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Aligned genetic linkage maps of apple rootstock cultivar ‘JM7’ and Malus sieboldii ‘Sanashi 63’ constructed with novel EST-SSRs

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Abstract

Identification of markers associated with genes of interest and quantitative trait loci (QTLs), combined with high-density genetic linkage maps, can help reduce labor and costs by enabling marker-assisted selection (MAS). In this study, a dwarfing apple rootstock cultivar ‘JM7’ (Malus prunifolia × Malus pumila ‘Malling 9’) and wild apple Malus sieboldii ‘Sanashi 63’ (section Sorbomalus) were used for constructing genetic linkage maps. Here, a species from section Sorbomalus was used for the first time as a target species in a genome-wide mapping study. We also developed and mapped 137 novel-expressed sequence tag-simple sequence repeat (EST-SSR) markers. The genetic linkage maps of ‘JM7’ and ‘Sanashi 63’ consisted of 415 and 310 loci and spanned 998.0 and 981.8 cM, respectively, comparable to the reference map of Malus × domestica ‘Discovery’. A BLASTN search revealed that all of the EST-SSR sequences used in this study exhibited very high homology to one or more previously characterized apple genome contigs. Although the most homologous contigs of 89 EST-SSRs were located within the same linkage groups (LGs) identified by mapping analysis, the other 48 EST-SSRs were aligned into contigs positioned in different LGs than those identified by mapping. When search criteria were expanded to include the five most homologous contigs of each EST-SSR, at least one of the top five contigs for 15 of these 48 EST-SSRs corresponded to the LG obtained by mapping. The maps of ‘JM7’ and ‘Sanashi 63’ may be useful for analyzing important rootstock characteristics and identifying markers for MAS.

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Acknowledgments

We thank Dr. T. Ueda of NARO Institute of Fruit Tree Science for valuable discussions and computer analysis. This work was supported by National Agriculture and Food Research Organization Research Project No. 211, “Establishment of Integrated Basis for Development and Application of Advanced Tools for DNA Marker-Assisted Selection in Horticultural Crops”.

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Author notes

  1. Nobuhiro Kotoda

    Present address: Okitsu Citrus Research Station, NARO Institute of Fruit Tree Science, Shimizuokitsunaka-cho, Shizuoka, Shizuoka, 424-0292, Japan

  2. Naozumi Mimida

    Present address: Faculty of Agriculture, Iwate University, Morioka, Iwate, 020-8550, Japan

Authors and Affiliations

  1. Apple Research Station, NARO Institute of Fruit Tree Science, Shimokuriyagawa, Morioka, Iwate, 020-0123, Japan

    Shigeki Moriya, Hiroshi Iwanami, Nobuhiro Kotoda, Takashi Haji, Kazuma Okada, Naozumi Mimida & Kazuyuki Abe

  2. NARO Institute of Fruit Tree Science, Fujimoto, Tsukuba, Ibaraki, 305-8605, Japan

    Shingo Terakami & Toshiya Yamamoto

Authors
  1. Shigeki Moriya
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  2. Hiroshi Iwanami
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Corresponding author

Correspondence to Shigeki Moriya.

Additional information

Communicated by E. Dirlewanger

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Supplementary Table 1

Apple EST-SSRs with predicted amino acid sequences showing significant homology to Arabidopsis thaliana proteins (DOC 161 kb)

Supplementary Table 2

Homology search of EST-SSR DNA sequences to determine their chromosome and genomic locations within Apple v1.0 genome assembly (DOC 161 kb)

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Moriya, S., Iwanami, H., Kotoda, N. et al. Aligned genetic linkage maps of apple rootstock cultivar ‘JM7’ and Malus sieboldii ‘Sanashi 63’ constructed with novel EST-SSRs. Tree Genetics & Genomes 8, 709–723 (2012). https://doi.org/10.1007/s11295-011-0458-3

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