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Title: Genetic marker anchoring by six-dimensional pools for development of a soybean physical map

Author
item WU, XIAOLEI - UNIVERSITY OF MISSOURI
item ZHONG, GUOHUA - UNIVERSITY OF MISSOURI
item FINDLEY, SETH - UNIVERSITY OF MISSOURI
item Cregan, Perry
item STACEY, GARY - UNIVERSITY OF MISSOURI
item NGUYEN, HENRY - UNIVERSITY OF MISSOURI

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2008
Publication Date: 1/22/2008
Citation: Wu, X., Zhong, G., Findley, S., Cregan, P.B., Stacey, G., Nguyen, H.T. 2008. Genetic marker anchoring by six-dimensional pools for development of a soybean physical map. Biomed Central (BMC) Genomics. 9:28.

Interpretive Summary: Geneticists create both genetic and physical maps of the chromosomes of the organisms they study. The genetic map of the complete set of chromosomes, referred to as the "genome", provides one measure of the distance between genes which is based on the frequency with which genes or genetic markers are seen to genetically recombine. The physical map is based upon the actual physical distance (amount of DNA) along the chromosome between the positions of genes or genetic markers. The physical map is constructed via the assembly of many thousands of DNA fragments or clones that are derived by cutting the genome into small DNA fragments of 50,000 to 300,000 DNA units in length. These fragments are individually preserved as bacterial artificial chromosome clones or BACs. The BAC clones are then “fingerprinted” in order to identify clones that overlap in an effort to re-assemble the BAC clones in the same order as they occur in the genome thereby creating the physical map. In the case of the soybean, well developed genetic and physical maps are available. In order to facilitate cloning of important genes it is necessary to “anchor” the physical map to the genetic map. This was done by using genetic markers with defined positions on the genetic map and identifying the BAC clones in which those DNA markers are located. The research reported here represents a large step forward in the anchoring of the physical map to the genetic map and will be used by soybean geneticists to discover genes controlling traits of importance and for the development of new genetic markers in specific genome regions of interest.

Technical Abstract: Integrated genetic and physical maps are extremely valuable for genomic studies and as important references for assembling of whole genome shotgun sequences. Screening of a BAC library using molecular markers is an indispensable procedure for integration of both physical and genetic maps of a genome. Molecular markers provide anchor points for integration of genetic and physical maps and also validate BAC contigs assembled based solely on BAC fingerprints. A six-dimensional BAC pooling strategy was employed to anchor molecular markers onto the soybean physical map. A total of 1,470 markers (580 SSRs and 890 STSs) were anchored by PCR on a subset of a Williams 82 BstY I BAC library pooled into 208 pools in six dimensions. This resulted in 7,463 clones (~1x genome equivalent) associated with 1470 markers, of which the majority of clones (6,157, 82.5%) were anchored by one marker and 1106 (17.5%) individual clones contained two or more markers. This contributed to 1184 contigs having anchor points through this 6-D pool screening effort. These results are being integrated with BAC fingerprints to assemble the BAC contigs (see soymap.org). Ultimately, these efforts will lead to an integrated soybean physical and genetic map resource.