Molecular Breeding

, 35:200 | Cite as

Fine mapping of the Rvi5 (Vm) apple scab resistance locus in the ‘Murray’ apple genotype

  • Valentina Cova
  • Nadeesha Lewke Bandara
  • Wei Liang
  • Stefano Tartarini
  • Andrea Patocchi
  • Michela Troggio
  • Riccardo Velasco
  • Matteo Komjanc


Apple scab, caused by the fungal pathogen Venturia inaequalis, is the most devastating pathogen in the apple-growing industry. In the last two decades, many studies have been initiated to identify new resistances to apple scab and to introgress them into new cultivars through breeding. The Rvi6 gene from Malus floribunda 821 has been the one most intensively used in breeding programmes worldwide, but the identification of new pathogen strains that are virulent to Rvi6 has increased the need for pyramiding of more than one resistance gene to obtain cultivars with durable resistance. Here, we report on the fine mapping of the Rvi5 apple scab resistance locus using two large segregating populations. A region of about 1 cM at the distal end of LG17 carrying the Rvi5 resistance gene was detailed by developing and mapping 10 molecular markers, including SCAR, SSR and SNP markers. The Rvi5 locus was restricted to a region of 228 kb on the ‘Golden Delicious’ reference genome between the two flanking SSR markers FMACH_Vm4 and FMACH_Vm2. Three co-segregating molecular markers were also developed (SSR FMACH_Vm3, Vm–SCAR1 and Vm-SNP5). All these markers will facilitate the development of marker-assisted selection protocols for this gene using both low-cost methods and high-throughput systems. The findings of this study will thus be useful for further investigation of the Rvi5 resistance locus of ‘Murray’, aimed at candidate gene identification and the physical isolation of the resistance gene.


Venturia inaequalis Apple scab Rvi5 Fine mapping Malus × domestica Murray 



This research was funded by the Agroalimentare research AGER project (grant no. 2010-2119) and by the Grant Office of the Autonomous Province of Trento. SNP development was funded under the EU Seventh Framework Programme through FruitBreedomics project no. 265582, ‘Integrated approach for increasing breeding efficiency in fruit tree crops’. The views expressed in this work are the sole responsibility of the authors and do not necessary reflect the views of the European Commission.

Supplementary material

11032_2015_396_MOESM1_ESM.docx (21 kb)
Supplementary material 1 (DOCX 21 kb)
11032_2015_396_MOESM2_ESM.docx (16 kb)
Supplementary material 2 (DOCX 16 kb)
11032_2015_396_MOESM3_ESM.docx (16 kb)
Supplementary material 3 (DOCX 16 kb)
11032_2015_396_MOESM4_ESM.docx (16 kb)
Supplementary material 4 (DOCX 15 kb)
11032_2015_396_MOESM5_ESM.png (201 kb)
Supplementary material 5 (PNG 201 kb)


