Advertisement

Tree Genetics & Genomes

, 15:25 | Cite as

Genetic mapping of the European canker (Neonectria ditissima) resistance locus Rnd1 from Malus ‘Robusta 5’

  • Vincent G. M. BusEmail author
  • Reiny W. A. Scheper
  • Monika Walter
  • Rebecca E. Campbell
  • Biff Kitson
  • Lauren Turner
  • Brent M. Fisher
  • Sarah L. Johnston
  • Chen Wu
  • Cecilia H. Deng
  • Gagandeep Singla
  • Deepa Bowatte
  • Linley K. Jesson
  • Duncan I. Hedderley
  • Richard K. Volz
  • David Chagné
  • Susan E. Gardiner
Original Article
  • 12 Downloads
Part of the following topical collections:
  1. Disease Resistance

Abstract

Current control strategies for the major apple disease European canker (EC) are laborious and expensive, and often do not prevent progression of the disease, which can lead to loss of trees and therefore production. Hence, the development of resistant cultivars is a significant goal for breeders supporting growers in maritime climates conducive to the disease. With genetic markers increasingly being used as a tool in marker-assisted selection for parental and seedling selection, genetic mapping of major effect loci controlling resistance to the pathogen is integral to most breeding programmes. We report the genetic mapping of EC resistance in a bi-parental progeny derived from a cross between moderately EC-resistant ‘Malling 9’ (‘M9’) and highly resistant Malus ‘Robusta 5’ (R5) using two resistance phenotyping techniques. Field inoculation of rasp wounds on the stem and lateral shoots of replicated plants grown on their own roots with a suspension of Neonectria ditissima conidia proved both easier to perform and more effective than inoculation onto leaf scars. Rasp wound phenotype data combined with a previously reported genetic map enabled us to identify a large-effect QTL for control of resistance to EC on linkage group 14 of R5, which we named Rnd1. The position of this QTL was confirmed using leaf scar phenotyping data from the field and glasshouse inoculations. We have developed new SNP markers for this locus, using a novel bioinformatic SNP filtering tool that searches aligned genomic sequences of multiple apple accessions. We have converted one of these markers into a high-throughput version for application in marker-assisted selection of apple.

Keywords

Apple Leaf scar Rasp wound QTL High-throughput marker Marker-assisted selection 

Notes

Acknowledgements

The research was funded by Prevar™ and the Strategic Science Investment Fund from the Ministry of Business, Innovation and Employment. We thank Gail Timmerman-Vaughan and Jibran Tahir for critical reading of the manuscript.

Data archiving statement

The complete data set for the summary of BLUPS data for the glasshouse and field evaluation of the M9×R5 family provided in Table 1 is presented in Supplementary Table 1. The genetic map of the M9×R5 has been submitted to GDR (https://www.rosaceae.org/node/1539159).

Supplementary material

11295_2019_1332_MOESM1_ESM.docx (509 kb)
Supplementary Fig. 1 Leaf scar identification in the glasshouse experiments using a white paint pen (a), and wound preparation using a rasp (b) for brush inoculation with Neonectria ditissima conidia (c) during field phenotyping for European canker resistance. (DOCX 508 kb)
11295_2019_1332_MOESM2_ESM.docx (932 kb)
Supplementary Fig. 2 European canker symptoms on ‘M9’ (a), ‘M9’ x ‘Robusta 5’ progeny AJ79 (b), AJ169 (c), AJ185 (d), AJ197 (e) and ‘Royal Gala’ (f) 15 weeks after inoculation, and ‘Robusta 5’ (g) showing no symptoms 10 months after leaf scar inoculation in the 2012 glasshouse experiment. (DOCX 932 kb)
11295_2019_1332_MOESM3_ESM.docx (596 kb)
Supplementary Fig. 3 Comparison of mean canker lesion length and disease incidence for the accessions showing lesions in the 2012 glasshouse experiment from nine observation times (8, 10, 12, 15, 17, 19, 21, 25 and 29 weeks after inoculation). Long lesions were exhibited by both high and low incidence accessions, i.e. lesion length and disease incidence was not correlated in our study. (DOCX 596 kb)
11295_2019_1332_MOESM4_ESM.docx (312 kb)
Supplementary Fig. 4 Simple dot plots showing association of the LG14_31201280 marker allele ab from crab apple ‘Robusta 5’ (R5) with European canker disease incidence (a, b), but not with lesion length (c, d) in progeny of the M9xR5 segregating population evaluated in the glasshouse 22 (in 2012) and 25 (in 2014) weeks after inoculation. ns = not significant at P = 0.05 (DOCX 312 kb)
11295_2019_1332_MOESM5_ESM.docx (59 kb)
Supplementary Table 1 The best linear unbiased prediction values for European canker disease incidence (proportion infected wounds as a percentage of the number of inoculated wounds) and area under the disease progress curve (AUDPC) on trees on their own roots in the field, for two inoculation methods, leaf scar and rasp wound, ranked by rasp wound incidence. (DOCX 59 kb)

