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The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca


Fragaria vesca is a short-lived perennial with a seasonal-flowering habit. Seasonality of flowering is widespread in the Rosaceae and is also found in the majority of temperate polycarpic perennials. Genetic analysis has shown that seasonal flowering is controlled by a single gene in F. vesca, the SEASONAL FLOWERING LOCUS (SFL). Here, we report progress towards the marker-assisted selection and positional cloning of SFL, in which three ISSR markers linked to SFL were converted to locus-specific sequence-characterized amplified region (SCAR1–SCAR3) markers to allow large-scale screening of mapping progenies. We believe this is the first study describing the development of SCAR markers from ISSR profiles. The work also provides useful insight into the nature of polymorphisms generated by the ISSR marker system. Our results indicate that the ISSR polymorphisms originally detected were probably caused by point mutations in the positions targeted by primer anchors (causing differential PCR failure), by indels within the amplicon (leading to variation in amplicon size) and by internal sequence differences (leading to variation in DNA folding and so in band mobility). The cause of the original ISSR polymorphism was important in the selection of appropriate strategies for SCAR-marker development. The SCAR markers produced were mapped using a F. vesca f. vesca × F. vesca f. semperflorens testcross population. Marker SCAR2 was inseparable from the SFL, whereas SCAR1 mapped 3.0 cM to the north of the gene and SCAR3 1.7 cM to its south.

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  1. Akiyama Y, Yamamoto Y, Ohmido N, Ohshima M, Fukui K (2001) Estimation of the nuclear DNA content of strawberries (Fragaria spp.) compared with Arabidopsis thaliana by using dual-step flow cytometry. Cytologia 66:431–436

  2. Albani M, Taylor S, Rodriguez Lopez C, Cekic C, Al-Sheikh M, Greenland A, Wetten A, Wilkinson M, Battey N (2001) Fragaria vesca . . . one way to understand flowering in perennials. Flowering Newsl 31:44–48

  3. Barrett SCH, Harder LD, Worley AC (1996) The comparative biology of pollination and mating in flowering plants. Philos Trans R Soc Lond Ser B Biol Sci 351:1271–1280

  4. Battey NH (2000) Aspects of seasonality. J Exp Bot 51:1769–1780

  5. Battey NH, Le Mière P, Tehranifar A, Cekic C, Taylor S, Shrives KJ, Hadley P, Greenland AJ, Darby J, Wilkinson MJ (1998) Genetic and environmental control of flowering in strawberry. In: Cockshull KE, Gray D, Seymour GB, Thomas B (eds) Genetic and environmental manipulation of horticultural crops. CAB International, Wallingford, UK, pp 111–131

  6. Bautista R, Canovas FM, Claros MG (2003) Genomic evidence for a repetitive nature of the RAPD polymorphisms in Olea europaea (olive-tree). Euphytica 130:185–190

  7. Behura SK, Nair S, Sahu SC, Mohan M (2000) An AFLP marker that differentiates biotypes of the Asian rice gall midge (Orseolia oryzae, Wood-Mason) is sex-linked and also linked to avirulence. Mol Gen Genet 263:328–334

  8. Brisse SC, Dujardin J, Tibayrenc M (2000) Identification of six Trypanosoma cruzi lineages by sequence-characterised amplified region markers. Mol Biochem Parasitol 111:95–105

  9. Brown T, Wareing PF (1965) The genetical control of the everbearing habit and three other characters in varieties of Fragaria vesca. Euphytica 14:97–112

  10. Cao W, Hughes GR, Ma H, Dong Z (2001) Identification of molecular markers for resistance to Septoria nodorum blotch in durum wheat. Theor Appl Genet 102:551–554

  11. Cekic C, Battey NH, Wilkinson MJ (2001) The potential of ISSR-PCR primer pair combinations for genetic linkage analysis using the SEASONAL FLOWERING LOCUS in Fragaria vesca as a model. Theor Appl Genet 103:540–546

