Identification of a major quantitative trait locus for resistance to fire blight in the wild apple species Malus fusca

Molecular Breeding

Volumn 34, Issue 2, 2014, Pages 407-419

  Emeriewen, Ofere ^a,b   Richter, Klaus ^b   Kilian, Andrzej ^c   Zini, Elena ^a   Hanke, Magda Viola ^b   Malnoy, Mickael ^a   Peil, Andreas ^b  

^a RESEARCH AND INNOVATION CENTRE   (Italy)

^b INSTITUTE FOR EPIDEMIOLOGY AND PATHOGEN DIAGNOSTICS   (Germany)

^c Triticarte P L   (Australia)

Author keywords

DArT markers; Erwiniaamylovora; Fire blight; Malus fusca; QTL mapping; SSR markers

Indexed keywords

BACTERIA; DNA SEQUENCES; FIRE RESISTANCE; FRUITS; PLANTS (BOTANY);

BACTERIAL DISEASE; DIVERSITY ARRAY TECHNOLOGY MARKER; ERWINIAAMYLOVORA; FIRE BLIGHT; GRAM-NEGATIVE BACTERIA; LINKAGE GROUPS; MALU FUSCA; QUANTITATIVE TRAIT LOCI MAPPINGS; QUANTITATIVE TRAIT LOCUS; SIMPLE SEQUENCE-REPEAT MARKERS;

MAPPING;

EID: 84919345963     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-014-0043-1     Document Type: Article

References (61)

