong [eds.], Flora of China. vol 12. Missouri Botanical Garden Press, St Louis, Missouri, USA.
dc.identifier.citedreferenceRokas, A., B. L. Williams, N. King, and S. B. Carroll. 2003. Genomeâ scale approaches to resolving incongruence in molecular phylogenies. Nature 425 ( 6960 ): 798.
dc.identifier.citedreferenceSawler, J., J.M. Stout., K.M. Gardner, D. Hudson, J. Vidmar, L. Butler, J.E. Page, and S. Myles. 2015. The genetic structure of marijuana and hemp. PloS One 10 ( 8 ): e0133292.
dc.identifier.citedreferenceSmith, S. A., and C. Dunn. 2008. Phyutility: a phyloinformatics utility for trees, alignments, and molecular data. Bioinformatics 24: 715 â 716.
dc.identifier.citedreferenceSoltis, P. S., D. E. Soltis, and M. W. Chase. 1999. Angiosperm phylogeny inferred from multiple genes as a tool for comparative biology. Nature 402 ( 6760 ): 402.
dc.identifier.citedreferenceStamatakis, A. 2014. RAxML Version 8: A tool for phylogenetic analysis and postâ analysis of large phylogenies. Bioinformatics 30 ( 9 ): 1312 â 1313.
dc.identifier.citedreferenceTerral, J. F., E. Tabard, L. Bouby, S. Ivorra, T. Pastor, I. Figueiral, S. Picq, et al. 2009. Evolution and history of grapevine ( Vitis vinifera ) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars. Annals of Botany 105 ( 3 ): 443 â 455.
dc.identifier.citedreferenceTröndle, D., Schröder S., H.H. Kassemeyer, C. Kiefer, M.A. Koch, and P. Nick. 2010. Molecular phylogeny of the genus Vitis (Vitaceae) based on plastid markers. American Journal of Botany 97 ( 7 ): 1168 â 1178.
dc.identifier.citedreferenceUribeâ Convers, S., M.L. Settles, and D.C. Tank. 2016. A phylogenomic approach based on PCR target enrichment and high throughput sequencing: Resolving the diversity within the South American species of Bartsia L. (Orobanchaceae). PloS One 11 ( 2 ): e0148203.
dc.identifier.citedreferenceWan, Y., H.R. Schwaninger, A.M. Baldo, J.A. Labate, G.â Y. Zhong, and C.J. Simon. 2013. A phylogenetic analysis of the grape genus ( Vitis L.) reveals broad reticulation and concurrent diversification during neogene and quaternary climate change. BMC Evolutionary Biology 13: 1 â 20.
dc.identifier.citedreferenceWarschefsky, E.J., L.L. Klein, M.H. Frank, D.H. Chitwood, J.P. Londo, von Wettberg E.J.B., and A.J. Miller. 2016. Rootstocks: diversity, domestication, and impacts on shoot phenotypes. Trends in Plant Science 21 ( 5 ): 418 â 437.
dc.identifier.citedreferenceWen, J., Z.L. Nie, A. Soejima, and Y. Meng. 2007. Phylogeny of Vitaceae based on the nuclear GAI1 gene sequences. Canadian Journal of Botany 85 ( 8 ): 731 â 745.
dc.identifier.citedreferenceWickham, H. 2009. Ggplot2: elegant graphics for data analysis. Springer Science & Business Media, Berlin. https://doi.org/10.1007/978-0-387-98141-3.
dc.identifier.citedreferenceZecca, G., J.R. Abbott, W.B. Sun, A. Spada, F. Sala, and F. Grassi. 2012. The timing and the mode of evolution of wild grapes ( Vitis ). Molecular Phylogenetics and Evolution 62 ( 2 ): 736 â 747.
dc.identifier.citedreferenceZhang, N., J. Wen, and E.A. Zimmer. 2015. Expression patterns of AP1, FUL, FT and LEAFY orthologs in Vitaceae support the homology of tendrils and inflorescences throughout the grape family. Journal of Systematics and Evolution 53 ( 5 ): 469 â 476.
dc.identifier.citedreferenceZohary, D., and P. Spiegelâ Roy. 1975. Beginnings of fruit growing in the old world. Science 187: 319 â 327.
