Theoretical and Applied Genetics

, Volume 115, Issue 6, pp 793–805

Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome

  • V. Laurent
  • P. Devaux
  • T. Thiel
  • F. Viard
  • S. Mielordt
  • P. Touzet
  • M. C. Quillet
Original Paper
  • 256 Downloads

Abstract

Sugar beet (Beta vulgaris) is an important root crop for sucrose production. A study was conducted to find a new abundant source of microsatellite (SSR) markers in order to develop marker assistance for breeding. Different sources of existing microsatellites were used and new ones were developed to compare their efficiency to reveal diversity in mapping population and mapping coverage. Forty-one microsatellite markers were isolated from a B. vulgaris ssp maritima genomic library and 201 SSRs were extracted from a B. vulgaris ssp vulgaris library. Data mining was applied on GenBank B. vulgaris expressed sequence tags (ESTs), 803 EST-SSRs were identified over 19,709 ESTs. Characteristics, polymorphism and cross-species transferability of these microsatellites were compared. Based on these markers, a high density genetic map was constructed using 92 F2 individuals from a cross between a sugar and a table beet. The map contains 284 markers, spans over 555 cM and covers the nine chromosomes of the species with an average markers density of one marker every 2.2 cM. A set of markers for assignation to the nine chromosomes of sugar beet is provided.

