Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes

Schneider K, Kulosa D, Rosleff Sörensen T, Möhring S, Heine M, Durstewitz G, Polley A, Weber E, Jamsari n.a., Lein J, Hohmann U, et al. (2007)
Theoretical and Applied Genetics 115(5): 601-615.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
DOI
Autor*in
Schneider, Katharina; Kulosa, Dagmar; Rosleff Sörensen, ThomasUniBi; Möhring, Silke; Heine, Martin; Durstewitz, Gregor; Polley, Andreas; Weber, Eberhard; Jamsari, n.a.; Lein, Jens; Hohmann, Uwe; Tahiro, Emma
Alle
Einrichtung
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Fakultät für Biologie > Genetik und Genomik der Pflanzen
Centrum für Biotechnologie > Arbeitsgruppe B. Weisshaar
Abstract / Bemerkung
A panel of 13 sugar beet lines and one genotype each of the Beta vulgaris cultivars red beet and Swiss chard, and B. vulgaris ssp. maritima were used to identify polymorphisms in alignments of genomic DNA sequences derived from 315 EST- and 43 non-coding RFLP-derived loci. In sugar beet lines, loci of expressed genes showed an average SNP frequency of 1/72 bp, 1 in 58 bp in non-coding sequences, increasing to 1/47 bp upon the addition of the remaining genotypes. Within analysed DNA fragments, alleles at different SNP positions displayed linkage disequilibrium indicative of haplotype structures. On average 2.7 haplotypes were found in sugar beet lines, and haplotype conservation in expressed genes appeared to exceed 500 bp in length. Seven different genotyping techniques including SNP detection by MALDI-TOF mass spectrometry, pyrosequencing and fluorescence scanning of labelled nucleotides were employed to perform 712 segregation analyses for 538 markers in three F2 populations. Functions were predicted for 492 mapped sequences. Genetic maps comprised 305 loci covering 599.8 cM in population K1, 241 loci distributed over 636.6 cM in population D2, and 166 loci over 507.1 cM in population K2, respectively. Based on 156 markers common to more than one population an integrated map was constructed with 524 loci covering 664.3 cM. For 377 loci the genome positions of the most similar sequences from A. thaliana were identified, but little evidence for previously presented ancestral genome structures was found.
Erscheinungsjahr
2007
Zeitschriftentitel
Theoretical and Applied Genetics
Band
115
Ausgabe
5
Seite(n)
601-615
ISSN
0040-5752
eISSN
1432-2242
Page URI
https://pub.uni-bielefeld.de/record/1632708

Zitieren

Schneider K, Kulosa D, Rosleff Sörensen T, et al. Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics. 2007;115(5):601-615.
Schneider, K., Kulosa, D., Rosleff Sörensen, T., Möhring, S., Heine, M., Durstewitz, G., Polley, A., et al. (2007). Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics, 115(5), 601-615. https://doi.org/10.1007/s00122-007-0591-4
Schneider, Katharina, Kulosa, Dagmar, Rosleff Sörensen, Thomas, Möhring, Silke, Heine, Martin, Durstewitz, Gregor, Polley, Andreas, et al. 2007. “Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes”. Theoretical and Applied Genetics 115 (5): 601-615.
Schneider, K., Kulosa, D., Rosleff Sörensen, T., Möhring, S., Heine, M., Durstewitz, G., Polley, A., Weber, E., Jamsari, n.a., Lein, J., et al. (2007). Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics 115, 601-615.
Schneider, K., et al., 2007. Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics, 115(5), p 601-615.
K. Schneider, et al., “Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes”, Theoretical and Applied Genetics, vol. 115, 2007, pp. 601-615.
Schneider, K., Kulosa, D., Rosleff Sörensen, T., Möhring, S., Heine, M., Durstewitz, G., Polley, A., Weber, E., Jamsari, n.a., Lein, J., Hohmann, U., Tahiro, E., Weisshaar, B., Schulz, B., Koch, G., Jung, C., Ganal, M.: Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theoretical and Applied Genetics. 115, 601-615 (2007).
Schneider, Katharina, Kulosa, Dagmar, Rosleff Sörensen, Thomas, Möhring, Silke, Heine, Martin, Durstewitz, Gregor, Polley, Andreas, Weber, Eberhard, Jamsari, n.a., Lein, Jens, Hohmann, Uwe, Tahiro, Emma, Weisshaar, Bernd, Schulz, Britta, Koch, Georg, Jung, Christian, and Ganal, Martin. “Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes”. Theoretical and Applied Genetics 115.5 (2007): 601-615.

