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

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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.

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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).

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Authors and Affiliations

  1. The New Zealand Institute for Plant and Food Research Ltd (Plant & Food Research), Hawke’s Bay Research Centre, Havelock North, New Zealand

    Vincent G. M. Bus, Reiny W. A. Scheper, Brent M. Fisher, Sarah L. Johnston, Gagandeep Singla, Linley K. Jesson & Richard K. Volz

  2. Plant & Food Research, Motueka Research Centre, Motueka, New Zealand

    Monika Walter, Rebecca E. Campbell, Biff Kitson & Lauren Turner

  3. Plant & Food Research, Mt Albert Research Centre, Auckland, New Zealand

    Chen Wu & Cecilia H. Deng

  4. Plant & Food Research, Palmerston North Research Centre, Palmerston North, New Zealand

    Deepa Bowatte, Duncan I. Hedderley, David Chagné & Susan E. Gardiner

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  1. Vincent G. M. Bus
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  2. Reiny W. A. Scheper
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Correspondence to Vincent G. M. Bus.

Additional information

Communicated by V. Decroocq

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Electronic supplementary material

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)

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)

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)

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)

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)

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Bus, V.G.M., Scheper, R.W.A., Walter, M. et al. Genetic mapping of the European canker (Neonectria ditissima) resistance locus Rnd1 from Malus ‘Robusta 5’. Tree Genetics & Genomes 15, 25 (2019). https://doi.org/10.1007/s11295-019-1332-y

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