References

  1. Alston FH (1970) Response of apple cultivars to canker, Nectria galligena. Rep East Malling Res Station For 1969:147–148Google Scholar
  2. Amponsah NT, Walter M, Beresford RM, Scheper RWA (2015) Seasonal wound presence and susceptibility to Neonectria ditissima infection in New Zealand apple trees. N Z Plant Protect 68:250–256Google Scholar
  3. Amponsah NT, Scheper RWA, Fisher B, Walter M, Smits JM, Jesson LK (2017) The effect of wood age on infection by Neonectria ditissima through artificial wounds on different apple cultivars. N Z Plant Protect 70:97–105Google Scholar
  4. Bagenal NB (1945) Fruit growing. Modern cultural methods. Ward, Lock & Co. Limited, London, p 416Google Scholar
  5. Bassett H, Malone M, Ward S, Foster T, Chagné D, Bus V (2015) Marker assisted selection in an apple rootstock breeding family. Acta Hortic 1100:25–28CrossRefGoogle Scholar
  6. Beresford RM, Kim KS (2011) Identification of regional climatic conditions favorable for development of European canker of apple. Phytopathology 101:135–146CrossRefGoogle Scholar
  7. Børve J, Kolltveit SA, Talgø V, Stensvand A (2017) Apple rootstocks may become infected by Neonectria ditissima during propagation. Acta Agric Scand Sect B Soil Plant Sci 68:16–25.  https://doi.org/10.1080/09064710.2017.1351578 CrossRefGoogle Scholar
  8. Bus VGM, Chagné D, Bassett HCM, Bowatte D, Calenge F, Celton J-M, Durel C-E, Malone MT, Patocchi A, Ranatunga AC, Rikkerink EHA, Tustin DS, Zhou J, Gardiner SE (2008) Genome mapping of three major resistance genes to woolly apple aphid (Eriosoma lanigerum Hausm.). Tree Genet Genomes 4:223–236CrossRefGoogle Scholar
  9. Bus VGM, Esmenjaud D, Buck E, Laurens F (2009) Application of genetic markers in rosaceous crops. In: Folta KM, Gardiner SE (eds) Genetics and genomics of the Rosaceae, plant genetics and genomics: crops and models 6, Springer Science+Business Media, p 563–599Google Scholar
  10. Bus V, Singla G, Ward S, Brewer L, Morgan C, Bowatte D, Bassett H, Attfield B, Colhoun C, Bastiaanse H, Walter M, Scheper R, Fisher B, Won K, Montanari S, Volz R, Chagné D, Gardiner SE (2017) Progress in pipfruit resistance breeding and research at Plant & Food Research. Acta Hortic 1172:7–14CrossRefGoogle Scholar
  11. Calenge F, Durel CE (2006) Both stable and unstable QTLs for resistance to powdery mildew are detected in apple after four years of field assessments. Mol Breed 17:329–339CrossRefGoogle Scholar
  12. Campbell RE, Roy S, Curnow T, Walter M (2016) Monitoring methods and spatial patterns of European canker disease in commercial orchards. N Z Plant Protect 69:213–220Google Scholar
  13. Celton J-M, Tustin DS, Chagné D, Gardiner S (2009) Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet Genomes 5:93–107CrossRefGoogle Scholar
  14. Chagné D, Gasic K, Crowhurst RN, Han Y, Bassett HC, Bowatte DR, Lawrence TJ, Rikkerink EHA, Gardiner SE, Korban SS (2008) Development of a set of SNP markers present in expressed genes of apple. Genomics 92:353–358CrossRefGoogle Scholar
  15. Cooke LR (1999) The influence of fungicide sprays on infection of apple cv. Bramley’s seedling by Nectria galligena. Eur J Plant Pathol 105:783–790CrossRefGoogle Scholar
  16. Daccord N, Celton C-M, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro EA, Gouzy J, Rees DJG, Guérif P, Muranty H, Durel C-E, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, Quesneville H, Weigel D, van de Weg E, Troggio M, Bucher E (2017) High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet 49:1099–1108CrossRefGoogle Scholar
  17. Dryden GH, Nelson MA, Smith JT, Walter M (2016) Postharvest foliar nitrogen applications increase Neonectria ditissima leaf scar infection in apple trees. N Z Plant Protect 69:230–237Google Scholar