1. Akbari M, Wenzel P, Caig V, Carling J, Xia L, Yang S, Uszynski G, Mohler V, Lehmenseik A, Kuchel H, Hayden MJ, Howes N, Sharp P, Vaughan P, Rathmell B, Huttner E, Kilian A (2006) Diversity arrays technology (DArT) for high throughput profiling of the hexaploid wheat genome. Theor Appl Genet 113:1409–1420
2. Aldwinckle HS, Beer SV (1979) Fire blight and its control. Hort Rev 1:425–476
3. Aldwinkle HS, Way RD, Livermore JL, Preczewski L, Beer SV (1976) Fire blight in the Geneva apple collection. Fruit Varieties J 30:42–55
4. 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 MalusInfinium whole genome genotyping array. BMC Genom 13:203. doi:10.1186/1471-2164-13-203
5. Bonn WG, Van der Zwet T (2000) Distribution and economic importance of fire blight. In: Vanneste JL (ed) Fire blight: the disease and its causative agent: Erwinia amylovora. CAB Intl, Wallingford, pp 37–53
6. Calenge F, Drouet D, Denance C, Van de Weg WE, Brisset MN, Paulin JP, Durel CE (2005) Identification of a major QTL together with several minor additive or espistatic QTLs for resistance to fire blight in apple in two related progenies. Theor Appl Genet 111:128–135
7. Conner PJ, Brown SK, Weeden NF (1997) Randomly amplified polymorphic DNA-based genetic linkage maps of three apple cultivars. J Am Soc Hort Sci 3:350–359
8. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leafs. Phytochem Bull 19:11–15
9. Durel CE, Denance C, Brisset MN (2009) Two distinct major QTL for resistance to fire blight co-localize on linkage group 12 in apple genotypes ‘Evereste’ and Malus floribunda clone 821. Genome 52:139–147
10. 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 9:237–251
11. Flachowsky H, Le Roux PM, Peil A, Patocchi A, Richter K, Hanke V (2011) Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker assisted selection. New Phytol 192:364–377
12. Gardiner SE, Norelli JL, De Silva N, Fazio G, Peil A, Malnoy M, Horner M, Bowatte D, Carlisle C, Wiedow C, Wan Y, Bassett CL, Baldo AM, Celton JM, Ritcher K, Aldwinckle HS, Bus VGM (2012) Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus ‘Robusta 5′ accessions. BMC Genet 13:25. doi:10.1186/1471-2156-13-25
13. Han Y, Zheng D, Vimolmangkang S, Khan MA, Beever J, Korban S (2011) Integration of physical and genetic maps in apples confirms whole-genome and segmental duplications in the apple genome. J Exp Bot 14:51117–51130
14. Hemmat M, Weeden NF, Manganaris AG, Lawson DM (1994) Molecular marker linkage map for apple. J Hered 85:4–11
15. Hua J (2013) Modulation of plant immunity by light, circadian rhythm and temperature. Curr Opin Plant Biol 16:1–8
16. Jaccoud D, Peng K, Feinstein D, Kilian A (2001) Diversity arrays: a solid state technology for sequence information independent genotyping. Nucleic Acids Res 29:e25. doi:10.1093/nar/29.4.e25
17. Johnson KB, Stockwell VO (1998) Management of fire blight: a case study in microbial ecology. Annu Rev Phytopathol 36:227–248
18. Jones AL, Schnabel E (2000) The development of streptomycin-resistant strains of Erwinia amylovora. In: Vanneste JL (ed) Fire blight: the disease and its causative agent: Erwinia amylovora. CAB Intl, Wallingford, pp 335–367
19. Jones CJ, Edwards KJ, Castaglione S, Winfield MO, Sala F, van de Wiel C, Bredemeijer G, Vosman B, Matthes M, Daly A, Brettschneider R, Bettini P, Buiatti M, Maestri E, Malcevschi A, Marmiroli N, Aert R, Volckaert G, Rueda J, Linacero R, Vazquez A, Karp A (1997) Reproducibility testing of RAPD, AFLP, and SSR markers in plants by a network of European laboratories. Mol Breed 3:381–390
20. Khan MA, Duffy B, Gessler C, Patocchi A (2006) QTL mapping of fire blight resistance. Mol Breed 17:299–306
21. Khan MW, Zhao YF, Korban SS (2012) Molecular mechanisms of pathogenesis and resistance to the bacterial pathogen Erwinia amylovora, causal agent of fire blight disease in Rosaceae. Plant Mol Biol Rep 30:247–260
22. Khan MW, Zhao YF, Korban SS (2013) Identification of genetic loci associated with fire blight resistance in Malus through combined use of QTL and association mapping. Physiol Plantarum 148:344–353. doi:10.1111/ppl.12068
