Analysis of DNA Polymorphisms in Sugar Beet (Beta Vulgaris L.) and Development of an SNP-based Map of Expressed Genes

Overview

Journal Theor Appl Genet

Publisher Springer

Specialty Genetics

Date 2007 Jul 12

PMID 17622508

Citations 24

Authors

Katharina Schneider

Dagmar Kulosa

Thomas Rosleff Soerensen

Silke Mohring

Martin Heine

Gregor Durstewitz

Andreas Polley

Eberhard Weber

Jamsari

Jens Lein

Uwe Hohmann

Emma Tahiro

Bernd Weisshaar

Britta Schulz

Georg Koch

Christian Jung

Martin Ganal

Affiliations

Soon will be listed here.

Abstract

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 F(2) 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.

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References

Syvanen A . Accessing genetic variation: genotyping single nucleotide polymorphisms. Nat Rev Genet. 2001; 2(12):930-42. DOI: 10.1038/35103535. View

Li W, Sadler L . Low nucleotide diversity in man. Genetics. 1991; 129(2):513-23. PMC: 1204640. DOI: 10.1093/genetics/129.2.513. View

Cogan N, Ponting R, Vecchies A, Drayton M, George J, Dracatos P . Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.). Mol Genet Genomics. 2006; 276(2):101-12. DOI: 10.1007/s00438-006-0126-8. View

Gordon D, Abajian C, Green P . Consed: a graphical tool for sequence finishing. Genome Res. 1998; 8(3):195-202. DOI: 10.1101/gr.8.3.195. View

Pillen K, Steinrucken G, Wricke G, Herrmann R, Jung C . A linkage map of sugar beet (Beta vulgaris L.). Theor Appl Genet. 2013; 84(1-2):129-35. DOI: 10.1007/BF00223992. View

Schneider K, Schafer-Pregl R, Borchardt C, Salamini F . Mapping QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers. Theor Appl Genet. 2003; 104(6-7):1107-1113. DOI: 10.1007/s00122-002-0890-8. View

Schmid K, Rosleff Sorensen T, Stracke R, Torjek O, Altmann T, Mitchell-Olds T . Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res. 2003; 13(6A):1250-7. PMC: 403656. DOI: 10.1101/gr.728603. View

Barzen E, Mechelke W, Ritter E, Schulte-Kappert E, Salamini F . An extended map of the sugar beet genome containing RFLP and RAPD loci. Theor Appl Genet. 2013; 90(2):189-93. DOI: 10.1007/BF00222201. View

Bennetzen J, Ma J . The genetic colinearity of rice and other cereals on the basis of genomic sequence analysis. Curr Opin Plant Biol. 2003; 6(2):128-33. DOI: 10.1016/s1369-5266(03)00015-3. View

10.

Herwig R, Schulz B, Weisshaar B, Hennig S, Steinfath M, Drungowski M . Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes. Plant J. 2002; 32(5):845-57. DOI: 10.1046/j.1365-313x.2002.01457.x. View

11.

Hunger S, Di Gaspero G, Mohring S, Bellin D, Schafer-Pregl R, Borchardt D . Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.). Genome. 2003; 46(1):70-82. DOI: 10.1139/g02-106. View

12.

Rickert A, Premstaller A, Gebhardt C, Oefner P . Genotyping of Snps in a polyploid genome by pyrosequencing. Biotechniques. 2002; 32(3):592-3, 596-8, 600 passim. DOI: 10.2144/02323rr01. View

13.

Ewing B, Green P . Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 1998; 8(3):186-94. View

14.

Rafalski A . Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol. 2002; 5(2):94-100. DOI: 10.1016/s1369-5266(02)00240-6. View

15.

Rostoks N, Mudie S, Cardle L, Russell J, Ramsay L, Booth A . Genome-wide SNP discovery and linkage analysis in barley based on genes responsive to abiotic stress. Mol Genet Genomics. 2005; 274(5):515-27. DOI: 10.1007/s00438-005-0046-z. View

16.

Dominguez I, Graziano E, Gebhardt C, Barakat A, Berry S, Arus P . Plant genome archaeology: evidence for conserved ancestral chromosome segments in dicotyledonous plant species. Plant Biotechnol J. 2006; 1(2):91-9. DOI: 10.1046/j.1467-7652.2003.00009.x. View

17.

Ragoussis J, Elvidge G, Kaur K, Colella S . Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research. PLoS Genet. 2006; 2(7):e100. PMC: 1523240. DOI: 10.1371/journal.pgen.0020100. View

18.

Gebhardt C, Schmidt R, Schneider K . Plant genome analysis: the state of the art. Int Rev Cytol. 2005; 247:223-84. DOI: 10.1016/S0074-7696(05)47005-9. View

19.

Van K, Hwang E, Kim M, Park H, Lee S, Cregan P . Discovery of SNPs in soybean genotypes frequently used as the parents of mapping populations in the United States and Korea. J Hered. 2005; 96(5):529-35. DOI: 10.1093/jhered/esi069. View

20.

Nei M, Li W . Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc Natl Acad Sci U S A. 1979; 76(10):5269-73. PMC: 413122. DOI: 10.1073/pnas.76.10.5269. View