References

  1. Andersen NS, Siegismund HR, Meyer V, Jorgensen RB (2005) Low level of gene flow from cultivated beets (Beta vulgaris L. ssp vulgaris) into Danish populations of sea beet (Beta vulgaris L. ssp. maritima (L.) Arcangeli). Mol Ecol 14:1391–1405PubMedCrossRefGoogle Scholar
  2. Arnaud JF, Viard F, Delescluse M, Cuguen J (2003) Evidence for gene flow via seed dispersal from crop to wild relatives in Beta vulgaris (Chenopodiaceae): consequences for the release of genetically modified crop species with weedy lineages. Proc R Soc Lond 1524:1565–1571CrossRefGoogle Scholar
  3. Areshchenkova T, Ganal M (2002) Comparative analysis of polymorphism and chromosomal location of tomato microsatellite markers isolated from three different sources. Theor Appl Genet 104:229–235PubMedCrossRefGoogle Scholar
  4. Barzen E, Mechelke W, Ritter E, Seitzer J, 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 2:601–611CrossRefGoogle Scholar
  5. Barzen E, Mechelke W, Ritter E, Schulte-Kappert E, Salamini F (1995) An extended map of the sugar beet genome containing RFLP and RAPD loci. Theor Appl Genet 90:189–193CrossRefGoogle Scholar
  6. Barzen E, Stahl R, Fuchs E, Borchardt D, Salamini F (1997) Development of coupling-repulsion-phase SCAR markers diagnostic for the sugar beet Rr1 allele conferring resistance to rhizomania. Mol Breed 3:231–238CrossRefGoogle Scholar
  7. Boudry P, Wieber R, Saumitou-Laprade P, Pillen K, VanDijk H, Jung C (1994) Identification of RFLP markers closely linked to the bolting gene B and their significance for the study of the annual habit in beets (Beta vulgaris L.). Theor Appl Genet 88:852–858CrossRefGoogle Scholar
  8. Butterfass T (1964) Die chloroplastenzahlen in verschiedenartigen zellen trisomer zuckerruben (Beta vulgaris L.). Z Bot 52:46–77Google Scholar
  9. Butterfass T (1968) Die Zuordnung des Locus R der Zuckerrübe (Hypokotylfarbe) zum Chromosom II. Theor Appl Genet 38:348–350CrossRefGoogle Scholar
  10. Cardle L, Ramsay L, Milbourne D, Macaulay M, Marshall D, Waugh R (2000) Computational and experimental characterization of physically clustered simple sequence repeats in plants. Genetics 156:847–854PubMedGoogle Scholar
  11. Cho Y, Ishii T, Temnykh S, Chen X, Lipovich L, McCouch S, Park W, Ayres N, Cartinhour S (2000) Diversity of microsatellites derived from genomic libraries and GenBank sequences in rice (Oryza sativa L.). Theor Appl Genet 100:713–722CrossRefGoogle Scholar
  12. Cureton A, Burns M, Ford-Lloyd B, Newbury H (2002) Development of simple sequence repeat (SSR) markers for the assesment of gene flow between sea beet (Beta vulgaris ssp. maritima) populations. Mol Ecol Note 2:402–403CrossRefGoogle Scholar
  13. Decroocq V, Fave M, Hagen L, Bordenave L, Decroocq S (2003) Development and transferability of apricot and grape EST microsatellite markers across taxa. Theor Appl Genet 106:912–922PubMedGoogle Scholar
  14. El-Mezawy A, Dreyer F, Jacobs G, Jung C (2002) High-resolution mapping of the mapping gene B of sugar beet. Theor Appl Genet 105:100–105PubMedCrossRefGoogle Scholar
  15. Eujayl I, Sorrells M, Baum M, Wolters P, Powell W (2001) Assessment of genotypic variation among cultivated durum wheat based on EST-SSRS and genomic SSRS. Euphytica 119:39–43CrossRefGoogle Scholar
  16. Friesen T, Weiland J, Aasheim M, Hunger S, Borchardt D, Lewellen R (2006) Identification of a SCAR marker associated with B m, the beet mosaic virus resistance gene, on chromosome 1 of sugar beet. Plant Breed 125:167–172CrossRefGoogle Scholar
  17. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554:17–22PubMedCrossRefGoogle Scholar
  18. Guo W, Wang W, Zhou B, Zhang T (2006) Cross-species transferability of G. arboreum-derived EST-SSRs in the diploid species of Gossypium. Theor Appl Genet 112:1573–1581PubMedCrossRefGoogle Scholar
  19. Hackauf B, Wehling P (2002) Identification of microsatellite polymorphisms in a expressed portion of the rye genome. Plant Breed 121:17–25CrossRefGoogle Scholar
  20. Hagihara E, Matsuhira H, Ueda M, Mikami T, Kubo T (2005) Sugar beet BAC library construction and assembly of a contig spanning Rf1, a restorer-of-fertility gene for Owen cytoplasmic male sterility. Mol Genet Genomics 4:1–8Google Scholar
  21. Halldén C, Hjerdin A, Rading I, Säll T, Fridlundh B, Johannisdottir G, Tuvesson S, Akesson C, Nilsson N (1996) A high density RFLP linkage map of sugar beet. Genome 39:634–645PubMedGoogle Scholar
  22. Hirata M, Cai H, Inoue M, Yuyama N, Miura Y, Komatsu T, Takamizo T, Fujimori M (2006) Development of simple sequence repeat (SSR) markers and construction of an SSR-based linkage map in Italian ryegrass (Lolium multiflorum Lam.). Theor Appl Genet 113:270–279PubMedCrossRefGoogle Scholar
  23. Hohmann S, Kadereit J, Kadereit G (2006) Understanding Mediterranean-Californian disjunctions: molecular evidence from Chenopodiaceae-Betoideae. Taxon 55:67–78CrossRefGoogle Scholar
