Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2003
Publication Date: 4/1/2004
Citation: Mudge, J., Huihuang, Y., Denny, R.L., Howe, D.K., Danesh, D., Marek, L.F., Retzel, E., Shoemaker, R.C., Young, N.D. 2004. Soybean bac contigs anchored with rflps: insights into genome duplication and gene clustering. Genome. v. 47. p. 361-372. Interpretive Summary: Understanding the way in which the hereditary material of an organism is put together is critical to planning strategies for decoding all of the organism's DNA. In this study the authors used special genetic markers to capture regions of the soybean chromosomes that are evolutionarily related and duplicated. The authors discovered that the molecular markers they chose were clustered together in about one-fourth of the total amount of DNA. They speculated that most of the genes in soybean are clustered in about one-fourth of the DNA. They also determined that the evolutionarily related DNA regions are very, very similar. This information is important to scientists planning to 'discover' soybean genes, and planning on decoding all of the important DNA of the soybean.
Technical Abstract: Surveying the soybean genome with 683 bacterial artificial chromosome (BAC) contiguous groups ('contigs') anchored by restriction fragment length polymorphisms (RFLPs) enabled us to explore microsyntenic relationships among duplicated regions, and also to examine the physical organization of hypomethylated (and presumably gene-rich) genomic regions. Numerous cases where non-homologous RFLPs hybridized to common BAC clones indicated that RFLPs were physically clustered in soybean, apparently in less than 25% of the genome. By extension, we speculate that most of the genes are clustered in less than 275 Mbp of the soybean genome. Approximately 40-45% of this gene-rich portion is associated with the RFLP-anchored contigs described in this study. Similarities in genome organization among BAC contigs from duplicate genomic regions were also examined. Homoeologous BAC contigs often exhibited extensive microsynteny. Furthermore, paralogs recovered from duplicate contigs shared 86-100% sequence identity.