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The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers

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Breeding in raspberry is time-consuming due to the highly heterozygous nature of this perennial fruit crop, coupled with relatively long periods of juvenility. The speed and precision of raspberry breeding can be improved by genetic linkage maps, thus facilitating the development of diagnostic markers for polygenic traits and the identification of genes controlling complex phenotypes. A genetic linkage map (789 cM) of the red raspberry Rubus idaeus has been constructed from a cross between two phenotypically different cultivars; the recent European cultivar Glen Moy and the older North American cultivar Latham. SSR markers were developed from both genomic and cDNA libraries from Glen Moy. These SSRs, together with AFLP markers, were utilised to create a linkage map. In order to test the utility of the genetic linkage map for QTL analysis, morphological data based on easily scoreable phenotypic traits were collected. The segregation of cane spininess, and the root sucker traits of density and spread from the mother plant, was quantified in two different environments. These traits were analysed for significant linkages to mapped markers using MapQTL and were found to be located on linkage group 2 for spines and group 8 for density and diameter. The availability of co-dominant markers allowed heterozygosities to be calculated for both cultivars.

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  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJJ (1990) Basic local alignment search tool. Mol Biol 215:403–410

    Article  CAS  PubMed  Google Scholar 

  • Antonius-Klemola K (1999) Molecular markers in Rubus (Rosaceae) research and breeding. J Hortic Sci Biotech 74:149–160

    CAS  Google Scholar 

  • Bradshaw HD Jr, Stettler RF (1994) Molecular genetics of growth and development in Populus. IV. Mapping QTLs with large effects on growth, form and phenology traits in a forest tree. Genetics 139:963–973

    Google Scholar 

  • Bradshaw HD Jr, Villar M, Watson BD, Otto KG, Stewart S, Stettler RF (1994) Molecular genetics of growth and development in Populus. III. A genetic linkage map of a hybrid poplar composed of RFLP, STS and RAPD markers. Theor Appl Genet 89:167–178

    CAS  Google Scholar 

  • Dale A, Moore PP, McNicol RJ, Sjulin TM, Burmistrov LA (1993) Genetic diversity of red raspberry varieties throughout the world. J Am Soc Hortic Sci 118:119–129

    Google Scholar 

  • Davis TM, Yu H (1997) A linkage map of the diploid strawberry Fragaria vesca. J Hered 88:215–221

    CAS  Google Scholar 

  • Ellis RP, McNicol JW, Baird E (1997) The use of AFLPs to examine genetic relatedness in barley. Mol Breed 3:359–369

    CAS  Google Scholar 

  • Fatahi R, Ebadi A, Bassil N, Mehlenbacher SA, Zamani Z (2003) Characterisation of Iranian grapevine cultivars using microsatellite markers. Vitis 42:185–192

    CAS  Google Scholar 

  • Galletta GJ (1983) Pollen and seed management. In. Moore JM, Janick J (eds) Methods in fruit breeding. Purdue University Press, West Lafayette pp 23–47

  • Graham J, McNicol RJ (1995) An examination of the ability of RAPD markers to determine the relationships within and between Rubus species. Theor Appl Genet 90:1128–1132

    CAS  Google Scholar 

  • Graham J, Smith K, Woodhead M, Russell J (2002) Development and use of simple sequence repeat SSR markers in Rubus species. Mol Ecol Notes 2:250–252

    Article  CAS  Google Scholar 

  • Graham J, Marshall B, Squire GR (2003) Genetic differentiation over a spatial environmental gradient in wild Rubus idaeus populations. New Phytol 157:667–675

    Article  Google Scholar 

  • Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137

    CAS  PubMed  Google Scholar 

  • Hall HK, Cohen D, Skirvin RM (1986) The inheritance of thornlessness from tissue culture derived “Thornless Evergreen” blackberry. Euphytica 54:891–898

    Google Scholar 

  • Haskell G (1960) The raspberry wild in Britain. Watsonia 4:238–255

    Google Scholar 

  • Hemmat M, Weeden NF, Brown SK (2003) Mapping and evaluation of Malus × domestica microsatellites in apple and pear. J Amer Soc Hort Sci 128:515–520

    CAS  Google Scholar 

  • Hokanson SC (2001) SNiPs, Chips, BACs and YACs: are small fruits part of the party mix? HortScience 36:859–871

    Google Scholar 

  • Jennings DL (1988) Raspberries and blackberries: their breeding, diseases and growth. Academic, London

    Google Scholar 

  • Jennings DL, Ingram R (1983) Hybrids of Rubus parvifolius (Nutt.) with raspberry and blackberry, and the inheritance of spinelessness derived from this species. Crop Res 23:95–101

    Google Scholar 

  • Knight RL, Keep E (1960) The genetics of suckering and tip rooting in the raspberry. In: Report of East Malling Research Station for 1959, pp 57–62

  • Lewis D (1939) Genetical studies in cultivated raspberries. I. Inheritance and linkage. J Genet 38:367–379