  18. Duan N, Bai Y, Sun H, Wang N, Ma Y, Li M, Wang X, Jiao C, Legall N, Mao L, Wan S, Wang K, He T, Feng S, Zhang Z, Mao Z, Shen X, Chen X, Jiang Y, Wu S, Yin C, Ge S, Yang L, Jiang S, Xu H, L J WD, Qu C, Wang Y, Zuo W, Xiang L, Liu C, Zhang D, Gao Y, Xu Y, Xu K, Chao T, Fazio G, Shu H, Zhong G-Y, Cheng L, Fei Z, Chen X (2017) Genome re-sequencing reveals the history of apple and supports a two-stage model for fruit enlargement. Nat Commun 8:249CrossRefGoogle Scholar
  19. Dubin HJ, English H (1974) Factors affecting apple leaf scar infection by Nectria galligena conidia. Phytopathology 64:1201–1203CrossRefGoogle Scholar
  20. Foster TM, Celton J-M, Chagné D, Tustin DS, Gardiner SE (2015) Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple. Hortic Res 2:15001CrossRefGoogle Scholar
  21. Gardiner SE (2017) Novel genetic marker technologies revolutionize apple breeding. Acta Hortic 1174:23–30CrossRefGoogle Scholar
  22. Gardiner SE, Norelli JL, da Silva N, Fazio G, Peil A, Malnoy M, Horner M, Bowatte D, Carlisle C, Wiedow C, Wan YZ, Bassett CL, Baldo AM, Celton J-M, Richter 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 13:25CrossRefGoogle Scholar
  23. Garkava-Gustavsson L, Zborowska A, Sehic J, Rur M, Nybom H, Englund J-E, Lateur M, van de Weg E, Holefors A (2013) Screening of apple cultivars for resistance to European canker, Nectria galligena. Acta Hortic 976:529–536CrossRefGoogle Scholar
  24. Garkava-Gustavsson L, Ghasemkhani M, Zborowska A, Englund JE, Lateur M, van de Weg E (2016) Approaches for evaluation of resistance to European canker (Neonectria ditissima) in apple. Acta Hortic 1127:75–81CrossRefGoogle Scholar
  25. Gelvonauskiene D, Sasnauskas A, Gelvonauskis B (2007) The breeding of apple tree resistant to European canker (Nectria galligena Bres.). Sodinink Darzinink 26:174–178Google Scholar
  26. Ghasemkhani M, Liljeroth E, Sehic J, Zborowska A, Nybom H (2015a) Cut-off shoots method for estimation of partial resistance in apple cultivars to fruit tree canker caused by Neonectria ditissima. Acta Agric Scand Sect B Soil Plant 65:412–421Google Scholar
  27. Ghasemkhani M, Sehic J, Ahmadi-Afzadi M, Nybom H, Garkava-Gustavsson L (2015b) Screening for partial resistance to fruit tree canker in apple cultivars. Acta Hortic 1099:687–690CrossRefGoogle Scholar
  28. Gómez-Cortecero A, Saville RJ, Scheper RWA, Bowen JK, Agripino De Medeiros H, Kingsnorth J, Xu X, Harrison RJ (2016) Variation in host and pathogen in the Neonectria/Malus interaction; toward an understanding of the genetic basis of resistance to European canker. Front Plant Sci 7:1365CrossRefGoogle Scholar
  29. Grove GG (1990) Nectria canker. In: Jones AL, Aldwinckle HS (eds) Compendium of apple and pear diseases. APS Press, St Paul, pp 35–36Google Scholar
  30. Kazlouskaya ZA, Marchuk YG (2013) Evaluation of susceptibility to Nectria canker as initial material for apple breeding. Acta Hortic 976:549–554CrossRefGoogle Scholar
  31. Krüger J (1983) Anfälligkeiten von Apfelsorten und Kreuzungsnachkommenschaften für den Obstbaumkrebs nach natürlicher und künstlicher Infektion. Erwerbstobstbau 114:114–116Google Scholar
  32. Langmead B, Salzberg S (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359CrossRefGoogle Scholar
  33. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25:2078–2079CrossRefGoogle Scholar
  34. Moore MH (1934) Some field observations on apple canker (Nectria galligena). Rep East Malling Res Station for 1933:166–175Google Scholar
  35. Moore MH (1960) Apple rootstocks susceptible to scab, mildew and canker for use in glasshouse and field experiments. Plant Pathol 9:84–87CrossRefGoogle Scholar
  36. Palm G, Harms F, Vollmer I (2011) Mehrjährige Befallsentwicklung des Obstbaukrebses an verschiedenen Apfelsorten an drei Standorten. Mitt OVR 66:360–363Google Scholar
  37. Peil A, Richter K, Garcia-Libreros T, Hanke MV, Flachowsky H, Celton J-M, Horner M, Gardiner S, Bus V (2008) Confirmation of the fire blight QTL of Malus x robusta 5 on linkage group 3. Acta Hortic 793:297–303CrossRefGoogle Scholar
