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Epistatic fire blight resistance QTL alleles in the apple cultivar ‘Enterprise’ and selection X-6398 discovered and characterized through pedigree-informed analysis

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Abstract

Most cultivated apple cultivars are highly susceptible to fire blight, caused by Erwinia amylovora. However, differences in resistance levels are observed among cultivars and could be used in breeding. In this paper, we investigated the genetic basis of fire blight resistance of the cultivar ‘Enterprise’ and the advanced breeding selection X-6398. Genotyped pedigrees were used for validating and curating historic pedigree records. Various quantitative trait locus (QTL) discovery approaches were applied on the full-sib families ‘Gala’ × ‘Enterprise’ (GaEn) and X-6398 × X-6683 (IW) with the software FlexQTL™ and MapQTL®. The paternal lineage of ‘Enterprise’ was reconstructed and showed to include ‘Cox’s Orange Pippin’. The QTLs found varied with the software used. Using FlexQTL™, two were found on linkage groups (LGs) 7 and 13, favourable alleles inherited by Enterprise from ‘Cox’s Orange Pippin’ and ‘Golden Delicious’, respectively. The former was identical to the previously named FB_F7 allele from ‘Fiesta’, while the latter is new and has been named FB_13GD. X-6398 had a QTL at the same position as FB_F7. Its favourable allele was new, originating from the unknown grandfather of X-4598, and was named FB_7X-6398. Using MapQTL® on GaEn, FB_F7 was also identified. Performing the same analysis on the subset of offspring that carried the favourable allele of FB_F7, two putative QTLs on LG8 and on top of LG13 were identified, which showed interactions with FB_F7. Implication of the findings for breeding for fire blight-resistant apples is discussed. Single nucleotide polymorphism data on Enterprise and its ancestors are provided.

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Acknowledgments

The authors are grateful to A. Peil (JKI Dresden, Germany), S. Tartarini (DCA Bologna, Italy) and G. Fazio of the USDA-ARS Plant Genetic Resources Unit at Geneva (NY, USA) for providing part of, respectively, the budwood of the individuals used in this study and freeze-dried leaves of a series of individuals that allowed the reconstruction of the pedigree of ‘Enterprise’. H. Muranty (INRA-Angers, France) is acknowledged for tracing the true historic pedigree data of the INRA selection X-6398. The authors also thank the INRA Experimental Unit (UE Horticole) for maintaining the IW populations in the field.

Funding

The research was partially funded by the ZUEFOS II Project (Züchtung feuerbrandtoleranter Obstsorten) of the Federal Office for Agriculture (FOAG, Switzerland). This work has also been partly funded under the EU Seventh Framework Program by the FruitBreedomics project no. 265582: Integrated Approach for increasing breeding efficiency in fruit tree crops.

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  1. Didier Socquet-Juglard

    Present address: New York State Agricultural Experiment Station, Cornell University, Geneva, NY, 14456, USA

Authors and Affiliations

  1. Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands

    Eric van de Weg & Mario Di Guardo

  2. Research and Innovation Centre, Foundation Edmund Mach, 38010, San Michele all’Adige, Trento, Italy

    Mario Di Guardo, Fabrizio Costa & Michela Troggio

  3. Agroscope, Division Plant Breeding, Schloss 1, 8820, Wädenswil, Switzerland

    Melanie Jänsch, Didier Socquet-Juglard, Isabelle Baumgartner, Giovanni A. L. Broggini, Markus Kellerhals & Andrea Patocchi

  4. Institut de Recherche en Horticulture et Semences (IRHS), INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, 42 rue Georges Morel, 49071, Beaucouzé, France

    François Laurens & Charles-Eric Durel

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  1. Eric van de Weg
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Correspondence to Andrea Patocchi.

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van de Weg, E., Di Guardo, M., Jänsch, M. et al. Epistatic fire blight resistance QTL alleles in the apple cultivar ‘Enterprise’ and selection X-6398 discovered and characterized through pedigree-informed analysis. Mol Breeding 38, 5 (2018). https://doi.org/10.1007/s11032-017-0755-0

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