30 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Report on the development of putative functional SSR and SNP markers in passion fruits.
da Costa ZP, Munhoz CF, Vieira MLC., BMC Res Notes 10(1), 2017
PMID: 28874179
Exploring potential of pearl millet germplasm association panel for association mapping of drought tolerance traits.
Sehgal D, Skot L, Singh R, Srivastava RK, Das SP, Taunk J, Sharma PC, Pal R, Raj B, Hash CT, Yadav RS., PLoS One 10(5), 2015
PMID: 25970600
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris).
Dohm JC, Minoche AE, Holtgräwe D, Capella-Gutiérrez S, Zakrzewski F, Tafer H, Rupp O, Sörensen TR, Stracke R, Reinhardt R, Goesmann A, Kraft T, Schulz B, Stadler PF, Schmidt T, Gabaldón T, Lehrach H, Weisshaar B, Himmelbauer H., Nature 505(7484), 2014
PMID: 24352233
The B2 flowering time locus of beet encodes a zinc finger transcription factor.
Dally N, Xiao K, Holtgräwe D, Jung C., Proc Natl Acad Sci U S A 111(28), 2014
PMID: 24965366
Genetic analysis of bolting after winter in sugar beet (Beta vulgaris L.).
Pfeiffer N, Tränkner C, Lemnian I, Grosse I, Müller AE, Jung C, Kopisch-Obuch FJ., Theor Appl Genet 127(11), 2014
PMID: 25212110
Reliable in silico identification of sequence polymorphisms and their application for extending the genetic map of sugar beet (Beta vulgaris).
Holtgräwe D, Sörensen TR, Viehöver P, Schneider J, Schulz B, Borchardt D, Kraft T, Himmelbauer H, Weisshaar B., PLoS One 9(10), 2014
PMID: 25302600
Multiple-line cross quantitative trait locus mapping in sugar beet (Beta vulgaris L.)
Schwegler DD, Liu W, Gowda M, Würschum T, Schulz B, Reif JC., Mol Breed 31(2), 2013
PMID: IND500628876
Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.).
Sun L, Zhang Q, Xu Z, Yang W, Guo Y, Lu J, Pan H, Cheng T, Cai M., BMC Genet 14(), 2013
PMID: 24093913
Integration of gene-based markers in a pearl millet genetic map for identification of candidate genes underlying drought tolerance quantitative trait loci.
Sehgal D, Rajaram V, Armstead IP, Vadez V, Yadav YP, Hash CT, Yadav RS., BMC Plant Biol 12(), 2012
PMID: 22251627
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, Sörensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H., Plant J 70(3), 2012
PMID: 22211633
A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses.
Mutasa-Göttgens ES, Joshi A, Holmes HF, Hedden P, Göttgens B., BMC Genomics 13(), 2012
PMID: 22429863
Genetic identification of a novel bolting locus in Beta vulgaris which promotes annuality independently of the bolting gene B
Abou-Elwafa SF, Büttner B, Kopisch-Obuch FJ, Jung C, Müller AE., Mol Breed 29(4), 2012
PMID: IND44650165
A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution.
Paesold S, Borchardt D, Schmidt T, Dechyeva D., Plant J 72(4), 2012
PMID: 22775355
Conservation and divergence of autonomous pathway genes in the flowering regulatory network of Beta vulgaris.
Abou-Elwafa SF, Büttner B, Chia T, Schulze-Buxloh G, Hohmann U, Mutasa-Göttgens E, Jung C, Müller AE., J Exp Bot 62(10), 2011
PMID: 20974738
Identification of SNP and SSR markers in eggplant using RAD tag sequencing.
Barchi L, Lanteri S, Portis E, Acquadro A, Valè G, Toppino L, Rotino GL., BMC Genomics 12(), 2011
PMID: 21663628
Genome-wide distribution of genetic diversity and linkage disequilibrium in elite sugar beet germplasm.
Li J, Lühmann AK, Weissleder K, Stich B., BMC Genomics 12(), 2011
PMID: 21970685
Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database.
Xie F, Sun G, Stiller JW, Zhang B., PLoS One 6(11), 2011
PMID: 22087239
High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.
Lange C, Mittermayr L, Dohm JC, Holtgräwe D, Weisshaar B, Himmelbauer H., Theor Appl Genet 121(3), 2010
PMID: 20379697
Strategies to develop polymorphic markers for Coffea arabica L
Zarate L-A, Cristancho M-A, Moncada P., Euphytica 173(2), 2010
PMID: IND44352412
A survey of EMS-induced biennial Beta vulgaris mutants reveals a novel bolting locus which is unlinked to the bolting gene B.
Büttner B, Abou-Elwafa SF, Zhang W, Jung C, Müller AE., Theor Appl Genet 121(6), 2010
PMID: 20563790
Gene discovery in the horned beetle Onthophagus taurus.
Choi JH, Kijimoto T, Snell-Rood E, Tae H, Yang Y, Moczek AP, Andrews J., BMC Genomics 11(), 2010
PMID: 21156066
Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.
Dohm JC, Lange C, Reinhardt R, Himmelbauer H., Plant J 57(1), 2009
PMID: 18764921
SNP identification in crop plants.
Ganal MW, Altmann T, Röder MS., Curr Opin Plant Biol 12(2), 2009
PMID: 19186095
Development and assessment of simple PCR markers for SNP genotyping in barley.
Hayden MJ, Tabone T, Mather DE., Theor Appl Genet 119(5), 2009
PMID: 19597725
A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits.
Li F, Kitashiba H, Inaba K, Nishio T., DNA Res 16(6), 2009
PMID: 19884167
Single strand conformation polymorphism based SNP and Indel markers for genetic mapping and synteny analysis of common bean (Phaseolus vulgaris L.).
Galeano CH, Fernández AC, Gómez M, Blair MW., BMC Genomics 10(), 2009
PMID: 20030833
Sugar beet contains a large CONSTANS-LIKE gene family including a CO homologue that is independent of the early-bolting (B) gene locus.
Chia TY, Müller A, Jung C, Mutasa-Göttgens ES., J Exp Bot 59(10), 2008
PMID: 18495636
Cloning and sequence diversity analysis of GmHs1 pro⁻¹ in Chinese domesticated and wild soybeans
Yuan C, Zhou G, Li Y, Wang K, Wang Z, Li X, Chang R, Qiu L., Mol Breed 22(4), 2008
PMID: IND44107406
Construction and characterization of a sugar beet (Beta vulgaris) fosmid library.
Lange C, Holtgräwe D, Schulz B, Weisshaar B, Himmelbauer H., Genome 51(11), 2008
PMID: 18956027
Mapping of rhizoctonia root rot resistance genes in sugar beet using pathogen response-related sequences as molecular markers
, Plant Breed 127(6), 2008
PMID: IND44130705

