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SSR-based linkage map with new markers using an intraspecific population of common wheat

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Abstract

Simple sequence repeats (SSRs) are valuable molecular markers in many plant species. In common wheat (Triticum aestivum L.), which is characteristic of its large genomes and alloploidy, SSRs are one of the most useful markers. To increase SSR marker sources and construct an SSR-based linkage map of appropriate density, we tried to develop new SSR markers from SSR-enriched genomic libraries and the public database. SSRs having (GA)n and (GT)n motifs were isolated from enriched libraries, and di- and tri-nucleotide repeats were mined from expressed sequence tags (ESTs) and DNA sequences of Triticum species in the public database. Of the 1,147 primer pairs designed, 842 primers gave accurate amplification products, and 478 primers showed polymorphism among the nine wheat lines examined. Using a doubled haploid (DH) population from an intraspecific cross between Kitamoe and Münstertaler (KM), we constructed an SSR-based linkage map that consisted of 464 loci: 185 loci from genomic libraries, 65 loci from the sequence database including ESTs, 213 loci from the SSR markers already reported, and 1 locus of morphological marker. Although newly developed SSR loci were distributed throughout all chromosomes, clustering of them around putative centromeric regions was found on several chromosomes. The total length of the KM map spanned 3,441 cM and corresponded to approximately 86% genome coverage. The KM map comprised of 23 linkage groups because two gaps of over 50 cM distance remained on chromosome 6A. This is a first report of SSR-based linkage map using single intraspecific population of common wheat. This mapping result suggests that it becomes possible to construct linkage maps with sufficient genome coverage using only SSR markers without RFLP markers, even in an intraspecific population of common wheat. Moreover, the new SSR markers will contribute to the enrichment of molecular marker resources in common wheat.

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Acknowledgements

I am grateful to Ms. Satoko Itoh for technical assistance. This work was supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project DM-2103). DH lines of Kitamoe/Münsterataler used in this study were developed in collaboration with Kitami Pref. Agric. Stn. Primer sequences developed in this study are available upon request.

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Authors and Affiliations

  1. Hokkaido Green-Bio Institute, Higashi-5 Kita-15, 069-1317, Naganuma, Hokkaido, Japan

    Atsushi Torada & Michiya Koike

  2. Integrated Genomics Research Team, RIKEN Plant Science Center (PSC), 1-7-22 Suehiro-cho, Tsurumi-ku, 230-0045, Yokohama Kanagawa, Japan

    Keiichi Mochida

  3. Kyoto Pref. University, 606-8522, Shimogamo, Kyoto, Japan

    Yasunari Ogihara

Authors
  1. Atsushi Torada
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  2. Michiya Koike
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  3. Keiichi Mochida
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  4. Yasunari Ogihara
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Correspondence to Atsushi Torada.

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Communicated by F. Salamini

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Torada, A., Koike, M., Mochida, K. et al. SSR-based linkage map with new markers using an intraspecific population of common wheat. Theor Appl Genet 112, 1042–1051 (2006). https://doi.org/10.1007/s00122-006-0206-5

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  • DOI: https://doi.org/10.1007/s00122-006-0206-5

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