Abstract
A set of single nucleotide polymorphism (SNP) markers has been developed for each of the nine linkage groups of sugar beet. Each set can monitor the polymorphic state at five to six linked marker loci. In each set, the loci selected for marker development are first amplified in a multiplexed reaction. These amplification products are the basis for sequence-specific elongation of primers adjacent to SNP positions. The extension step revealing SNP loci is based on fluorescently labelled nucleotides. In each set, primers developed to reveal SNP alleles differ in length to allow clear peak resolution in capillary electrophoresis. The nine linkage group (LG) −specific sets provide information on the polymorphism at a total of 52 SNP marker loci. Using the SNP-based tool, groups of concerned loci have been anchored to three different linkage maps of sugar beet. In a second experiment, sugar beet breeding lines have been fingerprinted. The use of the nine sets of LG-specific markers in sugar beet genetics and breeding is discussed. The information necessary to specify the 52 marker loci, as well as their map location, and all details concerning SNP assays, including allele type and nature of mutation, are reported.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Anderson J. A., Churchill G. A., Autrique J. E., Tanksley S. D. and Sorrells M. E. 1993. Optimizing parental selection for genetic linkage maps. Genome 36: 181-186.
Barzen E., Mechelke W., Ritter E., Seitzer J. F. and Salamini F. 1992. RFLP markers for sugar beet breeding: chromosomal linkage maps and location of major genes for rhizomania resistance, monogermy and hypocotyl colour. Plant J. 2: 601-611.
Barzen E., Mechelke W., Ritter E., Schulte-Kappert E. and Salamini F. 1995. An extended map of the sugar beet genome containing RFLP and RAPD loci. Theor. Appl. Genet. 90: 189-193.
Butterfass T. 1964. Die Chloroplastenzahlen in verschiedenartigen Zellen trisomer Zuckerrüben (Beta vulgaris L. ). Z. Botanik 52: 46-77.
Cai D., Kleine M., Kifle S., Harloff H. J., Sandal N. N., Marcker K. A., Klein-Lankhorst R. M., Salentijn E. M., Lange W., Stiekema W. J., Wyss U., Grundler F. M. and Jung C. 1997. Positional cloning of a gene for nematode resistance in sugar beet. Science 275: 832-834.
Gebhardt C., Ballvora A., Walkemeier B., Oberhagemann P. and Schüler K. 2004. Assessing genetic potential in germplasm collections of crop plants by marker-trait association: a case study for potatoes with quantitative variation of resistance to late blight and maturity type. Mol. Breeding 13: 93-102.
Hohmann U., Jacobs G., Telgmann A., Gaafar R. M., Alam S. and Jung C. 2003. A bacterial artificial chromosome (BAC) library of sugar beet and a physical map of the region encompassing the bolting gene B. Mol Genet Genomics 269: 126-136.
Hunger S., Di Gaspero G., Möhring S., Bellin D., Schäfer-Pregl R., Borchardt D. C., Durel C.-E., Werber M., Weisshaar B., Salamini F. and Schneider K. 2003. Isolation and linkage analy-sis of expressed disease. resistance gene analogues of sugar beet (Beta vulgaris L. ). Genome 46: 70-82.
Koornneef M., Hanhart C. J., von Loenen Martinet E. P., Peeters A. J. M., van der Veen J. H. 1987. Arabidopsis Inf. Serv. Frankfurt 23: 46-50.
Liu S., Saha S., Stelly D., Burr B. and Cantrell R. G. 2000. Chromosomal assignment of microsatellite loci in cotton. J. Hered. 91: 326-332.
Makridakis N. M. and Reichardt J. K. 2001. Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms. Biotechniques 31: 1374-1380.
Mitchell S. E., Kresovich S., Jester C. A., Hernandez C. J. and Szewc-McFadden A. K. 1997. Application of multiplex PCR and fluorescence-based, semi-automated allele sizing technology for genotyping plant genetic resources. Crop Sci. 37: 617-624.
Narvel J. M., Chu W.-C., Fehr W. R., Cregan P. B. and Shoemaker R. C. 2000. Development of multiplex sets of simple sequence repeat DNA markers covering the soybean genome. Mol. Breed. 6: 175-183.
