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Title: A CHROMOSOME BIN MAP OF 16,000 EST LOCI AND DISTRIBUTION OF GENES AMONG THE THREE GENOMES OF POLYPLOID WHEAT

Author
item QI, L - KANSAS STATE UNIVERSITY
item ECHALIER, B - KANSAS STATE UNIVERSITY
item Chao, Shiaoman
item Lazo, Gerard
item Anderson, Olin
item AKHUNOV, E - UNIV OF CALIFORNIA-DAVIS
item DVORAK, J - UNIV OF CALIFORNIA-DAVIS
item LINKIEWICZ, A - UNIV OF CALIFORNIA-DAVIS
item RATNASIRI, A - UNIV OF CALIFORNIA-DAVIS
item DUBCOVSKY, J - UNIV OF CALIFORNIA-DAVIS
item BERMUDEZ-KANDIANIS, C - CORNELL UNIVERSITY
item GREENE, R - CORNELL UNIVERSITY
item KANTETY, R - CORNELL UNIVERSITY
item LA ROTA, M - CORNELL UNIVERSITY
item MUNKVOLD, J - CORNELL UNIVERSITY
item SORRELLS, S - CORNELL UNIVERSITY
item SORRELLS, M - CORNELL UNIVERSITY
item DILBIRLIGI, M - WASHINGTON STATE UNIV
item SIDHU, D - WASHINGTON STATE UNIV
item ERYMAN, M - WASHINGTON STATE UNIV
item RANDHAWA, H - WASHINGTON STATE UNIV
item SANDHU, D - WASHINGTON STATE UNIV
item BONDAREVA, SVETLANA - WASHINGTON STATE UNIV
item GILL, K - WASHINGTON STATE UNIV
item MAHMOUD, A - UNIV OF MISSOURI-COLUMBIA
item MA, XEUFENG - UNIV OF MISSOURI-COLUMBIA
item MIFTAHUDIN - UNIV OF MISSOURI-COLUMBIA
item Gustafson, J
item WENNERLIND, E - UNIV OF MINNESOTA-ST PAUL
item NDUATI, V - UNIV OF MINNESOTA-ST PAUL
item GONZALEZ-HERNANDEZ, J - UNIV OF MINNESOTA-ST PAUL
item ANDERSON, J - UNIV OF MINNESOTA-ST PAUL
item PENG, J - COLORADO STATE UNIV
item LAPITAN, N L - COLORADO STATE UNIV
item HOSSAIN, K - NORTH DAKOTA STATE UNIV
item KALAVACHARLA, V - NORTH DAKOTA STATE UNIV
item KIANIAN, S - NORTH DAKOTA STATE UNIV
item PATHAN, M - UNIV OF MISSOURI-COLUMBIA
item ZHANG, D - TEXAS TECH UNIV-LUBBOCK
item NGUYEN, H - UNIV OF MISSOURI-COLUMBIA
item CHOI, D - UNIV OF CA-RIVERSIDE
item CLOSE, T - UNIV OF CA-RIVERSIDE
item MCGUIRE, P - UNIV OF CALIFORNIA-DAVIS
item QUALSET, C - UNIV OF CALIFORNIA-DAVIS
item GILL, B - KANSAS STATE UNIVERSITY

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/1/2004
Publication Date: 10/1/2004
Citation: Qi, L.L., Echalier, B., Chao, S., Lazo, G.R., Anderson, O.D., Akhunov, E.D., Dvorak, J., Linkiewicz, A.M., Ratnasiri, A., Dubcovsky, J., Bermudez-Kandianis, C.E., Greene, R.A., Kantety, R., La Rota, M., Munkvold, J.D., Sorrells, S.F., Sorrells, M.E., Dilbirligi, M., Sidhu, D., Eryman, M., Randhawa, H.S., Sandhu, D., Bondareva, S., Gill, K.S., Mahmoud, A., Ma, X., Miftahudin, Gustafson, J.P., Wennerlind, E.J., Nduati, V., Gonzalez-Hernandez, J.L., Anderson, J.A., Peng, J., Lapitan, N.V., Hossain, K.S., Kalavacharla, V., Kianian, S.F., Pathan, M.S., Zhang, D., Nguyen, H.T., Choi, D.W., Close, T.J., Mcguire, P.E., Qualset, C.O., Gill, B.S. 2004. A chromosome bin map of 16,000 est loci and distribution of genes among the three genomes of polyploid wheat. Genetics. 168:701-712.

Interpretive Summary: Because the hexaploid wheat genome is about 17,300 Mb in size, mapping of the expressed portion is the first step in gene discovery. We report on the mapping of 7104 expressed sequence tags (ESTs) into chromosome deletion bin maps. The EST density was higher depending on the particular region of the hexaploid wheat genome. In general, EST density increased relative to the physical distance from the middle of individual wheat chromosomes. It appears that most of the agronomically-important genes are located in these EST-dense regions. The chromosome bin map of ESTs is a unique resource available to wheat researchers for comparative mapping, structural, and functional analysis, and the study of polyploid evolution in wheat.

Technical Abstract: Because of the huge size (17,300 Mb) of the common wheat (Triticum aestivum L., 2n=6x=42, AABBDD) genome, sequencing and mapping of the expressed portion is a logical first step for gene discovery. Here, we report mapping of 7104 expressed sequence tag (EST) unigenes by Southern hybridization into a chromosome bin map using a set of wheat aneuploids. An EST detected an average of 4.8 restriction fragments and 2.8 loci were mapped per EST. More loci were mapped in the B genome (5774) than in the A (5173) or D (5146) genomes. The EST density was significantly higher for the D genome than for the A or B. In general, EST density increased relative to the physical distance from the centromere. The majority of EST-dense regions are in the distal parts of chromosomes. Most of the agronomically-important genes are located in EST-dense regions. The chromosome bin map of ESTs is a unique resource for SNP analysis, comparative mapping, structural and functional analysis, and polyploid evolution, as well as providing a framework for constructing a sequence-ready, BAC-contig map of the wheat genome.