  12. Charters YM, Robertson A, Wilkinson MJ, Ramsay G (1996) PCR analysis of oilseed rape cultivars (Brassica napus L. ssp. oleifera) using 5′-anchored simple sequence repeat (SSR) primers. Theor Appl Genet 92:442–447

  13. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

  14. Hauser MT, Adhami F, Dorner M, Fuchs E, Glossl J (1998) Generation of co-dominant PCR-based markers by duplex analysis on high resolution gels. Plant J 16:117–125

  15. Hunger S, Di Gaspero G, Mohring S, Bellin D, Schafer-Pregl R, Borchardt DC, Durel CE, Werber M, Weisshaar B, Salamini F, Schneider K (2003) Isolation and linkage analysis of expressed disease-resistance gene analogues of sugar beet (Beta vulgaris L.) Genome 46:70–82

  16. Jensen CS, Salchert K, Nielsen KK (2001) A TERMINAL FLOWER1-like gene from perennial ryegrass involved in floral transition and axillary meristem identity. Plant Physiol 125:1517–1528

  17. Kanazin V, Talbert H, See D, DeCamp P, Nevo E, Blake T (2002) Discovery and assay of single-nucleotide polymorphisms in barley (Hordeum vulgare). Plant Mol Biol 48:529–537

  18. Kim SJ, Moon J, Lee I, Maeng J, Kim SR (2003) Molecular cloning and expression analysis of a CONSTANS homologue, PnCOL1, from Pharbitis nil. J Exp Bot 54:1879–1887

  19. Meksem K, Ruben E, Hyten D, Triwitayakorn K, Lightfoot DA (2001) Conversion of AFLP bands into high-throughput DNA markers. Mol Gen Genet 265:207–214

  20. Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956

  21. Negi MS, Devic M, Delseny M, Lakshmikumaran M (2000) Identification of AFLP fragments linked to seed-coat colour in Brassica juncea and conversion to a SCAR marker for rapid selection. Theor Appl Genet 101:146–152

  22. Orita M, Iwahana H, Kanazawa H, Hayashi K, Sekiya T (1989) Detection of polymorphisms of human DNA by gel electrophoresis as single-stranded conformation polymorphisms. Proc Natl Acad Sci USA 86:2766–2770

  23. Rottmann WH, Meilan R, Sheppard LA, Brunner AM, Skinner JS, Ma C, Cheng S, Jouanin L, Pilate G, Strauss SH (2000) Diverse effects of overexpression of LEAFY and PTLF, a poplar (Populus) homologue of LEAFY/FLORICAULA, in transgenic poplar and Arabidopsis. Plant J 22:235–245

  24. Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards JA, Peacock WJ, Dennis ES (1999) The FLF MADS-box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458

  25. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JoinMap. Plant J 3:739–744

  26. Tartarini S, Gianfranceschi L, Sansavini S, Gessler C (1999) Development of reliable PCR markers for the selection of the Vf gene conferring scab resistance in apple. Plant Breed 118:183–186

  27. Wada M, Cao Q, Kotoda N, Soejima J, Masuda T (2002) Apple has two orthologues of FLORICAULA/LEAFY involved in flowering. Plant Mol Biol 49:567–577

  28. Wong A, Forbes MR, Smith ML (2001) Characterization of AFLP markers in damselflies: prevalence of codominant markers and implications for population genetics applications. Genome 44:677–684

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The authors thank Dr. Cetin Cekic for creating the BC1 mapping population and Dr. Vaseilios Stamatakos and Nicola Halstead for screening the mapping progenies with the SCAR markers. This study was supported by the UK Department for Environment, Food and Rural Affairs.

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Correspondence to M. J. Wilkinson.

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Communicated by H. Nybom

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Albani, M.C., Battey, N.H. & Wilkinson, M.J. The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca . Theor Appl Genet 109, 571–579 (2004).

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  • Bulk Segregant Analysis
  • ISSR Marker
  • Scar Marker
  • Internal Sequence
  • ISSR Primer