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DNA Research Advance Access published online on January 11, 2008
DNA Research, doi:10.1093/dnares/dsm025
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© The Author 2008. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Characterization of the Soybean Genome Using EST-derived Microsatellite Markers

Hiroshi Hisano1, Shusei Sato1, Sachiko Isobe1, Shigemi Sasamoto1, Tsuyuko Wada1, Ai Matsuno1, Tsunakazu Fujishiro1, Manabu Yamada1, Shinobu Nakayama1, Yasukazu Nakamura1, Satoshi Watanabe2, Kyuya Harada3 and Satoshi Tabata1,*

1 Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
2 Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
3 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

Received 26 September 2007 ; accepted 30 November 2007.

We generated a high-density genetic linkage map of soybean using expressed sequence tag (EST)-derived microsatellite markers. A total of 6920 primer pairs (10.9%) were designed to amplify simple sequence repeats (SSRs) from 63 676 publicly available non-redundant soybean ESTs. The polymorphism of two parent plants, the Japanese cultivar ‘Misuzudaizu’ and the Chinese line ‘Moshidou Gong 503’, were examined using 10% polyacrylamide gel electrophoresis. Primer pairs showing polymorphism were then used for genotyping 94 recombinant inbred lines (RILs) derived from a cross between the parents. In addition to previously reported markers, 680 EST-derived microsatellite markers were selected and subjected to linkage analysis. As a result, 935 marker loci were mapped successfully onto 20 linkage groups, which totaled 2700.3 cM in length; 693 loci were detected using the 668 EST-derived microsatellite markers developed in this study, the other 242 loci were detected with 105 RFLP markers, 136 genome-derived microsatellite markers, and one phenotypic marker. We examined allelic variation among 23 soybean cultivars/lines and a wild soybean line using 668 mapped EST-derived microsatellite markers (corresponding to 686 marker loci), in order to determine the transferability of the markers among soybean germplasms. A limited degree of macrosynteny was observed at the segmental level between the genomes of soybean and the model legume Lotus japonicus, which suggests that considerable genome shuffling occurred after separation of the species and during establishment of the paleopolyploid soybean genome.

Key words: soybean; microsatellite markers; genetic linkage map; polymorphism information content; comparative map

* To whom correspondence should be addressed. Tel. +81 438-52-3933. Fax. +81 438-52-3934. E-mail: tabata{at}kazusa.or.jp

Edited by Dr Kazuo Shinozaki.


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