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United States Department of Agriculture

Agricultural Research Service

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

Authors
item Van, K - SEOUL NATIONAL UNIV
item Kim, D - SEOUL NATIONAL UNIV
item Mei Cai, C - SEOUL NATIONAL UNIV
item Young Kim, M - SEOUL NATIONAL UNIV
item Shin, J - SEOUL NATIONAL UNIV
item Graham, Michelle
item Shoemaker, Randy
item Choi, B - SEOUL NATIONAL UNIV
item Yang, T - SEOUL NATIONAL UNIV
item Lee, S - SEOUL NATIONAL UNIV

Submitted to: DNA Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: January 16, 2008
Publication Date: March 11, 2008
Citation: Van, K., Kim, D., Mei Cai, C., Young Kim, M., Shin, J., Graham, M.A., Shoemaker, R.C., Choi, B., Yang, T., Lee, S. 2008. Sequence Level Analysis of Recently Duplicated Regions in the Soybean [Glycine max (L.) Merr.] Genome. DNA Research. 15:93-102.

Interpretive Summary: The hereditary material of many plants has undergone one to many doublings over millions of years. These doubling events result in duplications of genes. In this study the authors, while studying a disease resistance gene in soybean, identified a pair of these duplicated regions. They genetically mapped the regions and determined they were located on two different chromosomes. An analysis of the two regions identified DNA sequences involved in signalling and communication within the cell. They estimated the timing of the duplications to have been at 5 and 24 million years ago. This information will be of importance to geneticists and evolutionary biologists who are studying relationships among genes within gene families and who are studying the complexity of traits controlled by multiple genes.

Technical Abstract: A single recessive gene, rxp, on linkage group (LG) D2 controls bacterial leaf pustule resistance in soybean. Markers linked to rxp were used to develop BAC contigs spanning the Rxp region. We identified two homoeologous contigs (GmA and GmA’) composed of five bacterial artificial chromosomes (BACs). GmA correspond to the Rxp region on linkage group D2. SNP and SSR markers were used to place GmA’ on LG A1 using a RIL population develop from the cross of Pureunkong and Jinpumkong. Based on 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 24 and 5 million years ago, respectively. Distribution of synonymous substitution patterns, Ks, yielded a first secondary peak (mode Ks = 0.10 to 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.

Last Modified: 10/1/2014
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