Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris)

Dohm JC, Lange C, Holtgräwe D, Rosleff Sörensen T, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H (2012)
The Plant Journal 70(3): 528-540.

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ; ; ; ; ; ;
Abstract
Sugar beet (Beta vulgaris) is an important crop plant accounting for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons, and genomic characterization of sugar beet is essential in order to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps covering all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map comprising 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map we hybridized gene-derived oligomer probes against two BAC libraries with 9.5 fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs containing 8361 probes and 22,815 BAC clones. By using the gene order established with the physical map we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species involving 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet enabling future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species. © 2011 The Authors. The Plant Journal© 2011 Blackwell Publishing Ltd.
Publishing Year
ISSN
PUB-ID

Cite this

Dohm JC, Lange C, Holtgräwe D, et al. Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris). The Plant Journal. 2012;70(3):528-540.
Dohm, J. C., Lange, C., Holtgräwe, D., Rosleff Sörensen, T., Borchardt, D., Schulz, B., Lehrach, H., et al. (2012). Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris). The Plant Journal, 70(3), 528-540.
Dohm, J. C., Lange, C., Holtgräwe, D., Rosleff Sörensen, T., Borchardt, D., Schulz, B., Lehrach, H., Weisshaar, B., and Himmelbauer, H. (2012). Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris). The Plant Journal 70, 528-540.
Dohm, J.C., et al., 2012. Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris). The Plant Journal, 70(3), p 528-540.
J.C. Dohm, et al., “Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris)”, The Plant Journal, vol. 70, 2012, pp. 528-540.
Dohm, J.C., Lange, C., Holtgräwe, D., Rosleff Sörensen, T., Borchardt, D., Schulz, B., Lehrach, H., Weisshaar, B., Himmelbauer, H.: Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris). The Plant Journal. 70, 528-540 (2012).
Dohm, Juliane C., Lange, Cornelia, Holtgräwe, Daniela, Rosleff Sörensen, Thomas, Borchardt, Dietrich, Schulz, Britta, Lehrach, Hans, Weisshaar, Bernd, and Himmelbauer, Heinz. “Palaeohexaploid Ancestry for Caryophyllales Inferred from Extensive Gene-Based Physical and Genetic Mapping of the Sugar Beet Genome (Beta vulgaris)”. The Plant Journal 70.3 (2012): 528-540.
This data publication is cited in the following publications:
This publication cites the following data publications:

13 Citations in Europe PMC

Data provided by Europe PubMed Central.

A major QTL corresponding to the Rk locus for resistance to root-knot nematodes in cowpea (Vigna unguiculata L. Walp.).
Huynh BL, Matthews WC, Ehlers JD, Lucas MR, Santos JR, Ndeve A, Close TJ, Roberts PA., Theor. Appl. Genet. 129(1), 2016
PMID: 26450274
SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications.
Iquebal MA, Jaiswal S, Angadi UB, Sablok G, Arora V, Kumar S, Rai A, Kumar D., Database (Oxford) 2015(), 2015
PMID: 26647370
Exploiting single-molecule transcript sequencing for eukaryotic gene prediction.
Minoche AE, Dohm JC, Schneider J, Holtgrawe D, Viehover P, Montfort M, Sorensen TR, Weisshaar B, Himmelbauer H., Genome Biol. 16(), 2015
PMID: 26328666
Lineage-specific gene radiations underlie the evolution of novel betalain pigmentation in Caryophyllales.
Brockington SF, Yang Y, Gandia-Herrero F, Covshoff S, Hibberd JM, Sage RF, Wong GK, Moore MJ, Smith SA., New Phytol. 207(4), 2015
PMID: 25966996
Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing.
Yang Y, Moore MJ, Brockington SF, Soltis DE, Wong GK, Carpenter EJ, Zhang Y, Chen L, Yan Z, Xie Y, Sage RF, Covshoff S, Hibberd JM, Nelson MN, Smith SA., Mol. Biol. Evol. 32(8), 2015
PMID: 25837578
Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris).
Holtgrawe D, Sorensen TR, Viehover P, Schneider J, Schulz B, Borchardt D, Kraft T, Himmelbauer H, Weisshaar B., PLoS ONE 9(10), 2014
PMID: 25302600
Genome-wide identification and characterisation of R2R3-MYB genes in sugar beet (Beta vulgaris).
Stracke R, Holtgrawe D, Schneider J, Pucker B, Sorensen TR, Weisshaar B., BMC Plant Biol. 14(), 2014
PMID: 25249410
The B2 flowering time locus of beet encodes a zinc finger transcription factor.
Dally N, Xiao K, Holtgrawe D, Jung C., Proc. Natl. Acad. Sci. U.S.A. 111(28), 2014
PMID: 24965366
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
Dohm JC, Minoche AE, Holtgrawe D, Capella-Gutierrez S, Zakrzewski F, Tafer H, Rupp O, Sorensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldon T, Lehrach H, Weisshaar B, Himmelbauer H., Nature 505(7484), 2014
PMID: 24352233
Unusual and typical features of a novel restorer-of-fertility gene of sugar beet (Beta vulgaris L.).
Matsuhira H, Kagami H, Kurata M, Kitazaki K, Matsunaga M, Hamaguchi Y, Hagihara E, Ueda M, Harada M, Muramatsu A, Yui-Kurino R, Taguchi K, Tamagake H, Mikami T, Kubo T., Genetics 192(4), 2012
PMID: 22997236
Evolutionary reshuffling in the Errantivirus lineage Elbe within the Beta vulgaris genome.
Wollrab C, Heitkam T, Holtgrawe D, Weisshaar B, Minoche AE, Dohm JC, Himmelbauer H, Schmidt T., Plant J. 72(4), 2012
PMID: 22804913
The role of a pseudo-response regulator gene in life cycle adaptation and domestication of beet.
Pin PA, Zhang W, Vogt SH, Dally N, Buttner B, Schulze-Buxloh G, Jelly NS, Chia TY, Mutasa-Gottgens ES, Dohm JC, Himmelbauer H, Weisshaar B, Kraus J, Gielen JJ, Lommel M, Weyens G, Wahl B, Schechert A, Nilsson O, Jung C, Kraft T, Muller AE., Curr. Biol. 22(12), 2012
PMID: 22608508

