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DNA Research Advance Access published online on March 11, 2008
DNA Research, doi:10.1093/dnares/dsn001
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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

Sequence Level Analysis of Recently Duplicated Regions in Soybean [Glycine max (L.) Merr.] Genome

Kyujung Van1, Dong Hyun Kim1, Chun Mei Cai2, Moon Young Kim1,3, Jin Hee Shin1, Michelle A. Graham4, Randy C. Shoemaker4, Beom-Soon Choi5, Tae-Jin Yang1 and Suk-Ha Lee1,3,*

1 Department of Plant Science, Seoul National University, San 56-1, Sillim-dong, Gwanak-gu, Seoul 151-921, South Korea
2 National Institute of Crop Science, Suwon 441-857, South Korea
3 Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, South Korea
4 Corn Insect and Crop Genetics Research Unit, USDA-ARS, Iowa State University, Ames, IA 50011, USA
5 National Instrumentation Center for Environmental Management, Seoul National University, Seoul 151-921, South Korea

Received 15 November 2007 ; accepted 16 January 2008.

A single recessive gene, rxp, on linkage group (LG) D2 controls bacterial leaf-pustule resistance in soybean. We identified two homoeologous contigs (GmA and GmA') composed of five bacterial artificial chromosomes (BACs) during the selection of BAC clones around Rxp region. With the recombinant inbred line population from the cross of Pureunkong and Jinpumkong 2, single-nucleotide polymorphism and simple sequence repeat marker genotyping were able to locate GmA' on LG A1. On the basis of information in the Soybean Breeders Toolbox and our results, parts of LG A1 and LG D2 share duplicated regions. Alignment and annotation revealed that many homoeologous regions contained kinases and proteins related to signal transduction pathway. Interestingly, inserted sequences from GmA and GmA' had homology with transposase and integrase. Estimation of evolutionary events revealed that speciation of soybean from Medicago and the recent divergence of two soybean homoeologous regions occurred at 60 and 12 million years ago, respectively. Distribution of synonymous substitution patterns, Ks, yielded a first secondary peak (mode Ks = 0.10–0.15) followed by two smaller bulges were displayed between soybean homologous regions. Thus, diploidized paleopolyploidy of soybean genome was again supported by our study.

Key words: BAC; divergence time; duplication; Ks; Rxp; soybean

* To whom correspondence should be addressed. Tel. +82 2-880-4545. Fax. +82 2-873-2056. E-mail: sukhalee{at}snu.ac.kr

Edited by Satoshi Tabata


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