Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels

Ries D, Holtgräwe D, Viehöver P, Weisshaar B (2016)
BMC Genomics 17(1): 236.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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Abstract / Bemerkung
Background
The combination of bulk segregant analysis (BSA) and next generation sequencing (NGS), also known as mapping by sequencing (MBS), has been shown to significantly accelerate the identification of causal mutations for species with a reference genome sequence. The usual approach is to cross homozygous parents that differ for the monogenic trait to address, to perform deep sequencing of DNA from F2 plants pooled according to their phenotype, and subsequently to analyze the allele frequency distribution based on a marker table for the parents studied. The method has been successfully applied for EMS induced mutations as well as natural variation. Here, we show that pooling genetically diverse breeding lines according to a contrasting phenotype also allows high resolution mapping of the causal gene in a crop species. The test case was the monogenic locus causing red vs. green hypocotyl color in Beta vulgaris (R locus).
Results
We determined the allele frequencies of polymorphic sequences using sequence data from two diverging phenotypic pools of 180 B. vulgaris accessions each. A single interval of about 31 kbp among the nine chromosomes was identified which indeed contained the causative mutation.
Conclusions
By applying a variation of the mapping by sequencing approach, we demonstrated that phenotype-based pooling of diverse accessions from breeding panels and subsequent direct determination of the allele frequency distribution can be successfully applied for gene identification in a crop species. Our approach made it possible to identify a small interval around the causative gene. Sequencing of parents or individual lines was not necessary. Whenever the appropriate plant material is available, the approach described saves time compared to the generation of an F2 population. In addition, we provide clues for planning similar experiments with regard to pool size and the sequencing depth required.
Stichworte
Allele frequency; Beta vulgaris; Gene identification; Mapping by sequencing; Phenotypic pools; R locus; SNP detection; Sugar beet
Erscheinungsjahr
2016
Zeitschriftentitel
BMC Genomics
Band
17
Ausgabe
1
Art.-Nr.
236
ISSN
2041-1723
eISSN
1471-2164
Finanzierungs-Informationen
Open-Access-Publikationskosten wurden durch die Deutsche Forschungsgemeinschaft und die Universität Bielefeld gefördert.
Page URI
https://pub.uni-bielefeld.de/record/2901603

Zitieren

Ries D, Holtgräwe D, Viehöver P, Weisshaar B. Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels. BMC Genomics. 2016;17(1): 236.
Ries, D., Holtgräwe, D., Viehöver, P., & Weisshaar, B. (2016). Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels. BMC Genomics, 17(1), 236. doi:10.1186/s12864-016-2566-9
Ries, David, Holtgräwe, Daniela, Viehöver, Prisca, and Weisshaar, Bernd. 2016. “Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels”. BMC Genomics 17 (1): 236.
Ries, D., Holtgräwe, D., Viehöver, P., and Weisshaar, B. (2016). Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels. BMC Genomics 17:236.
Ries, D., et al., 2016. Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels. BMC Genomics, 17(1): 236.
D. Ries, et al., “Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels”, BMC Genomics, vol. 17, 2016, : 236.
Ries, D., Holtgräwe, D., Viehöver, P., Weisshaar, B.: Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels. BMC Genomics. 17, : 236 (2016).
Ries, David, Holtgräwe, Daniela, Viehöver, Prisca, and Weisshaar, Bernd. “Rapid gene identification in sugar beet using deep sequencing of DNA from phenotypic pools selected from breeding panels”. BMC Genomics 17.1 (2016): 236.
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2019-09-06T09:18:36Z
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3 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

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Shen F, Huang Z, Zhang B, Wang Y, Zhang X, Wu T, Xu X, Zhang X, Han Z., G3 (Bethesda) 9(5), 2019
PMID: 30910819
Sequencing of bulks of segregants allows dissection of genetic control of amylose content in rice.
Wambugu P, Ndjiondjop MN, Furtado A, Henry R., Plant Biotechnol J 16(1), 2018
PMID: 28499072
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

37 References

Daten bereitgestellt von Europe PubMed Central.

Harvesting the potential of induced biological diversity.
Waugh R, Leader DJ, McCallum N, Caldwell D., Trends Plant Sci. 11(2), 2006
PMID: 16406304
Bulk segregant analysis using single nucleotide polymorphism microarrays.
Becker A, Chao DY, Zhang X, Salt DE, Baxter I., PLoS ONE 6(1), 2011
PMID: 21297997
Bulk segregant analysis with molecular markers and its use for improving drought resistance in maize
Quarrie SA, Lazic-Jancic V, Kovacevic D, Steed A, Pekic S., 1999
DNA Pooling: a tool for large-scale association studies.
Sham P, Bader JS, Craig I, O'Donovan M, Owen M., Nat. Rev. Genet. 3(11), 2002
PMID: 12415316
Next-generation sequencing technologies and their implications for crop genetics and breeding.
Varshney RK, Nayak SN, May GD, Jackson SA., Trends Biotechnol. 27(9), 2009
PMID: 19679362
Plant genome sequencing - applications for crop improvement.
Bolger ME, Weisshaar B, Scholz U, Stein N, Usadel B, Mayer KF., Curr. Opin. Biotechnol. 26(), 2013
PMID: 24679255
Fast-forward genetics enabled by new sequencing technologies.
Schneeberger K, Weigel D., Trends Plant Sci. 16(5), 2011
PMID: 21439889
SHOREmap: simultaneous mapping and mutation identification by deep sequencing.
Schneeberger K, Ossowski S, Lanz C, Juul T, Petersen AH, Nielsen KL, Jorgensen JE, Weigel D, Andersen SU., Nat. Methods 6(8), 2009
PMID: 19644454
Fast isogenic mapping-by-sequencing of ethyl methanesulfonate-induced mutant bulks.
Hartwig B, James GV, Konrad K, Schneeberger K, Turck F., Plant Physiol. 160(2), 2012
PMID: 22837357

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Linkage disequilibrium: what history has to tell us.
Nordborg M, Tavare S., Trends Genet. 18(2), 2002
PMID: 11818140

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Pigment evolution in the Caryophyllales: a Systematic Overview
Clement JS, Mabry TJ., 1996
Inheritance of some major color types in beets
Keller W., 1936
Linkage among the R, Y and Bl loci in table beet.
Goldman IL, Austin D., Theor. Appl. Genet. 100(3/4), 2000
PMID: IND22069524

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
The statistics of bulk segregant analysis using next generation sequencing.
Magwene PM, Willis JH, Kelly JK., PLoS Comput. Biol. 7(11), 2011
PMID: 22072954

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
Sequencing depth and coverage: key considerations in genomic analyses.
Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP., Nat. Rev. Genet. 15(2), 2014
PMID: 24434847
Identification of a spontaneous frame shift mutation in a nonreference Arabidopsis accession using whole genome sequencing.
Laitinen RA, Schneeberger K, Jelly NS, Ossowski S, Weigel D., Plant Physiol. 153(2), 2010
PMID: 20388671

AUTHOR UNKNOWN, 0
Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404

AUTHOR UNKNOWN, 0
Fast and accurate short read alignment with Burrows-Wheeler transform.
Li H, Durbin R., Bioinformatics 25(14), 2009
PMID: 19451168

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0

AUTHOR UNKNOWN, 0
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