38 References

Data provided by Europe PubMed Central.

Mapping and sequencing complex genomes: let's get physical!
Meyers BC, Scalabrin S, Morgante M., Nat. Rev. Genet. 5(8), 2004
PMID: 15266340
Algorithms and software tools for ordering clone libraries: application to the mapping of the genome of Schizosaccharomyces pombe.
Mott R, Grigoriev A, Maier E, Hoheisel J, Lehrach H., Nucleic Acids Res. 21(8), 1993
PMID: 8493107
Sequence-based physical mapping of complex genomes by whole genome profiling.
van Oeveren J, de Ruiter M, Jesse T, van der Poel H, Tang J, Yalcin F, Janssen A, Volpin H, Stormo KE, Bogden R, van Eijk MJ, Prins M., Genome Res. 21(4), 2011
PMID: 21324881
A linkage map of sugar beet (Beta vulgaris L.).
Pillen K, Steinrucken G, Wricke G, Herrmann RG, Jung C., Theor. Appl. Genet. 84(1/2), 1992
PMID: IND92056176
Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals.
Salse J, Abrouk M, Bolot S, Guilhot N, Courcelle E, Faraut T, Waugh R, Close TJ, Messing J, Feuillet C., Proc. Natl. Acad. Sci. U.S.A. 106(35), 2009
PMID: 19706486
Genome sequence of the palaeopolyploid soybean.
Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA., Nature 463(7278), 2010
PMID: 20075913
Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes.
Schneider K, Kulosa D, Soerensen TR, Mohring S, Heine M, Durstewitz G, Polley A, Weber E, Jamsari , Lein J, Hohmann U, Tahiro E, Weisshaar B, Schulz B, Koch G, Jung C, Ganal M., Theor. Appl. Genet. 115(5), 2007
PMID: 17622508
Integration of AFLP markers into a linkage map of sugar beet (Beta vulgaris L.).
Schondelmaier J, Steinrucken G, Jung C., Plant Breed. 115(4), 1996
PMID: IND20559576
Synteny and collinearity in plant genomes.
Tang H, Bowers JE, Wang X, Ming R, Alam M, Paterson AH., Science 320(5875), 2008
PMID: 18436778
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps.
Tang H, Wang X, Bowers JE, Ming R, Alam M, Paterson AH., Genome Res. 18(12), 2008
PMID: 18832442
The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
Tuskan GA, Difazio S, Jansson S, Bohlmann J, Grigoriev I, Hellsten U, Putnam N, Ralph S, Rombauts S, Salamov A, Schein J, Sterck L, Aerts A, Bhalerao RR, Bhalerao RP, Blaudez D, Boerjan W, Brun A, Brunner A, Busov V, Campbell M, Carlson J, Chalot M, Chapman J, Chen GL, Cooper D, Coutinho PM, Couturier J, Covert S, Cronk Q, Cunningham R, Davis J, Degroeve S, Dejardin A, Depamphilis C, Detter J, Dirks B, Dubchak I, Duplessis S, Ehlting J, Ellis B, Gendler K, Goodstein D, Gribskov M, Grimwood J, Groover A, Gunter L, Hamberger B, Heinze B, Helariutta Y, Henrissat B, Holligan D, Holt R, Huang W, Islam-Faridi N, Jones S, Jones-Rhoades M, Jorgensen R, Joshi C, Kangasjarvi J, Karlsson J, Kelleher C, Kirkpatrick R, Kirst M, Kohler A, Kalluri U, Larimer F, Leebens-Mack J, Leple JC, Locascio P, Lou Y, Lucas S, Martin F, Montanini B, Napoli C, Nelson DR, Nelson C, Nieminen K, Nilsson O, Pereda V, Peter G, Philippe R, Pilate G, Poliakov A, Razumovskaya J, Richardson P, Rinaldi C, Ritland K, Rouze P, Ryaboy D, Schmutz J, Schrader J, Segerman B, Shin H, Siddiqui A, Sterky F, Terry A, Tsai CJ, Uberbacher E, Unneberg P, Vahala J, Wall K, Wessler S, Yang G, Yin T, Douglas C, Marra M, Sandberg G, Van de Peer Y, Rokhsar D., Science 313(5793), 2006
PMID: 16973872
More genomic resources for less-studied crops.
Varshney RK, Glaszmann JC, Leung H, Ribaut JM., Trends Biotechnol. 28(9), 2010
PMID: 20692061

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 22211633
PubMed | Europe PMC

Search this title in

Google Scholar