47 References

Daten bereitgestellt von Europe PubMed Central.


S, Proc Natl Acad Sci 90(), 1993
Homoeologous relationships of rice, wheat and maize chromosomes.
Ahn S, Anderson JA, Sorrells ME, Tanksley SD., Mol. Gen. Genet. 241(5-6), 1993
PMID: 7903411
Optimizing parental selection for genetic linkage maps.
Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME., Genome 36(1), 1993
PMID: 18469981

K, Plant Mol Biol Rep 9(), 1991

E, Plant J 2(), 1992
An extended map of the sugar beet genome containing RFLP and RAPD loci.
Barzen E, Mechelke W, Ritter E, Schulte-Kappert E, Salamini F., Theor. Appl. Genet. 90(2), 1995
PMID: 24173890

D, Plant Biol 4(), 2002
The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis.
Bennetzen JL, Ma J., Curr. Opin. Plant Biol. 6(2), 2003
PMID: 12667868
SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines.
Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ., BMC Genet. 3(), 2002
PMID: 12366868
Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.).
Cogan NO, Ponting RC, Vecchies AC, Drayton MC, George J, Dracatos PM, Dobrowolski MP, Sawbridge TI, Smith KF, Spangenberg GC, Forster JW., Mol. Genet. Genomics 276(2), 2006
PMID: 16708235
Re-evaluating the relevance of ancestral shared synteny as a tool for crop improvement.
Delseny M., Curr. Opin. Plant Biol. 7(2), 2004
PMID: 15003211
Plant genome archaeology: evidence for conserved ancestral chromosome segments in dicotyledonous plant species.
Dominguez I, Graziano E, Gebhardt C, Barakat A, Berry S, Arus P, Delseny M, Barnes S., Plant Biotechnol. J. 1(2), 2003
PMID: 17147746
Base-calling of automated sequencer traces using phred. II. Error probabilities.
Ewing B, Green P., Genome Res. 8(3), 1998
PMID: 9521922
Base-calling of automated sequencer traces using phred. I. Accuracy assessment.
Ewing B, Hillier L, Wendl MC, Green P., Genome Res. 8(3), 1998
PMID: 9521921
Plant genome analysis: the state of the art.
Gebhardt C, Schmidt R, Schneider K., Int. Rev. Cytol. 247(), 2005
PMID: 16344114
Consed: a graphical tool for sequence finishing.
Gordon D, Abajian C, Green P., Genome Res. 8(3), 1998
PMID: 9521923
Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes.
Herwig R, Schulz B, Weisshaar B, Hennig S, Steinfath M, Drungowski M, Stahl D, Wruck W, Menze A, O'Brien J, Lehrach H, Radelof U., Plant J. 32(5), 2002
PMID: 12472698
Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.).
Hunger S, Di Gaspero G, Mohring S, Bellin D, Schafer-Pregl R, Borchardt DC, Durel CE, Werber M, Weisshaar B, Salamini F, Schneider K., Genome 46(1), 2003
PMID: 12669798
A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers.
Konieczny A, Ausubel FM., Plant J. 4(2), 1993
PMID: 8106085

