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United States Department of Agriculture

Agricultural Research Service

Title: Integration of Genetic and Physical Data in 2,585 Contigs

Authors
item Coe Jr, Edward
item Cone, Karen - UNIV OF MISSOURI-COLUMBIA
item Wei, Fusheng - UNIV OF ARIZONA-TUCSON
item Nelson, Will - UNIV OF ARIZONA-TUCSON
item Goicoechea, Jose - UNIV OF ARIZONA-TUCSON
item Bergstrom, Dean - UNIV OF MISSOURI-COLUMBIA
item Engler, Fred - UNIV OF ARIZONA-TUCSON
item Lee, Seunghee - UNIV OF ARIZONA-TUCSON
item Butler, Ed - UNIV OF ARIZONA-TUCSON
item Kim, Hyeran - UNIV OF ARIZONA-TUCSON
item Schroeder, Steven - UNIV OF MISSOURI-COLUMBIA
item Fang, Zhiwei - UNIV OF MISSOURI-COLUMBIA
item McMullen, Michael
item Bi, Irie Vroh - UNIV OF MISSOURI-COLUMBIA
item Davis, Georgia - UNIV OF MISSOURI-COLUMBIA
item Sanchez-Villeda, Hector - UNIV OF MISSOURI-COLUMBIA
item Yim, Young-Sun - UNIV OF MISSOURI-COLUMBIA
item Havermann, Seth - UNIV OF MISSOURI-COLUMBIA
item Bowers, John - UNIV OF GEORGIA-ATHENS
item Paterson, Andrew - UNIV OF GEORGIA-ATHENS
item Schaeffer, Mary
item Gardiner, Jack - UNIV OF MISSOURI-COLUMBIA
item Soderlund, Cari - UNIV OF ARIZONA-TUCSON
item Wing, Rod - UNIV OF ARIZONA-TUCSON

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract Only
Publication Acceptance Date: January 5, 2004
Publication Date: March 11, 2004
Citation: Coe Jr, E.H., Cone, K., Wei, F., Nelson, W., Goicoechea, J.L., Bergstrom, D., Engler, F., Lee, S., Butler, E., Kim, H., Schroeder, S., Fang, Z., Mcmullen, M.D., Bi, I., Davis, G., Sanchez-Villeda, H., Yim, Y., Havermann, S., Bowers, J., Paterson, A., Polacco, M.L., Gardiner, J., Soderlund, C., Wing, R.A. 2004. Integration of genetic and physical data in 2,585 contigs [abstract]. Maize Genetics Conference. 46:106-107.

Technical Abstract: High-resolution genetic maps and deep physical maps of maize, anchored inter se, are ready for targeted research, and for tiling and sequencing. The 2,300-Mb genome assembles readily, even though highly duplicated and rife with recently diverged, nested retrotransposons and other repetitive sequences. From HindIII, EcoRI, and MboI BAC libraries of B73, 290,000 agarose BAC fingerprints (15X) were assembled initially into contigs using FPC. Phase I manual editing for the June 2003 build drew together 3,500 contigs assembled at 10e-12 with the aid of an end-joining utility and over 15,400 markers, including 9,300 unigenes addressed to the BACs with 40-bp overgos. Physical addressing of genetically mapped markers by PCR on 48 x 48 x 48, 6-dimensional BAC pools proved to be an efficient and trustworthy aid. Targeted SNP mapping is on EST unigenes that are associated with unanchored contigs. These data and tools have largely anchored the contigs, some exceeding 8 Mb, to the genetic map. Contig order and orientation devolves from over 2000 markers mapped genetically at high resolution, which give virtually perfect correlation with physical order. A "neighbors" map, derived by intercalation of loci from other informative populations, combines over 5,800 mapped loci in approximate order, and assists editing. Phase II editing for the January 2004 build drew together 2,585 contigs with 18,649 markers, representing 2050 Mb of the genome, 56% anchored to the genetic map.. Software tools to systematize, validate, link, pipe, and integrate large, diverse, high-throughput datasets are available. See www.maizemap.org and genome.Arizona.edu/fpc/maize/ for views and downloads. Side-by-side dynamic views of the physical and genetic map from a database environment are in the iMap presentation at www.maizemap.org/iMapDB/iMap.html. Supported by NSF #9872655.

Last Modified: 4/23/2014
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