    Google Scholar 

  • Macaulay M, Ramsay L, Powell W, Waugh R (2001) A representative, highly informative ‘genotyping set’ of barley SSRs. Theor Appl Genet 102:801–809

    CAS  Google Scholar 

  • Maliepaard C, Van Ooijen JW (1994) QTL mapping in a full-sib family of an outcrossing species. In: Van Ooijen JW, Jansen J (eds) Biometrics in plant breeding: applications of molecular markers. Proceedings of the ninth meeting of the Eucarpia section biometrics in plant breeding, Wageningen, The Netherlands

  • Maliepaard C, Jansen J, Van Ooijen JW (1997) Linkage analysis in a full-sib family of an outbreeding plant species: overview and consequences for applications. Genet Res 70:237–250

    Article  Google Scholar 

  • McNicol RJ, Graham J (1992) Temperate small fruits. In: Hammerschlag FA, Litz RE (eds) Biotechnology of perennial fruit crops. CAB International, Wallingford, pp 303–321

  • McPheeters K, Skirvin RM (1983) Histogenic layer manipulation in chimeral “Thornless Evergreen” trailing blackberry. Euphytica 32:351–360

    Google Scholar 

  • Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with non-repetitive DNA in plant genomes. Nature Genet 30:194–200

    CAS  PubMed  Google Scholar 

  • Nybom H (1985) Chromosome numbers and reproduction in Rubus subgen. Malachobatus. Pl Syst Evol 152:211–218

    Google Scholar 

  • Pool RA, Ingram R, Abbot RJ, Jennings DL, Topham PB (1981) Karyotype variation in Rubus with special reference to R. idaeus L. and R. coreanus Miquel. Cytologia 46:125–132

    Google Scholar 

  • Qu LP, Hancock JF (1997) Randomly amplified polymorphic DNA-(RAPD-) based genetic linkage map of blueberry derived from an interspecific cross between diploid Vaccinium darrowi and tetraploid V. corymbosum. J Amer Soc Hort Sci 122:69–73

    CAS  Google Scholar 

  • Rafalski JA (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci 162:329–330

    Article  CAS  Google Scholar 

  • Ritter E, Gebhardt C, Salamini F (1990) Estimation of recombination frequencies and construction of RFLP linkage maps in plants from crosses between heterozygous parents. Genetics 125:645–654

    CAS  PubMed  Google Scholar 

  • Roach FA (1985) Cultivated fruits of Britain: their origin and history. Blackwell, Oxford

    Google Scholar 

  • Rosati P, Gaggioli D, Giunchi L (1986) Genetic stability of micropropagated Loganberry plants. J Hort Sci 61:33–41

    Google Scholar 

  • Rosati P, Hall HK, Jennings DL, Gaggiolo D (1988) A dominant gene for thornlessness obtained from the chimeral thornless Loganberry. HortScience 23:899–902

    Google Scholar 

  • Rowland LJ, Levi A (1994) RAPD-based genetic linkage map of blueberry derived from a cross between diploid species (Vaccinium darrowi and V. elliottii). Theor Appl Genet 87:863–868

    CAS  Google Scholar 

  • Rozen S, Skaletsky HJ (1998) Primer 3. Code available at

  • Sanford JC (1983) Ploidy manipulations. In: Moore JM, Janick J (eds) Methods in fruit breeding, Purdue University Press, pp 100–123

  • Sargent DJ, Hadonou AM, Simpson DW (2003) Development and characterisation of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Mol Ecol Notes 3:550–552

    Article  CAS  Google Scholar 

  • Spielman RS, McGuiness RE, Ewens WJ (1993) Transmission tests for linkage disequilibrium: the insulin gene region and insulin dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506–516

    PubMed  Google Scholar 

  • Stam P, Van Ooijen JW (1995) JoinmapTM version 2.0: Software for the calculation of genetic linkage maps. CPRO-DLO, Wageningen

  • Struss D, Ahmad R, Southwick SM, Boritzki M (2003) Analysis of sweet cherry (Prunus avium L.) cultivars using SSR and AFLP markers. J Amer Soc Hort Sci 128:904–909

    CAS  Google Scholar 

  • Van Ooijen JW, Maliepaard C (1996) MapQTLTM version 3.0: Software for the calculation of QTL positions on genetic linkage maps. CPRO-DLO, Wageningen

  • Woodhead M, Taylor M, Davies HV, Brennan RM, McNicol RJ (1997) Isolation of RNA from blackcurrant (Ribes nigrum L.) fruit. Mol Biotech 7:1–4

    CAS  Google Scholar 

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This work was financially supported by the Scottish Executive Environment and Rural Affairs Department. With thanks to W.B.T. Thomas, J.E. Bradshaw, D. Marshall, J. Russell, and N. Jennings for helpful discussions on the manuscript and linkage mapping.

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Correspondence to J. Graham.

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Communicated by H. Nybom

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Graham, J., Smith, K., MacKenzie, K. et al. The construction of a genetic linkage map of red raspberry (Rubus idaeus subsp. idaeus) based on AFLPs, genomic-SSR and EST-SSR markers. Theor Appl Genet 109, 740–749 (2004).

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