DD, Ann Eugen 12(), 1944
Low nucleotide diversity in man.
Li WH, Sadler LA., Genetics 129(2), 1991
PMID: 1743489

S, Molecular Breed 14(), 2004

M, 1987

M, Proc Natl Acad Sci USA 76(), 1979
PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing.
Nickerson DA, Tobe VO, Taylor SL., Nucleic Acids Res. 25(14), 1997
PMID: 9207020
The candidate gene approach in plant genetics: a review.
Pflieger S, Lefebvre V, Causse M., Mol. Breed. 7(4), 2001
PMID: IND23247209
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: 24203039

K, Plant Breed 111(), 1993

A, Curr Op Plant Biol 5(), 2002
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.
Ragoussis J, Elvidge GP, Kaur K, Colella S., PLoS Genet. 2(7), 2006
PMID: 16895448

AUTHOR UNKNOWN, 0
Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress.
Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A, Svensson JT, Wanamaker SI, Walia H, Rodriguez EM, Hedley PE, Liu H, Morris J, Close TJ, Marshall DF, Waugh R., Mol. Genet. Genomics 274(5), 2005
PMID: 16244872
openSputnik--a database to ESTablish comparative plant genomics using unsaturated sequence collections.
Rudd S., Nucleic Acids Res. 33(Database issue), 2005
PMID: 15608275
Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana.
Schmid KJ, Sorensen TR, Stracke R, Torjek O, Altmann T, Mitchell-Olds T, Weisshaar B., Genome Res. 13(6A), 2003
PMID: 12799357
PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris.
Schneider K, Borchardt DC, Schafer-Pregl R, Nagl N, Glass C, Jeppsson A, Gebhardt C, Salamini F., Mol. Gen. Genet. 262(3), 1999
PMID: 10589840
SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes.
Schneider K, Weisshaar B, Borchardt DC, Salamini F., Mol. Breed. 8(1), 2001
PMID: IND23254631
Mapping QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers.
Schneider K, Schafer-Pregl R, Borchardt C, Salamini F., Theor. Appl. Genet. 104(6-7), 2002
PMID: 12582619
Chromosomal assignment of the nine linkage groups of sugar beet (Beta vulgaris L.) using primary trisomics.
Schondelmaier J, Jung C., Theor. Appl. Genet. 95(4), 1997
PMID: IND20800264

K, Plant Breed 116(), 1997

P, Plant J 3(), 1993

AUTHOR UNKNOWN, 0

AC, Nature Rev Genet 2(), 2002
The absence of TIR-type resistance gene analogues in the sugar beet (Beta vulgaris L.) genome.
Tian Y, Fan L, Thurau T, Jung C, Cai D., J. Mol. Evol. 58(1), 2004
PMID: 14743313
Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea.
Van K, Hwang EY, Kim MY, Park HJ, Lee SH, Cregan PB., J. Hered. 96(5), 2005
PMID: 15994422
MapChart: software for the graphical presentation of linkage maps and QTLs.
Voorrips RE., J. Hered. 93(1), 2002
PMID: 12011185
The Genomes of Oryza sativa: a history of duplications.
Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK, Yang H., PLoS Biol. 3(2), 2005
PMID: 15685292
Single-nucleotide polymorphisms in soybean.
Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB., Genetics 163(3), 2003
PMID: 12663549
Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®
Quellen

PMID: 17622508
PubMed | Europe PMC

Suchen in

Google Scholar