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410CrossRefPubMedGoogle Scholar
  2. Anderson PA, Lawrence GJ, Morrish BC, Ayliffe MA, Finnegan EJ, Ellis JG (1997) Inactivation of the flax rust resistance gene M associated with loss of a repeated unit within the leucine-rich repeat coding region. Plant Cell 9:641–651PubMedCentralCrossRefPubMedGoogle Scholar
  3. Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ (2012) Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genom 13:203CrossRefGoogle Scholar
  4. Baldi P, Wolters PJ, Komjanc M, Viola R, Velasco R, Salvi S (2013) Genetic and physical characterisation of the locus controlling columnar habit in apple (Malus × domestica Borkh.). Mol Breed 31:429–440CrossRefGoogle Scholar
  5. Bastiaanse H, Bassett HCM, Kirk C, Gardiner SE, Deng C, Groenworld R, Chagne D, Bus VGM (2015) Scab resistance in ‘Geneva’ apple is conditioned by a resistance gene cluster with complex genetic control. Mol plant Pathol. doi: 10.1111/MPP.12269
  6. Beckerman J (2009) A 33-year evaluation of resistance and pathogenicity in the apple scab-crabapples pathosystem. HortScience 44:599–608Google Scholar
  7. Belfanti E, Silfverberg-Dilworth E, Tartarini S, Patocchi A, Barbieri M, Zhu J, Vinatzer BA, Gianfranceschi L, Gessler C, Sansavini S (2004) The HcrVf2 gene from a wild apple confers scab resistance to a transgenic cultivated variety. Proc Natl Acad Sci USA 101:886–890PubMedCentralCrossRefPubMedGoogle Scholar
  8. Bénaouf G, Parisi L (2000) Genetics of host-pathogen relationships between Venturia inaequalis races 6 and 7 and Malus species. Phytopathology 90:236–242CrossRefPubMedGoogle Scholar
  9. Botella MA, Parker JE, Frost LN, Bittner-Eddy PD, Beynon JL, Daniels MJ, Holub E, Jones JD (1998) Three genes of the Arabidopsis RPP1 complex resistance locus recognize distinct Peronospora parasitica avirulence determinants. Plant Cell 10:1847–1860PubMedCentralCrossRefPubMedGoogle Scholar
  10. Broggini GAL, Galli P, Parravicini G, Gianfranceschi L, Gessler C, Patocchi A (2009) HcrVf paralogs are present on linkage groups 1 and 6 of Malus. Genome 52:129–138CrossRefPubMedGoogle Scholar
  11. Broggini GAL, Fahrentrapp TWJ, Kost TD, Flachowsky H, Peil A, Hanke MV, Richter K, Patocchi A, Gessler C (2014) Engineering fire blight resistance into the apple cultivar ‘Gala’ using the FB_MR5 CC-NBS-LRR resistance gene of Malus × robusta 5. Plant Biotech 12:728–733CrossRefGoogle Scholar
  12. Bus VGM, Rikkerink EHA, Caffier V, Durel CE, Plummer KM (2011) Revision of the nomenclature of the differential host-pathogen interactions of Venturia inaequalis and Malus. Ann Rev Phytopathol 49:391–413CrossRefGoogle Scholar
  13. Cheng FS, Weeden NF, Brown SK, Aldwinckle HS, Gardiner SE, Bus VG (1998) Development of a DNA marker for Vm, a gene conferring resistance to apple scab. Genome 41:208–214CrossRefGoogle Scholar
  14. Chevalier M, Lespinasse Y, Renaudin S (1991) A microscopic study of different classes of symptoms coded by the Vf gene in apple for resistance to scab (Venturia inaequalis). Plant Pathol 40:249–256CrossRefGoogle Scholar
  15. Cova V, Lasserre P, Piazza S, Cestaro A, Velasco R, Durel CE, Malnoy M (2015) High-resolution genetic and physical map of the Rvi1 (Vg) apple scab resistance locus. Mol Breed 35:16. doi: 10.1007/s11032-015-0245-1 CrossRefGoogle Scholar
  16. Erdin N, Tartarini S, Broggini G, Gennari F, Sansavini S, Gessler C, Patocchi A (2006) Mapping of the apple scab resistance gene Vb. Genome 49:1238–1245CrossRefPubMedGoogle Scholar
  17. Fahrentrapp J, Broggini GAL, Kellerhals M, Peil A, Richter K, Zini E, Gessler C (2013) A candidate gene for fire blight resistance in Malus × robusta 5 is coding for a CC–NBS–LRR. Tree Genet Genomes 9:237–251CrossRefGoogle Scholar
