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United States Department of Agriculture

Agricultural Research Service


item Coe jr, Edward
item Cone, Karen
item Wei, Fusheng
item Nelson, Will
item Goicoechea, Jose
item Bergstrom, Dean
item Engler, Fred
item Lee, Seunghee
item Butler, Ed
item Kim, Hyeran
item Schroeder, Steven
item Fang, Zhiwei
item Mcmullen, Michael
item Bi, Irie vroh
item Davis, Georgia
item Sanchez-villeda, Hector
item Yim, Young-sun
item Havermann, Seth
item Bowers, John
item Paterson, Andrew
item Schaeffer, Mary
item Gardiner, Jack
item Soderlund, Cari
item Wing, Rod

Submitted to: Maize Genetics Conference Abstracts
Publication Type: Abstract only
Publication Acceptance Date: 1/5/2004
Publication Date: 3/11/2004
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.

Interpretive Summary:

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 and 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 Supported by NSF #9872655.

Last Modified: 8/24/2016
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