dc.identifier.citedreferenceAdamâ Blondon, A. F., O. Jaillon, S. Vezzulli, A. Zharkikh, M. Troggio, R. Velasco, and J. Martinezâ Zapater. 2011. Genome sequence initiatives. In A. F. Adamâ Blondon, J. M. Martinezâ Zapater, and C. Kole [eds.], Genetics, Genomics, and Breeding of Grapes, 211 â 234. CRC Press, Boca Raton, Florida, USA.
dc.identifier.citedreferenceBailey, L. H. 1934. The species of grapes peculiar to North America. Gentes Herbarum 3: 151 â 244.
dc.identifier.citedreferenceBarakat, A., M. Staton, C. H. Cheng, J. Park, N. M. B. Yassin, S. Ficklin, C. C. Yeh, et al. 2012. Chestnut resistance to the blight disease: insights from transcriptome analysis. BMC Plant Biology 12: 38.
dc.identifier.citedreferenceBielenberg, D. G., B. Rauh, S. Fan, K. Gasic, A. G. Abbott, G. L. Reighard, W. R. Okie, and C. E. Wells. 2015. Genotyping by sequencing for SNPâ based linkage map construction and QTL analysis of chilling requirement and bloom date in peach [ Prunus persica (L.) Batsch]. PloS One 10 ( 10 ): e0139406.
dc.identifier.citedreferenceCadleâ Davidson, L. 2008. Variation Within and between Vitis spp. for Foliar Resistance to the Downy Mildew Pathogen Plasmopara viticola. Plant Disease 92 ( 11 ): 1577 â 1584.
dc.identifier.citedreferenceCadleâ Davidson, L., D. R. Chicoine, and N. H. Consolie. 2011. Variation within and among Vitis spp. for foliar resistance to the powdery mildew pathogen Erysiphe necator. Plant Disease 95 ( 2 ): 202 â 211.
dc.identifier.citedreferenceCallen, S. T., L. L. Klein, and A. J. Miller. 2016. Climatic niche characterization of 13 North American Vitis species. American Journal of Enology and Viticulture 67: 339 â 349.
dc.identifier.citedreferenceCavenderâ Bares, J., A. Gonzálezâ Rodríguez, D. A. R. Eaton, A. A. L. Hipp, A. Beulke, and P. S. Manos. 2015. Phylogeny and biogeography of the American live oaks ( Quercus subsection Virentes ): A genomic and population genetics approach. Molecular Ecology 24 ( 14 ): 3668 â 3687.
dc.identifier.citedreferenceChifman, J., and L. Kubatko. 2014. Quartet inference from SNP data under the coalescent model. Bioinformatics 30 ( 23 ): 3317 â 3324.
dc.identifier.citedreferenceChifman, J., and L. Kubatko. 2015. Identifiability of the unrooted species tree topology under the coalescent model with timeâ reversible substitution processes, siteâ specific rate variation, and invariable sites. Journal of Theoretical Biology 374: 35 â 47.
dc.identifier.citedreferenceChitwood, D. H., L. L. Klein, R. O’Hanlon, S. Chacko, M. Greg, C. Kitchen, A. J. Miller, and J. P. Londo. 2016a. Latent developmental and evolutionary shapes embedded within the grapevine leaf. New Phytologist 210 ( 1 ): 343 â 355.
dc.identifier.citedreferenceChitwood, D. H., A. Ranjan, C. C. Martinez, L. R. Headland, T. Thiem, R. Kumar, M. F. Covington, et al. 2014. A modern ampelography: a genetic basis for leaf shape and venation patterning in grape. Plant Physiology 164 ( 1 ): 259 â 272.
dc.identifier.citedreferenceChitwood, D. H., S. M. Rundell, D. Y. Li, Q. L. Woodford, T. T. Yu, J. R. Lopez, D. Greenblatt, et al. 2016b. Climate and developmental plasticity: interannual variability in grapevine leaf morphology. Plant Physiology 170 ( 3 ): 1825 â 2015.