Nei M. 1987. Molecular evolutionary genetics. Columbia Univ. Press, New York, USA, pp. 512.
Nei M. and Li W.-H. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76: 5269-5273.
Powell W., Morgante M., Andre C., Hanafey M., Vogel J., Tingey S. and Rafalski A. 1996. The comparison of RFLP, RAPD, AFLP and SSR (microsatellite) markers for germplasm analysis. Mol. Breeding 2: 225-238.
Rafalski A. 2002. Applications of single nucleotide polymorphisms in crop genetics. Curr. Op. Plant Biol. 5: 94-100.
Roig C., Pozzi C., Santi L., Müller J., Stanca M. and Salamini F. 2004. The genetics of barley Hooded suppression. Genetics 167: 439-448.
Schneider K., Borchardt D. C., Schäfer-Pregl R., Nagl N., Glass C., Jeppson A., Gebhardt C. and Salamini F. 1999. PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris. Mol. Gen. Genet. 262: 515-524.
Schneider K., Schäfer-Pregl R., Borchardt D. C. and Salamini F. 2002. Mapping QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers. Theor. Appl. Genet. 104: 1107-1113.
Schneider K., Weisshaar B., Borchardt D. C. and Salamini F. 2001. SNP frequency and allelic haplotype structure of Beta vulgaris expressed genes. Mol. Breeding 8: 63-74.
Schondelmaier J. and Jung C. 1997. Chromosomal assignment of the nine linkage groups of sugar beet (Beta vulgaris L. ) using primary trisomics. Theor. Appl. Genet. 95: 590-596.
Schumacher K., Schondelmaier J., Barzen E., Steinruecken G., Borchardt D., Weber W. E., Jung C. and Salamini F. 1997. Combining different linkage maps in sugar beet (Beta vulgaris L.) to make one map. Plant Breeding 116: 23-38.
Stam P. 1993. Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J. 3: 739-744.
Stam P. and Van Ooijen J. W. 1995. JoinMap version 2.0: Software for the calculation of genetic linkage maps. CPRODLO, Wageningen, The Netherlands.
Syvanen A.-C. 2002. Accessing genetic variation: Genotyping single nucleotide polymorphisms. Nature Rev. Genet. 2: 930-942.
Tang S., Kishore V. K. and Knapp S. 2003. PCR-multiplexes for a genome-wide framework of simple sequence repeat marker loci in cultivated sunflower. Theor. Appl. Genet. 107: 6-19.
Tanksley S. D., Grandillo S., Fulton T. M., Zamir D., Eshed Y., Petiard V., Lopez J. and Beckbunn T. 1996. Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor. Appl. Genet. 92: 213-224.
Thornsberry J. M., Goodman M. M., Doebley J., Kresovich S., Nielsen D. and Buckler E. S. 2001. Dwarf8 polymorphisms associate with variation in flowering time. Nat. Genet. 28: 286-289.
Törjék O., Berger D., Meyer R. C., Müssig C., Schmid K. J., Rosleff Sörensen T., Weisshaar B., Mitchell-Olds T. and Altmann T. 2003. Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis. Plant J. 36: 122-140.
Van de Peer Y. and De Wachter R. 1994. TREECON for Windows: a software package for the construction and drawing of evolutionary trees for the Microsoft Windows environment. Comput. Applic. Biosci. 10: 569-570.
Voorrips R. E. 2002. MapChart: Software for the graphical presentation of linkage maps and QTLs. The Journal of Heredity 93: 77-78.
Whitt S. R., Wilson L. M., Tenaillon M. I., Gaut B. S. and Buckler E. S. 2002. Genetic diversity and selection in the maize starch pathway. Proc. Nat. Acad. Sci. U.S. A. 99: 12959-12962.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Möhring, S., Salamini, F. & Schneider, K. Multiplexed, linkage group-specific SNP marker sets for rapid genetic mapping and fingerprinting of sugar beet (Beta vulgaris L.). Molecular Breeding 14, 475–488 (2004). https://doi.org/10.1007/s11032-004-0900-4
Issue Date:
DOI: https://doi.org/10.1007/s11032-004-0900-4