  18. Galli P, Broggini GAL, Kellerhals M, Gessler C, Patocchi A (2010a) High-resolution genetic map of the Rvi15 (Vr2) apple scab resistance locus. Mol Breed 26:561–572CrossRefGoogle Scholar
  19. Galli P, Patocchi A, Broggini GAL, Gessler C (2010b) The Rvi15 (Vr2) apple scab resistance locus contains three TIR-NBS-LRR genes. Mol Plant-Microbe Interact 23:608–617CrossRefPubMedGoogle Scholar
  20. Gessler C, Patocchi A, Sansavini S, Tartarini S, Gianfranceschi L (2006) Venturia inaequalis resistance in apple. Crit Rev Plant Sci 25:1–31CrossRefGoogle Scholar
  21. Gygax M, Gianfranceschi L, Liebhard R, Kellerhals M, Gessler C, Patocchi A (2004) Molecular markers linked to the apple scab resistance gene Vbj derived from Malus baccata jackii. Theor Appl Genet 109:1702–1709CrossRefPubMedGoogle Scholar
  22. Hayden MJ, Tabone T, Mather DE (2009) Development and assessment of simple PCR markers for SNP genotyping in barley. Theor Appl Genet 119:939–951CrossRefPubMedGoogle Scholar
  23. Jänsch M, Broggini GAL, Weger J, Bus VGM, Gardiner SE, Bassett H, Patocchi A (2015) Identification of SNPs linked to eight apple disease resistance loci. Mol Breed 35:45. doi: 10.1007/s11032-015-0242-4 CrossRefGoogle Scholar
  24. Jha G, Thakur K, Thakur P (2009) The Venturia apple pathosystem: pathogenicity mechanisms and plant defense responses. J Biomed Biotechnol. doi: 10.1155/2009/680160 Google Scholar
  25. Joshi SG, Schaart JG, Groenwold R, Jacobsen E, Schouten HJ, Krens FA (2011) Functional analysis and expression profiling of HcrVf1 and HcrVf2 for development of scab resistant cisgenic and intragenic apples. Plant Mol Biol 75:579–591PubMedCentralCrossRefPubMedGoogle Scholar
  26. Lawrence GJ, Finnegan EJ, Ayliffe MA, Ellis JG (1995) The L6 gene for flax rust resistance is related to the Arabidopsis bacterial resistance gene Rps2 and the tobacco viral resistance gene N. Plant Cell 7:1195–1206PubMedCentralCrossRefPubMedGoogle Scholar
  27. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van de Weg E, Gessler C (2002) Development and characterization of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 10:217–241CrossRefGoogle Scholar
  28. MacHardy WE (1996) Apple scab, biology, epidemiology and management. APS Press, St. PaulGoogle Scholar
  29. Maguire TL, Collins GG, Sedgley M (1994) A modified CTAB DNA extraction procedure for plants belonging to the family Proteaceae. Plant Mol Biol Rep 12:106–109CrossRefGoogle Scholar
  30. Michael TP, Jackson S (2013) The first 50 plant genomes. Plant Genome 6:1–7CrossRefGoogle Scholar
  31. Parker JE, Coleman MJ, Szabo V, Frost LN, Schmidt R, Van der Biezen EA, Moores T, Dean C, Daniels MJ, Jones JDG (1997) The Arabidopsis downy mildew resistance gene RPP5 shares similarity to the toll and interleukin-1 receptors with N and L6. Plant Cell 9:879–894PubMedCentralCrossRefPubMedGoogle Scholar
  32. Parravicini G, Gessler C, Denancé C, Lasserre-Zuber P, Vergne E, Brisset MN, Patocchi A, Durel CE, Broggini GAL (2011) Identification of serine/threonine kinase and nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes in the fire blight resistance quantitative trait locus of apple cultivar ‘Evereste’. Mol Plant Pathol 12:493–505CrossRefPubMedGoogle Scholar
  33. Patocchi A, Gianfranceschi L, Gessler C (1999) Towards the map-based cloning of Vf: fine and physical mapping of the Vf Region. Theor Appl Genet 99:1012–1017CrossRefGoogle Scholar
  34. Patocchi A, Walser M, Tartarini S, Broggini GAL, Gennari F, Sansavini S, Gessler C (2005) Identification by genome scanning approach (GSA) of a microsatellite tightly associated with the apple scab resistance gene Vm. Genome 48:630–663CrossRefPubMedGoogle Scholar
