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Determination of partial genomic sequences and development of a CAPS system of the S-RNase gene for the identification of 22 S haplotypes of apple (Malus × domestica Borkh.)

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Abstract

Information about self-incompatibility (S) genotypes of apple cultivars is important for the selection of pollen donors for fruit production and breeding. Although S genotyping systems using S haplotype-specific PCR of S-RNase, the pistil S gene, are useful, they are sometimes associated with false-positive/negative problems and are unable to identify new S haplotypes. The CAPS (cleaved amplified polymorphic sequences) system is expected to overcome these problems, however, the genomic sequences needed to establish this system are not available for many S-RNases. Here, we determined partial genomic sequences of eight S-RNases, and used the information to design new primer and to select 17 restriction enzymes for the discrimination of 22 S-RNases by CAPS. Using the system, the S genotypes of three cultivars were determined. The genomic sequence-based CAPS system would be useful for S genotyping and analyzing new S haplotypes of apple.

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Abbreviations

GSI:

Gametophytic self-incompatibility

PCR:

Polymerase chain reaction

RFLP:

Restriction fragment length polymorphism

CAPS:

Cleaved amplified polymorphic sequences

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Acknowledgments

We thank Mr. Y. Inagawa and Mr. M. Kurushima of Hokkaido Central Agricultural Experimental Station for their suggestions, and Dr. K. Abe of the Department of Apple Research, National Institute of Fruit Tree Science for plant materials. H.K. was supported by JSPS Postdoctoral Fellowship for Foreign Researchers.

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Author notes

  1. Hoytaek Kim

    Present address: Fruit Genome Research Team, National Institute of Fruit Tree Science, 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan

  2. Nobuhiro Kotoda

    Present address: Fruit Genome Research Team, National Institute of Fruit Tree Science, 485-6 Okitsu-nakacho, Shimizu, Shizuoka, 424-0292, Japan

Authors and Affiliations

  1. Faculty of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan

    Hoytaek Kim, Takato Koba & Hidenori Sassa

  2. Graduate School of Science and Technology, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan

    Hiroyuki Kakui

  3. Department of Apple Research, National Institute of Fruit Tree Science, National Agricultural Research Organization, Shimo-Kuriyagawa, Morioka, 020-0123, Japan

    Nobuhiro Kotoda

  4. Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai, Fuchu, Tokyo, 183-8509, Japan

    Yutaka Hirata

Authors
  1. Hoytaek Kim
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  2. Hiroyuki Kakui
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Correspondence to Hidenori Sassa.

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Kim, H., Kakui, H., Kotoda, N. et al. Determination of partial genomic sequences and development of a CAPS system of the S-RNase gene for the identification of 22 S haplotypes of apple (Malus × domestica Borkh.). Mol Breeding 23, 463–472 (2009). https://doi.org/10.1007/s11032-008-9249-4

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  • DOI: https://doi.org/10.1007/s11032-008-9249-4

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