  24. Holton T, Christopher J, McClure L, Harker N, Henry R (2002) Identification and mapping of polymorphic SSR markers from expressed gene sequences of barley and wheat. Mol Breed 9:63–71CrossRefGoogle Scholar
  25. Kantety R, La Rota M, Matthews D, Sorrells M (2002) Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol Biol 48:501–510PubMedCrossRefGoogle Scholar
  26. Kosambi D (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  27. Lawson M, Zhang L (2006) Distinct patterns of SSR distribution in the Arabidopsis thaliana and rice genomes. Genome Biol 7:R14PubMedCrossRefGoogle Scholar
  28. Liewlaksaneeyanawin C, Ritland C, El-Kassaby Y, Ritland K (2004) Single-copy, species-transferable microsatellite markers developed from loblolly pine ESTs. Theor Appl Genet 109:361–369PubMedCrossRefGoogle Scholar
  29. Mielordt S (2005) Gene prediction in Arabidopsis thaliana. Master thesis in bioinformatics, FU Berlin (2005)Google Scholar
  30. Milbourne D, Meyer R, Collins A, Ramsay I, Gebhardt C, Waugh R (1998) Isolation, characterization and mapping of simple sequence repeat loci in potato. Mol Gen Genet 259:233–245PubMedCrossRefGoogle Scholar
  31. McGrath JM, Trebbi D, Fenwick A, Panella L, Schultz B, Laurent V, Barnes S, Murray S (2007) An open-source first-generation molecular genetic map from a sugar × table beet cross and its extension to physical mapping. Plant Genome, a Supp to Crop Sci 47:S49–S66Google Scholar
  32. Metzgar D, Bytof J, Wills C (2000) Selection against frameshift mutations limits microstellite expansion in coding DNA. Genome Res 10:72–80PubMedGoogle Scholar
  33. Monfort A, Vilanova S, Davis T, Arus P (2006) A new set of polymorphic simple sequence repeat (SSR) markers from a wild strawberry (Fragaria vesca) are transferable to other diploid Fragaria species and to Fragaria × ananassa. Mol Ecol Note 6:197–200CrossRefGoogle Scholar
  34. Monforte A (2003) Development and mapping of SSR markers from melon ESTs. 7th international congress on plant molecular biology. ISPMB 2003, Barcelona, 23–28 JuneGoogle Scholar
  35. Mörchen M, Cuguen J, Michaelis G, Hänni C, Saumitou-Laprade P (1996) Abundance and length polymorphism of microsatellite repeat in Beta vulgaris L. Theor Appl Genet 92:326–333CrossRefGoogle Scholar
  36. Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with nonrepetitive DNA in plant genomes. Nat Genet 30:194–200PubMedCrossRefGoogle Scholar
  37. Nilsson N, Halldén C, Hansen M, Hjerdin A, Säll T (1997) Comparing the distribution of RAPD and RFLP markers in a high density linkage map of sugar beet. Genome 40:644–651CrossRefPubMedGoogle Scholar
  38. Nilsson N, Hansen M, Panagopoulos A, Tuvesson S, Ehlde M, Christiansson M, Rading I, Rissler M, Kraft T (1999) QTL analysis of Cercospora leaf spot resistance in sugar beet. Plant Breed 118:327–334CrossRefGoogle Scholar
  39. Pelsy F, Merdinoglu D (1996) Identification and mapping of random amplified polymorphic DNA markers linked to a rhizomania resistance gene in sugar beet (Beta vulgaris L.) by bulked segregant analysis. Plant Breed 115:371–377CrossRefGoogle Scholar
  40. Pillen K, Steinrücken G, Wricke G, Herrmann R, Jung C (1992) A linkage map of sugar beet (Beta vulgaris L.). Theor Appl Genet 84:129–135CrossRefGoogle Scholar
  41. Qureshi S, Saha S, Kantety R, Jenkins J (2004) EST-SSR: a new class of genetic markers in cotton. J Cotton Sci 8:112–123Google Scholar
  42. Rae S, Aldam C, Domingez I, Hoebrechts M, Barnes S, Edwards K (2000) Development and incorporation of microsatellite markers into the linkage map of sugar beet (Beta vulgaris L.). Theor Appl Genet 100:1240–1248CrossRefGoogle Scholar
  43. Richards C, Brownson M, Mitchell S, Kresovich S, Panella L (2004) Polymorphic microsatellite markers for inferring diversity in wild and domesticated sugar beet (Beta vulgaris). Mol Ecol Notes 4:243CrossRefGoogle Scholar
  44. Röder M, Plaschke J, König S, Börner A, Sorrells M, Tanksley S, Ganal M (1995) Abundance, variability and chromosomal location of microsatellites in wheat. Mol Gen Genet 246:327–333PubMedCrossRefGoogle Scholar
  45. Roundy T, Theurer J (1974) Linkage and inheritance studies involving an annual pollen restorer and other genetic characters in sugar beets. Crop Sci 14:230–232CrossRefGoogle Scholar
  46. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar
  47. Rudd S, Mewes H, Mayer K (2003) SPUTNIK: a database platform for comparative plant genomics. Nucleic Acids Res 31:128–132PubMedCrossRefGoogle Scholar
  48. Saha M, Mian M, Eujayl I, Zwonitzer J, Wang L, May G (2004) Tall fescue EST-SSR markers with transferability across several grass species. Theor Appl Genet 109:783–791PubMedCrossRefGoogle Scholar