23. Kilian A, Wenzl P, Huttner E, Carling J, Xia L, Blois H, Craig V, Heller-Uszynska K, Jaccoud D, Hopper C, Aschenbrenner-Kilian M, Evers M, Peng K, Cayla C, Hok P, Uszynski G (2012) Diversity arrays technology: a generic genome profiling technology on open platforms. Methods Mol Biol 888:67–89. doi:10.1007/978-1-61779-870-2_5
24. Kleinhempel H, Kegler H, Ficke W, Schaefer HJ (1984) Methods of testing apples for resistance to fire blight. Acta Hort 151:261–265
25. Korban SS, Ries SM, Klopmeyer MJ, Morissey JF, Hattermann DR (1988) Genotype responses of scab-resistant apple cultivar/selections to two strains of Erwinia amylovora and the inheritance of resistance to fire blight. Ann Appl Biol 113:101–105
26. Le Roux PMF, Khan MA, Broggini GAL, Duffy B, Gessler C, Patocchi A (2010) Mapping of quantitative trait loci for fire blight resistance in the apple cultivars ‘Florina’ and ‘Nova Easygro’. Genome 53:710–722
27. Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, Van de Weg WE, Gessler C (2002) Development and characterisation of 140 new microsatellites in apple (Malus × domestica Borkh.). Mol Breed 10:217–241
28. Lu XP, Gui YJ, Xiao BG, Li YP, Tong ZJ, Liu Y, Bai XF, Wu WR, Xia L, Huttner E, Kilian A, Fan LJ (2013) Development of DArT markers for a linkage map of flue-cured tobacco. Chin Sci Bull 58:641–648. doi:10.1007/s11434-012-5453-z
29. Mace ES, Xia L, Jordan DR, Halloran K, Parh DK, Hunter E, Wenzl P, Kilian A (2008) DArT markers: diversity analyses and mapping in Sorghum bicolor. BMC Genom 9:26. doi:10.1186/1471-2229-9-13
30. Maliepaard C, Alston FH, van Arkel G, Brown LM, Chevreau E, Dunemann F, Evans KM, Gardiner S, Guilford P, van Heusden AW, Janse J, Laurens F, Lynn JR, Manganaris AG, Nijs APM, Periam N, Rikkerink E, Roche P, Ryder C, Sansavini S, Schmidt H, Tartarini S, den Verhaegh JJ, Vrielink van Ginkel M, King GJ (1998) Aligning male and female linkage maps of apple (Malus pumila Mill.) using multi-allelic markers. Theor Appl Genet 97:60–73
31. Malnoy M, Martens S, Norelli JL, Barny M, Sundin GW, Smiths THM, Brion D (2012) Fire blight: applied genomic insights of the pathogen and host. Annu Rev Phytopathol 50:475–494
32. McManus PS, Stockwell VO, Sundin GW, Jones AL (2002) Antibiotic use in plant agriculture. Annu Rev Phytopathol 40:443–465
33. Micheletti D, Troggio M, Zharkikh A, Costa F, Malnoy M, Velasco R, Salvi S (2011) Genetic diversity of the genus Malus and implications for linkage mapping with SNPs. Tree Genet Genomes 7:857–868
34. Norelli JN, Aldwinckle HS (1986) Differential susceptibility of Malus spp. cultivars Robusta 5, Novole, and Ottawa 523 to Erwinia amylovora. Plant Dis 70:1017–1019
35. Norelli JL, Jones AL, Aldwinkle HS (2003) Fire blight management in the twenty-first century—using new technologies that enhance host resistance in apple. Plant Dis 87:756–765
36. Oh C-S, Beer SV (2005) Molecular genetics of Erwinia amylovora involved in the development of fire blight. FEMS Microbiol Lett 253:185–192
37. Parravicini G, Gessler C, Denance 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 12:493–505
38. Peil A, Garcia-Libreros T, Richter K, Trognitz FC, Trognitz B, Hanke MV, Flachowsky H (2007) Strong evidence for a fire blight resistance gene of Malus robusta located on linkage group 3. Plant Breed 126:270–475
39. Peil A, Hanke MV, Flachowsky H, Richter K, Garcia-Libreros T, Celton JM, Gardiner S, Horner M, Bus V (2008) Confirmation of the fire blight QTL of Malus × robusta 5 on linkage group 3. Acta Hort 793:297–303
40. Peil A, Bus VGM, Geider K, Richter K, Flachowsky H, Hanke MV (2009) Improvement of fire blight resistance in apple and pear. Int J Plant Breed 3:1–27
41. Peil A, Flachowsky H, Hanke M-V, Richter K, Rode J (2011) Inoculation of Malus × robusta 5 progeny with a strain breaking resistance to fire blight reveals a minor QTL on LG5. Acta Hort 986:357–362
