Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)

Holtgräwe D, Rosleff Sörensen T, Viehöver P, Schneider J, Schulz B, Borchardt D, Kraft T, Himmelbauer H, Weisshaar B (2014)
PLoS ONE 9(10): e110113.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Holtgräwe, DanielaUniBi ; Rosleff Sörensen, ThomasUniBi; Viehöver, PriscaUniBi; Schneider, JessicaUniBi; Schulz, Britta; Borchardt, Dietrich; Kraft, Thomas; Himmelbauer, Heinz; Weisshaar, BerndUniBi
Abstract / Bemerkung
Molecular markers are a highly valuable tool for creating genetic maps. Like in many other crops, sugar beet (Beta vulgaris L.) breeding is increasingly supported by the application of such genetic markers. Single nucleotide polymorphism (SNP) based markers have a high potential for automated analysis and high-throughput genotyping. We developed a bioinformatics workflow that uses Sanger and 2nd-generation sequence data for detection, evaluation and verification of new transcript-associated SNPs from sugar beet. RNAseq data from one parent of an established mapping population were produced by 454-FLX sequencing and compared to Sanger ESTs derived from the other parent. The workflow established for SNP detection considers the quality values of both types of reads, provides polymorphic alignments as well as selection criteria for reliable SNP detection and allows painless generation of new genetic markers within genes. We obtained a total of 14,323 genic SNPs and InDels. According to empirically optimised settings for the quality parameters, we classified these SNPs into four usability categories. Validation of a subset of the in silico detected SNPs by genotyping the mapping population indicated a high success rate of the SNP detection. Finally, a total of 307 new markers were integrated with existing data into a new genetic map of sugar beet which offers improved resolution and the integration of terminal markers.
Erscheinungsjahr
2014
Zeitschriftentitel
PLoS ONE
Band
9
Ausgabe
10
Art.-Nr.
e110113
ISSN
1932-6203
eISSN
1932-6203
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2699085

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Holtgräwe D, Rosleff Sörensen T, Viehöver P, et al. Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris). PLoS ONE. 2014;9(10): e110113.
Holtgräwe, D., Rosleff Sörensen, T., Viehöver, P., Schneider, J., Schulz, B., Borchardt, D., Kraft, T., et al. (2014). Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris). PLoS ONE, 9(10), e110113. doi:10.1371/journal.pone.0110113
Holtgräwe, Daniela, Rosleff Sörensen, Thomas, Viehöver, Prisca, Schneider, Jessica, Schulz, Britta, Borchardt, Dietrich, Kraft, Thomas, Himmelbauer, Heinz, and Weisshaar, Bernd. 2014. “Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)”. PLoS ONE 9 (10): e110113.
Holtgräwe, D., Rosleff Sörensen, T., Viehöver, P., Schneider, J., Schulz, B., Borchardt, D., Kraft, T., Himmelbauer, H., and Weisshaar, B. (2014). Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris). PLoS ONE 9:e110113.
Holtgräwe, D., et al., 2014. Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris). PLoS ONE, 9(10): e110113.
D. Holtgräwe, et al., “Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)”, PLoS ONE, vol. 9, 2014, : e110113.
Holtgräwe, D., Rosleff Sörensen, T., Viehöver, P., Schneider, J., Schulz, B., Borchardt, D., Kraft, T., Himmelbauer, H., Weisshaar, B.: Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris). PLoS ONE. 9, : e110113 (2014).
Holtgräwe, Daniela, Rosleff Sörensen, Thomas, Viehöver, Prisca, Schneider, Jessica, Schulz, Britta, Borchardt, Dietrich, Kraft, Thomas, Himmelbauer, Heinz, and Weisshaar, Bernd. “Reliable In Silico Identification of Sequence Polymorphisms and Their Application for Extending the Genetic Map of Sugar Beet (Beta vulgaris)”. PLoS ONE 9.10 (2014): e110113.
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5 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Two sugar beet chitinase genes, BvSP2 and BvSE2, analysed with SNP Amplifluor-like markers, are highly expressed after Fusarium root rot inoculations and field susceptibility trial.
Yerzhebayeva R, Abekova A, Konysbekov K, Bastaubayeva S, Kabdrakhmanova A, Absattarova A, Shavrukov Y., PeerJ 6(), 2018
PMID: 29967753
Crop wild relative populations of Beta vulgaris allow direct mapping of agronomically important genes.
Capistrano-Gossmann GG, Ries D, Holtgräwe D, Minoche A, Kraft T, Frerichmann SLM, Rosleff Soerensen T, Dohm JC, González I, Schilhabel M, Varrelmann M, Tschoep H, Uphoff H, Schütze K, Borchardt D, Toerjek O, Mechelke W, Lein JC, Schechert AW, Frese L, Himmelbauer H, Weisshaar B, Kopisch-Obuch FJ., Nat Commun 8(), 2017
PMID: 28585529
The Genetics of Plant Metabolism.
Fernie AR, Tohge T., Annu Rev Genet 51(), 2017
PMID: 28876980
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

43 References

Daten bereitgestellt von Europe PubMed Central.