  49. Santoni S, Bervillé A (1992) Two different satellite DNAs in Beta vulgaris L.: evolution, quantification and distribution in the genus. Theor Appl Genet 84:1009–1016CrossRefGoogle Scholar
  50. Schäfer-Pregl R, Borchardt D, Barzen E, Glass C, Mechelke W, Seitzer J, Salamini F (1999) Localization of QTLs for tolerance to Cercospora beticola on sugar beet linkage groups. Theor Appl Genet 99:829–836CrossRefGoogle Scholar
  51. Schmidt T, Heslop-Harrison J (1996) The physical and genomic organization of microsatellites in sugar beet. Proc Natl Acad Sci USA 93:8761–8765PubMedCrossRefGoogle Scholar
  52. Schneider K, Borchardt D, Schäfer-Pregl R, Nagl N, Glass C, Jeppsson A, Gebhardt C, Salamini F (1999) PCR-based cloning and segregation analysis of functional gene homologues in Beta vulgaris. Mol Gen Genet 262:515–524PubMedCrossRefGoogle Scholar
  53. Schneider K, Schäfer-Pregl R, Borchardt D, Salamini F (2002) Mapping QTLs for sucrose content, yield and quality in a sugar beet population fingerprinted by EST-related markers. Theor Appl Genet 104:1107–1113PubMedCrossRefGoogle Scholar
  54. Scholten O, Klein-Lankhorst R, Esselink D, De Bock T, Lange W (1997) Identification and mapping of random amplified polymorphic DNA (RAPD) markers linked to resistance against beet necrotic yellow vein virus (BNYVV) in Beta accessions. Theor Appl Genet 94:123–130CrossRefPubMedGoogle Scholar
  55. Schondelmaier J, Steinrücken G, Jung C (1996) Integration of AFLP markers into a linkage map of sugar beet (Beta vulgaris L.). Plant Breed 115:231–237CrossRefGoogle Scholar
  56. Schondelmaier J, Jung C (1997) Chromosomal assignment of the nine linkage groups of sugar beet (Beta vulgaris L.) using primary trisomics. Theor Appl Genet 95:590–596CrossRefGoogle Scholar
  57. Schumacher K, Schondelmaier J, Barzen E, Steinrücken G, Borchardt D, Weber W, Jung C, Salamini F (1997) Combining different linkage maps in sugar beet (Beta vulgaris L.) to make one map. Plant Breed 116:23–38CrossRefGoogle Scholar
  58. Sorrells M (2000) The evolution of comparative plant genetics. In: Gustafson JP (ed) Genomes. Proceedings of 22nd stadler symposium (6–8 june 1998, Columbia). Kluwer academic publishers, BostonGoogle Scholar
  59. Temnykh S, DeClerck G, Lukashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452PubMedCrossRefGoogle Scholar
  60. Thiel T, Michalek W, Varshney R, Graner A (2003) Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  61. Uphoff H, Wricke G (1995) A genetic map of sugar beet (Beta vulgaris) based on RAPD markers. Plant Breed 114:355–357CrossRefGoogle Scholar
  62. Van Ooijen J, Voorrips R (2001) Joinmap® 3.0, Software for the calculation of genetics linkage maps. Plant Research International, WageningenGoogle Scholar
  63. Viard F, Bernard J, Desplanque B (2002) Crop–weed interactions in the Beta vulgaris complex at a local scale: allelic diversity and gene flow within sugar beet fields. Theor Appl Genet 104:688–697PubMedCrossRefGoogle Scholar
  64. Viard F, Arnaud JF, Delescluse M, Cuguen J (2004) Tracing back seed and pollen flow within the crop–wild Beta vulgaris complex: genetic distinctiveness vs. hot spots of hybridization over a regional scale. Mol Ecol 13:1357–1364PubMedCrossRefGoogle Scholar
  65. Wagner H, Weber W, Wricke G (1992) Estimating linkage relationship of isozyme markers and morphological markers in sugar beet (Beta vulgaris L.) including families with distorted segregations. Plant Breed 108:89–96CrossRefGoogle Scholar
  66. Weber W, Borchardt D, Koch G (1999) Combined linkage maps and QTLs in sugar beet (Beta vulgaris L.) from different populations. Plant Breed 118:193–204CrossRefGoogle Scholar
  67. Weber W, Borchardt D, Koch G (2000) Markers analysis for quantitative traits in sugar beet. Plant Breed 119:97–106CrossRefGoogle Scholar
  68. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16PubMedCrossRefGoogle Scholar
  69. Zhang L, Bernard M, Leroy P, Feuillet C, Sourdille P (2005) High transferability of bread wheat EST-derived SSRs to other cereals. Theor Appl Genet 111:677–687PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  • V. Laurent
    • 1
    • 3
  • P. Devaux
    • 1
  • T. Thiel
    • 2
  • F. Viard
    • 4
    • 5
  • S. Mielordt
    • 2
  • P. Touzet
    • 4
  • M. C. Quillet
    • 3
  1. 1.Laboratoire de BiotechnologiesEts Florimond DesprezCappelle-en-PévèleFrance
  2. 2.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
  3. 3.Laboratoire «Stress abiotiques et différenciation des végétaux», UMR INRA 1281Université des Sciences et Technologies de LilleVilleneuve d’Ascq cedexFrance
  4. 4.Laboratoire de Génétique et Evolution des Populations Végétales, UMR CNRS 8016Université des Sciences et Technologies de LilleVilleneuve d’Ascq cedexFrance
  5. 5.Laboratoire «Adaptation et Diversité en Milieu Marin», UMR CNRS-UPMC 7144Station Biologique de RoscoffRoscoff cedexFrance

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