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United States Department of Agriculture

Agricultural Research Service

Title: Soybean Genomic Survey: Bac-End Sequences Near Rflp and Ssr Markers

Authors
item Marek, Laura - IOWA STATE UNIVERSITY
item Mudge, Joann - UNIVERSITY OF MINNESOTA
item Darnielle, Lalitree
item Grant, David
item Hanson, Nadja
item Paz, Margie - IOWA STATE UNIVERSITY
item Huihuang, Yan - UNIVERSITY OF MINNESOTA
item Denny, Roxanne - UNIVERSITY OF MINNESOTA
item Larson, Karin - UNIVERSITY OF MINNESOTA
item Shoemaker, Randy

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: April 20, 2001
Publication Date: N/A

Interpretive Summary: Deciphering the genetic code of the soybean would be critical to improving the crop for better yield, nutrition, and health benefits. Unfortunately there is too much DNA in soybean to decode without great expense of time and money. In this paper the authors devised a method to sample the DNA sequences at known positions across chromosomes. They found broad range of fgenes as well as repetitive DNA sequences that probably represents a sampling of what exists on the chromosomes. This information tells researchers much about the organization and composition of the genome and may help to design strategies to clone important genes which will result in increased breeding efficiencies.

Technical Abstract: We are building a framework physical infrastructure across the soybean genome by using SSR (simple sequence repeat) and RFLP (restriction fragment length polymorphism) markers to identify BACs from two soybean BAC libraries. The libraries were prepared from two genotypes each digested with a different restriction enzyme. The BACs identified from each marker were grouped into contigs. We have obtained BAC-end sequence from the BAC within each contig. The sequences (1515) were analyzed by using BLAST algorithms to search nucleotide and protein databases by the University of Minnesota Computational Biology Centers. The SSR-identified BACs had a higher percentage of significant BLAST hits than did the RFLP-identified BACs. This difference was largely accounted for by a higher percentage of hits to repetitive-type sequences for the SSR-identified BACs. Both library screens had a similar percentage of BAC-end sequences with significant hits to experimentally defined genes (6-8% of total sequences) These genes represent a wide range of metabolic functions. In these analyses, repetitive sequences from RFLP-identified contigs and sequences with significant similarity to experimentally determined genes from both SSR- and RFLP-identified contigs were not clustered. Only repetitive sequences from SSR-identified contigs appeared to be clustered. The BAC- end sequences also allowed us to identify microsynteny between soybean and the model plants Arabidopsis and Medicago truncatula. This map-based approach to genome sampling provides a means to assay soybean genome structure and organization.

Last Modified: 10/21/2014
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