Bioscience for sustainable agriculture and food

Category: Standard Studentships

Characterising Malus koreana as a source of pest and disease resistance for utilisation in apple rootstock breeding

Project No. 2133

Primary Supervisor

Dr Suzanne Litthauer – NIAB EMR


Dr Marta Farré Belmonte – University of Kent


Apple (Malus domestica Borkh.) is a widely cultivated crop, yet many commercial cultivars are susceptible to diseases.1,2

Apple (Malus domestica Borkh.) is a widely cultivated crop, yet many commercial cultivars are susceptible to diseases.1,2 With pesticides increasingly restricted and ineffective, host resistance is imperative to sustainable apple production.3,4

Resistant rootstocks can reduce the need for pesticides and prevent tree losses.3,5 Breeding for disease resistance is a major objective of the East Malling Rootstock Club (EMRC), with focus on Phytophthora cactorum (collar rot) and the aphid Eriosoma lanigerum. A marker-assisted breeding (MAB) approach is also employed to incorporate quantitative trait loci (QTLs)6-9 linked to fire blight (Erwinia amylovora) resistance.

Identifying new resistance sources is essential in breeding resilient rootstocks.3 Recent EMRC investigations revealed that a wild accession of Malus koreana is resistant to a pathogenic strain of E. amylovora. The accession also exhibits resistance to E. lanigerum and partial tolerance to Neonectria dittisima (apple canker). Since these disease resistances have not yet been reported in Malus koreana, the PhD studentship aims to investigate Malus koreana as a source of disease resistance for utilisation in rootstock breeding.  Work will be divided into three packages:


Sequence and assemble the whole genome of Malus koreana for employment as a resource in MAB: genome sequencing and assembly, and comparison of the genome to the available Malus domestica reference genome10 and to genome data for rootstock M.9 (available at NIAB EMR).


Characterise the resistance of Malus koreana to fire blight: inoculate a Malus koreana x M.9 seedling population with E. amylovora, investigate segregation of resistance, map resistance loci using publicly available SNP arrays,11,12 and develop linked markers for MAB.


Explore Malus koreana as a source of additional traits desirable in apple rootstock breeding: investigate adventitious rooting efficiency; and perform controlled inoculations to phenotype resistance to different strains of Erwinia amylovora, different isolates of Phytophthora cactorum, and tolerance to N. dittisima.


  1. Wang, Y., Li, W., Xu, X., Qiu, C., Wu, T., Wei, Q., Ma, F., and Han, Z. (2019). Progress of apple rootstock breeding and its use. Hortic Plant J. 5 (5) 183-191.
  2. Schlathölter, I., Jänsch, M., Flachowsky, H., Broggini, G.A.L, Hanke, M.V, Patocchi, A. (2018) Generation of advanced fire blight-resistant apple (Malus × domestica) selections of the fifth generation within 7 years of applying the early flowering approach. Planta 247 (6), 1475-1488.
  3. Kellerhals, M., Schütz, S., and Patocchi, A. (2017). Breeding for host resistance to fire blight.  Plant Pathol.99, 37–43.
  4. Migicovsky, Z., and Myles, S. (2017). Exploiting wild relatives for genomics-assisted breeding of perennial crops. Front Plant Sci.8, 460.
  5. Albacete, A., Martínez-Andújar, C., Martínez-Pérez, A., Thompson, A. J., Dodd, I. C., and Pérez-Alfocea, F. (2015). Unravelling rootstock×scion interactions to improve food security. J Exp Bot.66(8), 2211–2226.
  6. Peil, A., Garcia-Libreros, T., Richter, K., Trognitz, F.C., Trognitz, B., Hanke, M.-V., Flachowsky, H. (2007). Strong evidence for a fire blight resistance gene of Malus robustalocated on linkage group 3. Plant Breed. 126 (5), 270–475.
  7. Gardiner, S.E., Norelli, J.L., de Silva, N., Fazio, G., Peil, A., Malnoy, M., Horner, M., Bowatte, D., Carlisle., C, Wiedow, C., et al. (2012). Putative resistance gene markers associated with quantitative trait loci for fire blight resistance in Malus‘Robusta 5’ accessions. BMC Genet. 13, 25.
  8. Durel, C.-E., Denance, C., and Brisset, M.N. (2009). Two distinct major QTL for resistance to fire blight co-localize on linkage group 12 in apple genotypes ‘Evereste’ and Malus floribundaclone 821. Genome 52 (2), 139–147
  9. Fahrentrapp, J., Broggini, G.A.L., Kellerhals, M., Peil, A., Richter, K., Zini, E., and 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 (1), 237–251
  10. Daccord N., Celton J. M., Linsmith G., Becker C., Choisne N., Schijlen E., et al. (2017). High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Genet. 49 (7), 1099–1106.
  11. Bianco, L., Cestaro, A., Sargent, D. J., Banchi, E., Derdak, S., Di Guardo, M., Salvi, S., Jansen, J., Viola, R., Gut, I., Laurens, F., Chagné, D., Velasco, R., van de Weg, E., & Troggio, M. (2014). Development and validation of a 20K single nucleotide polymorphism (SNP) whole genome genotyping array for apple (Malus × domestica Borkh). PloS one 9(10).
  12. Bianco L, Cestaro A, Linsmith G, et al. (2016) Development and validation of the Axiom® Apple480K SNP genotyping array. Plant J. 86(1), 62-74.