  35. Patocchi A, Frei A, Frey JE, Kellerhals M (2009) Towards improvement of marker assisted selection of apple scab resistant cultivars: Venturia inaequalis virulence surveys and standardization of molecular marker alleles associated with resistance genes. Mol Breed 24:337–347CrossRefGoogle Scholar
  36. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132:365–386PubMedGoogle Scholar
  37. Salamov A, Solovyev V (2000) Ab initio gene finding in Drosophila genomic DNA. Genome Res 10:516–522PubMedCentralCrossRefPubMedGoogle Scholar
  38. Schouten HJ, Brinkhuis J, van der Burgh A, Schaart JG, Groenwold R, Broggini GAL, Gessler C (2014) Cloning and functional characterization of the Rvi15 (Vr2) gene for apple scab resistance. Tree Genet Genomes 10:251–260CrossRefGoogle Scholar
  39. Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet Genomes 2:202–224CrossRefGoogle Scholar
  40. Soriano JM, Joshi SG, van Kaauwen M, Noordijk Y, Groenwold R, Henken B, van de Weg WE, Schouten HJ (2009) Identification and mapping of the novel apple scab resistance gene Vd3. Tree Genet Genomes 5:475–482CrossRefGoogle Scholar
  41. Soriano JM, Madduri M, Schaart JG, Burge AVD, Kaauwen MPWV, Tomic L, Groenwold R, Velasco R, Van de Weg E, Schouten HJ (2014) Fine mapping of the gene Rvi18 (V25) for broad spectrum resistance to apple scab, and development of a linked SSR marker suitable for marker assisted breeding. Mol Breed 34:2021–2032CrossRefGoogle Scholar
  42. Temnykh S, Lukashova A, Cartinhour S, DeClerck G, Lipovich L, 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 11:1441–1452PubMedCentralCrossRefPubMedGoogle Scholar
  43. Van Ooijen JW (2006) JoinMap_4.0, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, WageningenGoogle Scholar
  44. Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D et al (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nature Genet 42:833–839CrossRefPubMedGoogle Scholar
  45. Vinatzer BA, Patocchi A, Gianfranceschi L, Tartarini S, Zhang HB, Gessler C, Sansavini S (2001) Apple contains receptor-like genes homologous to the Cladosporium fulvum resistance gene family of tomato with a cluster of genes co-segregating with Vf apple scab resistance. Mol Plant-Microbe Interact 14:508–515CrossRefPubMedGoogle Scholar
  46. Vinatzer BA, Patocchi A, Tartarini S, Gianfranceschi L, Sansavini S, Gessler C (2004) Isolation of two microsatellite markers from bac clones of the Vf scab resistance region and molecular characterization of scab-resistant accessions in Malus germplasm. Plant Breed 123:321–326CrossRefGoogle Scholar
  47. Voorrips R (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78CrossRefPubMedGoogle Scholar
  48. Warner J, Potter C (1988) Performance of scab resistant apple cultivars at the Smithfield Experimental farm. Fruit Var J 42:96–102Google Scholar
  49. Williams EB, Brown AG (1968) A new physiological race of Venturia inaequalis incitant of apple scab. Plant Dis Rep 52:799–801Google Scholar
  50. Williams EB, Kuc J (1969) Resistance in Malus to Venturia inaequalis. Annu Rev Phytopathol 7:223–246CrossRefGoogle Scholar
  51. Win J, Greenwood DR, Plummer KM (2003) Characterization of a protein from Venturia inaequalis that induces necrosis in Malus carrying the Vm resistance gene. Physiol Mol Plant Pathol 62:193–202CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2015

Authors and Affiliations

  1. 1.Research and Innovation CentreFondazione Edmund MachS. Michele All’adigeItaly
  2. 2.Department of Fruit Tree and Woody Plant ScienceUniversity of BolognaBolognaItaly
  3. 3.Agroscope, Institute for Plant Production Science IPSWädenswilSwitzerland

Personalised recommendations