  38. Rusholme Pilcher RL, Celton J-M, Gardiner SE, Tustin DS (2008) Genetic markers linked to the dwarfing trait of apple rootstock ‘Malling 9’. J Am Soc Hortic Sci 133:100–106CrossRefGoogle Scholar
  39. Scheper RWA, Stevenson OD, Hedderley (2016) Protection of budding wounds in apple nursery trees from European canker. N Z Plant Protect 69:207–212Google Scholar
  40. Scheper RWA, Frijters L, Fisher BM, Hedderley DI (2015) Effect of freezing of Neonectria ditissima inoculum on its pathogenicity. N Z Plant Protect 68:257–263Google Scholar
  41. Scheper RWA, Walter M, Fisher BM, Johnston SL, Curnow T, Amponsah NT, Hedderley DI (2017) Resistance of apple and pear rootstocks to Neonectria ditissima and their effect on scion susceptibility. N Z Plant Protect 70:324Google Scholar
  42. Umpleby E, Swarbrick T (1936) The incidence of canker in young cider apple trees. Ann Rep Long Ashton Agric Hortic Res Station for 1935:98–103Google Scholar
  43. Van de Weg WE (1987) Note on an inoculation method to infect young apple seedlings with Nectria galligena Bres. Euphytica 36:853–854CrossRefGoogle Scholar
  44. Van de Weg WE (1989) Screening for resistance to Nectria galligena Bres. in cut shoots of apple. Euphytica 43:233–240CrossRefGoogle Scholar
  45. Walter M, Stevenson OD, Amponsah NT, Scheper RWA, Rainham D, Hornblow C, Kerer U, Dryden G, Latter I, Butler RC (2015) Control of Neonectria ditissima with copper based products in New Zealand. N Z Plant Protect 68:241–249Google Scholar
  46. Walter M, Roy S, Fisher BM, Mackle L, Amponsah NT, Curnow T, Campbell RE, Braun P, Reinecke A, Scheper RWA (2016) How many conidia are required for wound infection of apple plants by Neonectria ditissima? N Z Plant Protect 69:238–245Google Scholar
  47. Walter M, Campbell RE, Amponsah NT, Turner L, Rainham D, Kerer U, Butler RC (2017) Can biological products control Neonectria ditissima picking wound and leaf scar infections in apples? N Z Plant Protect 70:63–72Google Scholar
  48. Wan Y, Fazio G (2011) Confirmation by QTL mapping of the Malus robusta (‘Robusta 5’) derived powdery mildew resistance gene Pl1. Acta Hortic 903:95–99CrossRefGoogle Scholar
  49. Weber RWS (2014) Biology and control of the apple canker fungus Neonectria ditissima (syn. N. galligena) from a northwestern European perspective. Erwerbs-Obstbau 56:95–107CrossRefGoogle Scholar
  50. Wenneker M, Goedhart PW, Van der Steeg P, Van de Weg WE, Schouten HJ (2017) Methods for the quantification of resistance of apple genotypes to European fruit tree canker caused by Neonectria ditissima. Plant Dis 101:2012–2019CrossRefGoogle Scholar
  51. Wormald H (1955) Diseases of fruits and hops. Crosby Lockwood & Son Ltd, London, p 325Google Scholar
  52. Xu X-M, Butt DJ, Ridout MS (1998) The effects of inoculum dose, duration of wet period, temperature and wound age on infection by Nectria galligena of pruning wounds on apple. Eur J Plant Pathol 104:511–519CrossRefGoogle Scholar
  53. Zagaja SW, Millikan DF, Kaminski W, Myszka T (1971) Field resistance to Nectria canker in apple. Plant Dis Rep 55:445–447Google Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Vincent G. M. Bus
    • 1
    Email author
  • Reiny W. A. Scheper
    • 1
  • Monika Walter
    • 2
  • Rebecca E. Campbell
    • 2
  • Biff Kitson
    • 2
  • Lauren Turner
    • 2
  • Brent M. Fisher
    • 1
  • Sarah L. Johnston
    • 1
  • Chen Wu
    • 3
  • Cecilia H. Deng
    • 3
  • Gagandeep Singla
    • 1
  • Deepa Bowatte
    • 4
  • Linley K. Jesson
    • 1
  • Duncan I. Hedderley
    • 4
  • Richard K. Volz
    • 1
  • David Chagné
    • 4
  • Susan E. Gardiner
    • 4
  1. 1.The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research)Hawke’s Bay Research CentreHavelock NorthNew Zealand
  2. 2.Plant & Food ResearchMotueka Research CentreMotuekaNew Zealand
  3. 3.Plant & Food ResearchMt Albert Research CentreAucklandNew Zealand
  4. 4.Plant & Food ResearchPalmerston North Research CentrePalmerston NorthNew Zealand

Personalised recommendations