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DNA Research Advance Access published online on January 11, 2008
DNA Research, doi:10.1093/dnares/dsm027
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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

An Integrated High-density Linkage Map of Soybean with RFLP, SSR, STS, and AFLP Markers Using A Single F2 Population

Zhengjun Xia1,2, Yasutaka Tsubokura1,2, Masako Hoshi1, Masayoshi Hanawa1 {dagger}, Chizuru Yano1, Kayo Okamura1 {ddagger}, Talaat A. Ahmed1,3, Toyoaki Anai4, Satoshi Watanabe5, Masaki Hayashi1,2, Takashi Kawai1 ¶, Khwaja G. Hossain1,6, Hirokazu Masaki1 §, Kazumi Asai1 ||, Naoki Yamanaka7, Nakao Kubo1 #, Koh-ichi Kadowaki2 **, Yoshiaki Nagamura2, Masahiro Yano2, Takuji Sasaki2 and Kyuya Harada,1,2,*

1 Faculty of Horticulture, Chiba University, 648 Matsudo, Chiba 271-8510, Japan
2 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
3 Faculty of Agriculture, Agronomy Department, Assiut University, Assiut 71515, Egypt
4 Faculty of Agriculture, Saga University, Honjo-machi 1, Saga 840-8502, Japan
5 Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
6 Division of Science and Mathematics, Mayville State University, 330 3rd Street NE, Mayville, ND 58257, USA
7 Japan International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan

Received 25 September 2007 ; accepted 29 November 2007.

Soybean [Glycine max (L.) Merrill] is the most important leguminous crop in the world due to its high contents of high-quality protein and oil for human and animal consumption as well as for industrial uses. An accurate and saturated genetic linkage map of soybean is an essential tool for studies on modern soybean genomics. In order to update the linkage map of a F2 population derived from a cross between Misuzudaizu and Moshidou Gong 503 and to make it more informative and useful to the soybean genome research community, a total of 318 AFLP, 121 SSR, 108 RFLP, and 126 STS markers were newly developed and integrated into the framework of the previously described linkage map. The updated genetic map is composed of 509 RFLP, 318 SSR, 318 AFLP, 97 AFLP-derived STS, 29 BAC-end or EST-derived STS, 1 RAPD, and five morphological markers, covering a map distance of 3080 cM (Kosambi function) in 20 linkage groups (LGs). To our knowledge, this is presently the densest linkage map developed from a single F2 population in soybean. The average intermarker distance was reduced to 2.41 from 5.78 cM in the earlier version of the linkage map. Most SSR and RFLP markers were relatively evenly distributed among different LGs in contrast to the moderately clustered AFLP markers. The number of gaps of more than 25 cM was reduced to 6 from 19 in the earlier version of the linkage map. The coverage of the linkage map was extended since 17 markers were mapped beyond the distal ends of the previous linkage map. In particular, 17 markers were tagged in a 5.7 cM interval between CE47M5a and Satt100 on LG C2, where several important QTLs were clustered. This newly updated soybean linkage map will enable to streamline positional cloning of agronomically important trait locus genes, and promote the development of physical maps, genome sequencing, and other genomic research activities.

Key words: soybean; linkage map; SSR; RFLP; AFLP; STS

* To whom correspondence should be addressed. Tel/Fax. +81 29-838-7452. E-mail: haradaq{at}nias.affrc.go.jp

Edited by Kazuo Shinozaki

{dagger} Present address: Sinary Company, Ltd, 2-11-13 Kamiosahi, Sinagawa-ku, Tokyo 141-0021, Japan

{ddagger} Present address: Colorado State Department of Agriculture, 2331 West 31st Avenue, Denver, CO 80211, USA

Present address: GE Heathcare Bio-Sciences KK, 3-25-1 Hyakunincho, Shinjuku-ku, Tokyo 169-0073, Japan

§ Present address: Metropolitan Police Department, 1-15-15 Kitaohtsuku, Toshima-ku, Tokyo 170-0004, Japan

|| Present address: Institute for Environmental Science, University of Shizuoka, 52-1 Yada, Suruga, Shizuoka 422-8526, Japan

# Present address: Graduate School of Agriculture, Kyoto Prefectural University, 74 Oji, Kitainayazuma, Seika, Soraku, Kyoto 619-0244, Japan

** Present address: Ministry of Agriculture, Forestry and Fisheries, 1-2-1 Kasumigaseki, Chiyoda-ku, Tokyo 100-8950, Japan


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