dc.identifier.citedreferenceClark, A. G., M. J. Hubisz, C. D. Bustamante, S. H. Williamson, and R. Nielsen. 2005. Ascertainment bias in studies of human genomeâ wide polymorphism. Genome Research 15 ( 11 ): 1496 â 1502.
dc.identifier.citedreferenceCook, B. I., and E. M. Wolkovich. 2016. Climate change decouples drought from early wine grape harvests in France. Nature Climate Change 6 ( 7 ): 715 â 719.
dc.identifier.citedreferenceDanecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks, M. A. DePristo, R. Handsaker, et al. 2011. The Variant Call Format and VCFtools. Bioinformatics 27 ( 15 ): 2156 â 2158.
dc.identifier.citedreferenceDavey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen, and M. L. Blaxter. 2011. Genomeâ wide genetic marker discovery and genotyping using nextâ generation sequencing. Nature Reviews Genetics 12 ( 7 ): 499 â 510.
dc.identifier.citedreferenceDavid, B., R. Bouckaert, J. Felsenstein, N. A. Rosenberg, and A. R. Choudhury. 2012. Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis. Molecular Biology and Evolution 29 ( 8 ): 1917 â 1932.
dc.identifier.citedreferenceDempewolf, H., G. Baute, J. Anderson, B. Kilian, C. Smith, and L. Guarino. 2017. Past and future use of wild relatives in crop breeding. Crop Science 57 ( 3 ): 1070 â 1082.
dc.identifier.citedreferenceDrummond, A. J., M. A. Suchard, D. Xie, and A. Rambaut. 2012. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Molecular Biology and Evolution 29: 1969 â 1973.
dc.identifier.citedreferenceElshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto, E. S. Buckler, and S. E. Mitchell. 2011. A robust, simple genotypingâ byâ sequencing (GBS) approach for high diversity species. PloS One 6 ( 5 ): e19379.
dc.identifier.citedreferenceFielder, H., P. Brotherton, J. Hosking, J. J. Hopkins, B. Fordâ Lloyd, and N. Maxted. 2015. Enhancing the conservation of crop wild relatives in England. PloS One 10 ( 6 ): e0130804.
dc.identifier.citedreferenceGalet, P. 1979. A Practical Ampelography. Cornell University Press, Ithaca, New York, USA.
dc.identifier.citedreferenceGalet, P. 1988. Cépages et vignobles de France. Tome 1. Les vignes Américaines, 2nd ed. Pierre Galet, Montpellier, France.
dc.identifier.citedreferenceGlaubitz, J., T. Casstevens, F. Lu, J. Harriman, R. Elshire, Q. Sun, and E. Buckler. 2014. TASSELâ GBS: A High Capacity Genotyping by Sequencing Analysis Pipeline. PloS One 9 ( 2 ): e90346.
dc.identifier.citedreferenceGross, B. L., C. M. Richards, P. A. Reeves, A. D. Henk, P. L. Forsline, A. Szewcâ McFadden, G. Fazio, and C. T. Chao. 2013. Diversity Captured in the USDAâ ARS National Plant Germplasm System Apple Core Collection. Journal of the American Society for Horticultural Science 138 ( 5 ): 375 â 381.
dc.identifier.citedreferenceHannah, L., P.R. Roehrdanz, M. Ikegami, A.V. Shepard, M.R. Shaw, G. Tabor, L. Zhi, et al. 2013. Climate change, wine, and conservation. Proceedings of the National Academy of Sciences 110 ( 17 ): 6907 â 6912.
dc.identifier.citedreferenceHe, J., X. Zhao, A. Laroche, Z.X. Lu, H. Liu, and Z. Li. 2014. Genotypingâ byâ sequencing (GBS), an ultimate markerâ assisted selection (MAS) tool to accelerate plant breeding. Frontiers in Plant Science 5: 1 â 8.
dc.identifier.citedreferenceHipp, A. L., D. A. R. Eaton, J. Cavenderâ Bares, E. Fitzek, R. Nipper, and P. S. Manos. 2014. A framework phylogeny of the American Oak clade based on sequenced RAD data. PloS One 9 ( 4 ): e93975.