42. Rademacher W, Kober R (2003) Efficient use of Prohexadione-Ca in pome fruits. Eur J Hort Sci 68:101–107
43. Rozen S, Skaletsky HJ (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, Totowa, NJ, pp 365–386
44. Schouten HJ, van de Weg EW, Carling J, Khan SA, McKay SJ, van Kaauwen PW, Wittenberg AHJ, Koehorst van Putten HJJ, Noordijk Y, Gao Z, Rees DJG, Van Dyk MM, Jaccoud D, Considine MJ, Kilian A (2012) Diversity array technology (DArT) markers in apple for genetic linkage maps. Mol Breed 29:645–660. doi:10.1007/s11032-011-9579-5
45. Schuelke M (2000) An economic method for the fluorescent labelling of PCR fragments. Nat Biotechnol 18:233–234
46. Silfverberg-Dilworth E, Matasci CL, Vande Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patacchi A (2006) Microsatellite markers spanning the apple (Malus v domestica Borkh) genome. Tree Genet Genomes 2:202–224
47. Soriano JM, Joshi SG, Van Kaauwen M, Noordijk J, 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 5:475–482
48. Thomson SV (2000) Epidemiology of fire blight. In: Vanneste JL (ed) Fire blight: the disease and its causative agent, Erwinia amylovora. CAB International, Wallingford, pp 9–36
49. Tinker NA, Kilian A, Wight CP, Heller-Uszynska K, Wenzel P, Rines HW, Bjornstad, Howarth CJ, Jannink JL, Anderson JM, Rossnagel BG, Stuthman DD, Sorrells ME, Jackson EW, Tuvesson S, Kolb FL, Olsson O, Federizzi LC, Carson ML, Ohm HW, Molnar SJ, Scoles GJ, Eckstein PE, Bonman JM, Ceplitis A, Langdon T (2009) New DArT markers for oat provide enhanced map coverage and global germplasm characterization. BMC Genom 21:10–39
50. Tobler A, Short S, Andersen M, Paner T, Briggs J, Lambert S, Wu P, Wang Y, Spoonde A, Koehler R, Peyret N, Chen C, Broomer A, Ridzon D, Zhou H, Hoo B, Hayashibara K, Leong L, Ma C, Rosenblum B, Day J, Ziegle J, De La Vega F, Rhodes M, Hennessy K, Wenz H (2005) The SNPlex genotyping system: a flexible and scalable platform for SNP genotyping. J Biomol Technol 16:398–406
51. ® 5 Software for the mapping of quantitative trait loci in experimental populations. Plant Research International, Wageningen, The Netherlands
52. Van Ooijen JW, Maliepaard C (1996) MapQTL 4.0. Software for the calculation of QTL positions on genetic maps. CPRO-DLO, Wageningen, The Netherlands
53. ® 3.0, Software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands
54. Vanneste JL (2000) What is fire blight? Who is Erwinia amylovora? How to control it? In: Vanneste JL (ed) Fire blight: the disease and its causative agent: Erwinia amylovora. CAB International, Wallingford, pp 1–6
55. 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.). Nat Genet 42:833–839
56. Vogt I, Wöhner T, Richter K, Flachowsky H, Sundin GW, Wensing A, Savory EA, Geider K, Day B, Hanke MV, Peil A (2013) Gene-for-gene relationship in the host-pathogen system Malus × robusta 5-Erwinia amylovora. New Phytol 197:1262–1275
57. Wenzel P, Carling J, Kudrna D, Jaccoud D, Huttner E, Kleinhofs A, Kilian A (2004) Diversity arrays technology (DArT) for whole-genome profiling of barley. Proc Natl Acad Sci USA 101:9915–9920
58. White J, Law JR, McKay I, Chalmers KJ, Smith JSC, Kilian A, Powell W (2008) The genetic diversity of UK, US and Australian cultivars of Triticum aestivum measured by DArT markers and considered by genome. Theor Appl Genet 116:439–453
59. Wittenberg AHJ, Van der Lee T, Cayla C, Kilian A, Visser RGF, Schouten HJ (2005) Validation of the high throughput marker technology DArT using the model plant Arabidopsis thaliana. Mol Genet Genomics 274:30–39
60. Xia L, Peng K, Yang S, Wenzl P, de Vicente MC, Fregene M, Kilian A (2005) DArT of high-throughput genotyping of cassava (Manihot esculenta) and its wild relatives. Theor Appl Genet 110:1092–1098
61. Yang S, Pang W, Ash G, Harper J, Carling J, Wenzl P, Huttner E, Zong X, Kilian A (2006) Low level of genetic diversity in cultivated pigeon pea compared to its wild relatives is revealed by diversity arrays technology (DArT). Theor Appl Genet 113:585–595