Direct prediction of bioethanol yield in sugar beet pulp using near infrared spectroscopy.
Magana C, Nunez-Sanchez N, Fernandez-Cabanas VM, Garcia P, Serrano A, Perez-Marin D, Peman JM, Alcalde E., Bioresour. Technol. 102(20), 2011
PMID: 21872469
Unintended consequences of bioethanol feedstock choice in China.
Liang S, Xu M, Zhang T., Bioresour. Technol. 125(), 2012
PMID: 23070140
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), 2013
PMID: 24352233
Nuclear DNA content of some important plant species
AUTHOR UNKNOWN, 1991
High-throughput identification of genetic markers using representational oligonucleotide microarray analysis.
Lange C, Mittermayr L, Dohm JC, Holtgrawe D, Weisshaar B, Himmelbauer H., Theor. Appl. Genet. 121(3), 2010
PMID: 20379697
Genome-wide association mapping of agronomic traits in sugar beet.
Wurschum T, Maurer HP, Kraft T, Janssen G, Nilsson C, Reif JC., Theor. Appl. Genet. 123(7), 2011
PMID: 21761161
Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene-based physical and genetic mapping of the sugar beet genome (Beta vulgaris).
Dohm JC, Lange C, Holtgrawe D, Sorensen TR, Borchardt D, Schulz B, Lehrach H, Weisshaar B, Himmelbauer H., Plant J. 70(3), 2012
PMID: 22211633
Applications of single nucleotide polymorphisms in crop genetics.
Rafalski A., Curr. Opin. Plant Biol. 5(2), 2002
PMID: 11856602
Next-generation transcriptome assembly.
Martin JA, Wang Z., Nat. Rev. Genet. 12(10), 2011
PMID: 21897427
A general approach to single-nucleotide polymorphism discovery.
Marth GT, Korf I, Yandell MD, Yeh RT, Gu Z, Zakeri H, Stitziel NO, Hillier L, Kwok PY, Gish WR., Nat. Genet. 23(4), 1999
PMID: 10581034
Redundancy based detection of sequence polymorphisms in expressed sequence tag data using autoSNP.
Barker G, Batley J, O' Sullivan H, Edwards KJ, Edwards D., Bioinformatics 19(3), 2003
PMID: 12584131
QualitySNP: a pipeline for detecting single nucleotide polymorphisms and insertions/deletions in EST data from diploid and polyploid species.
Tang J, Vosman B, Voorrips RE, van der Linden CG, Leunissen JA., BMC Bioinformatics 7(), 2006
PMID: 17029635
Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences.
Dantec LL, Chagne D, Pot D, Cantin O, Garnier-Gere P, Bedon F, Frigerio JM, Chaumeil P, Leger P, Garcia V, Laigret F, De Daruvar A, Plomion C., Plant Mol. Biol. 54(3), 2004
PMID: 15284499
SNP discovery via 454 transcriptome sequencing.
Barbazuk WB, Emrich SJ, Chen HD, Li L, Schnable PS., Plant J. 51(5), 2007
PMID: 17662031
Calling SNPs without a reference sequence.
Ratan A, Zhang Y, Hayes VM, Schuster SC, Miller W., BMC Bioinformatics 11(), 2010
PMID: 20230626
An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics.
Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B., Plant Mol. Biol. 53(1-2), 2003
PMID: 14756321

AUTHOR UNKNOWN, 0
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
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
Trimming and clustering sugarcane ESTs
AUTHOR UNKNOWN, 2001
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ., Nucleic Acids Res. 25(17), 1997
PMID: 9254694

AUTHOR UNKNOWN, 0
Multiple alignment of DNA sequences with MAFFT.
Katoh K, Asimenos G, Toh H., Methods Mol. Biol. 537(), 2009
PMID: 19378139

AUTHOR UNKNOWN, 0
Primer3 on the WWW for general users and for biologist programmers.
Rozen S, Skaletsky H., Methods Mol. Biol. 132(), 2000
PMID: 10547847

AUTHOR UNKNOWN, 0
Constructing dense genetic linkage maps.
Jansen J, Jong AGde, Ooijen JWvan., Theor. Appl. Genet. 102(6/7), 2001
PMID: IND23221059

AUTHOR UNKNOWN, 0
RECORD: a novel method for ordering loci on a genetic linkage map.
Van Os H, Stam P, Visser RG, Van Eck HJ., Theor. Appl. Genet. 112(1), 2005
PMID: 16228189
Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes.
Dohm JC, Lange C, Reinhardt R, Himmelbauer H., Plant J. 57(1), 2008
PMID: 18764921
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
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
An SNP map of the human genome generated by reduced representation shotgun sequencing.
Altshuler D, Pollara VJ, Cowles CR, Van Etten WJ, Baldwin J, Linton L, Lander ES., Nature 407(6803), 2000
PMID: 11029002
Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools.
Norton N, Williams NM, Williams HJ, Spurlock G, Kirov G, Morris DW, Hoogendoorn B, Owen MJ, O'Donovan MC., Hum. Genet. 110(5), 2002
PMID: 12073018

AUTHOR UNKNOWN, 0
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