dc.identifier.citedreferenceHyma, K., P. Barba, M. Wang, J. Londo, C. Acharya, S. Mitchell, Q. Sun, et al. 2015. Heterozygous mapping strategy (HetMappS) for high resolution genotypingâ byâ sequencing markers: A case study in grapevine. PloS One 10 ( 8 ): e0134880.
dc.identifier.citedreferenceJaillon, O., J.â M. Aury, B. Noel, N. Choisne, C. Jubin, C. Dasilva, J. Poulain, et al. 2007. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449 ( 7161 ): 463 â 467.
dc.identifier.citedreferenceKearse, M., R. Moir, A. Wilson, S. Stonesâ Havas, M. Cheung, S. Sturrock, S. Buxton, et al. 2012. Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28 ( 12 ): 1647 â 1649.
dc.identifier.citedreferenceKliman, T. 2010. The Wild Vine: A Forgotten Grape and the Untold Story of American Wwine. Broadway Books, New York, New York, USA.
dc.identifier.citedreferenceLeaché, A. D., B. L. Banbury, J. Felsenstein, A. N. M. de Oca, and A. Stamatakis. 2015. Short tree, long tree, right tree, wrong tree: new acquisition bias corrections for inferring SNP phylogenies. Systematic Biology 64 ( 6 ): 1032 â 1047.
dc.identifier.citedreferenceLi, H., and R. Durbin. 2009. Fast and accurate short read alignment with Burrowsâ Wheeler transform. Bioinformatics 25 ( 14 ): 1754 â 1760.
dc.identifier.citedreferenceLiu, X. Q., S. M. Ickertâ Bond, Z. L. Nie, Z. Zhou, L. Q. Chen, and J. Wen. 2016. Phylogeny of the Ampelocissus â Vitis clade in Vitaceae supports the New World origin of the grape genus. Molecular Phylogenetics and Evolution 95: 217 â 228.
dc.identifier.citedreferenceMcAllister, C. A., and A. J. Miller. 2016. SNP discovery via genotypingâ byâ sequencing for assessment of population genetic structure and recurrent polyploidization in big bluestem ( Andropogon gerardii ). American Journal of Botany. 103: 1326 â 1335.
dc.identifier.citedreferenceMcKey, D., M. Elias, B. Pujol, and A. Duputié. 2010. The evolutionary ecology of clonally propagated domesticated plants. New Phytologist 186: 318 â 332.
dc.identifier.citedreferenceMigicovsky, Z., and S. Myles. 2017. Exploiting wild relatives for genomicsâ assisted breeding of perennial crops. Frontiers in Plant Science 8: 460.
dc.identifier.citedreferenceMigicovsky, Z., J. Sawler, K. M. Gardner, M. K. Aradhya, B. H. Prins, H. R. Schwaninger, C. D. Bustamante, et al. 2017. Patterns of genomic and phenomic diversity in wine and table grapes. Horticulture Research 4: 17035.
dc.identifier.citedreferenceMigicovsky, Z., J. Sawler, D. Money, R. Eibach, A. J. Miller, J. J. Luby, A. R. Jamieson, et al. 2016. Genomic ancestry estimation quantifies use of wild species in grape breeding. BMC Genomics 17 ( 1 ): 478.
dc.identifier.citedreferenceMiller, A. J., and B. L. Gross. 2011. From forest to field: perennial fruit crop domestication. American Journal of Botany 98 ( 9 ): 1389 â 1414.
dc.identifier.citedreferenceMiller, A.J., N. Matasci, H. Schwaninger, M.K. Aradhya, B. Prins, G.â Y. Zhong, C. Simon, et al. 2013. Vitis phylogenomics: hybridization intensities from a SNP array outperform genotype calls. PloS One 8 ( 11 ): e78680.
dc.identifier.citedreferenceMiller, M.A., W. Pfeiffer, and T. Schwartz. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees in Proceedings of the Gateway Computing Environments Workshop (GCE), 14 Nov. New Orleans, Louisiana, USA.
dc.identifier.citedreferenceMoore, M.O., 1991. Classification and systematics of eastern North American Vitis L. (Vitaceae) north of Mexico. SIDA Contributions to Botany 14 ( 3 ): 339 â 367.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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