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QTL analysis of crown gall disease resistance in apple: first plant R gene candidates effective against Rhizobium rhizogenes (Ti)

Tree Genetics & Genomes volume 17, Article number: 25 (2021) Cite this article

Abstract

In apple (Malus spp.), crown gall disease, caused by the bacterial pathogens Rhizobium radiobacter (Ti) and R. rhizogenes (Ti), can be severe. To control the disease, breeding of apple rootstocks that exhibit crown gall resistance is a promising approach. In this study, we used a full-sib F1 population derived from a ‘JM7’ (susceptible) × Sanashi 63 (resistant) cross to identify quantitative trait loci (QTLs) that control resistance to tumour-inducing Rhizobium isolates found in apple production areas in Japan. Three stable QTLs, associated with a wide range of crown gall resistances, were identified in three linkage groups (LGs). QTLs for resistance to isolates Peach CG8331, Nagano 1 and Nagano 2 co-localised at the middle of LG 2 in Sanashi 63, where the crown gall resistance gene Cg (renamed as Rrr1 in this study) was previously identified. Similarly, in ‘JM7’, QTLs were identified on LG 11 for resistance to isolates ARAT-001, ARAT-002 and Kazuno 2, and on LG 15 for resistance to isolate ARAT-001. Fine-mapping of Rrr1 and nucleotide sequencing of a contig obtained from two bacterial artificial chromosome (BAC) clones delimited the Rrr1 gene to a region spanning 217 kb. In silico gene prediction from the region identified four genes encoding the Toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat (TIR-NBS-LRR) class plant resistance genes.

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Data availability

Data generated or analysed during this study are included in this published article (and its supplementary information files) or in public database.

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Funding

A part of this work was supported by JSPS KAKENHI Grant Number 20K06039.

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Author notes

  1. Takashi Haji, Kazuma Okada & Kazuyuki Abe

    Present address: Institute of Fruit Tree Science, NARO, Tsukuba, 305-8605, Japan

  2. Naoko Kitamoto

    Present address: Akita Prefectural University, Ogata, Minami-Akita, 010-0444, Japan

  3. Toshiya Yamamoto

    Present address: Intellectual Property Department, NARO, Tsukuba, 305-8517, Japan

Authors and Affiliations

  1. Apple Research Station, Institute of Fruit Tree Science, National Agriculture and Food Research Organization (NARO), Morioka, 020-0123, Japan

    Shigeki Moriya, Hiroshi Iwanami, Takashi Haji, Kazuma Okada, Taku Shimizu, Koichi Suzaki, Naoko Kitamoto & Kazuyuki Abe

  2. Institute of Crop Science, NARO, Tsukuba, 305-8518, Japan

    Yuichi Katayose & Jianzhong Wu

  3. Institute of Fruit Tree Science, NARO, Tsukuba, 305-8605, Japan

    Toshiya Yamamoto

Authors
  1. Shigeki Moriya
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Contributions

S.M., H.I. and K.A. conceived and designed the study. S.M., H.I., T.H., K.O., T. S., K.S. and K.A. performed phenotyping. S.M., N.K., Y.K. and J.W. constructed the BAC library and performed screening of clones. S.M., N.K. and T.Y. performed genotyping and in silico gene prediction. S.M. analysed data and drafted the manuscript. All authors revised and approved the manuscript.

Corresponding author

Correspondence to Shigeki Moriya.

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Conflict of interest

The authors declare no competing interests.

Data Archiving Statement

The nucleotide sequence of the BAC contig was deposited to DDBJ under the accession number LC592177.

Additional information

Communicated by D. Chagné

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Moriya, S., Iwanami, H., Haji, T. et al. QTL analysis of crown gall disease resistance in apple: first plant R gene candidates effective against Rhizobium rhizogenes (Ti). Tree Genetics & Genomes 17, 25 (2021). https://doi.org/10.1007/s11295-021-01508-9

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  • DOI: https://doi.org/10.1007/s11295-021-01508-9

Keywords

  • Linkage mapping
  • Disease resistance
  • Fine-mapping
  • Bacterial artificial chromosome library