ARS | Publication request: A 2600-LOCUS CHROMOSOME BIN MAP OF WHEAT HOMOEOLOGOUS GROUP 2 REVEALS INTERSTITIAL GENE-RICH ISLANDS AND COLINEARITY WITH RICE

Submitted to: Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: June 1, 2004
Publication Date: October 1, 2004
Citation: Wennerlind, E., Nduati, V., Gonzalez-Hernandez, J.L., Mesfin, A., Trudeau-Spanjers, M., Chao, S., Lazo, G.R., Hummel, D., Anderson, O.D., Qi, L.L., Gill, B.S., Echalier, B., Linkiewicz, A.M., Akhunov, E.D., Dubcovsky, J., Peng, J., Lapitan, N.V., Zhang, D., Nguyen, H.T., Miftahudin, Gustafson, J.P., Greene, R.A., Sorrells, M.E., Hossain, K.S., Kalavacharla, V., Kianian, S.F., Sidhu, D., Dilbirligi, M., Gill, K.S., Fenton, R.D., Close, T.J., Mcguire, P.E., Qualset, C.O., Anderson, J.A. 2004. A 2600-locus chromosome bin map of wheat homoeologous group 2 reveals interstitial gene-rich islands and colinearity with rice. Genetics. 168:625-637.

Interpretive Summary: Expressed DNA sequences were taken from 47 cDNA libraries and were physically mapped to specific chromosome regions of wheat homoeologous group 2 chromosomes. We found that the expressed sequences were not scattered from one end to the other of the group 2 chromosomes, but seemed to be clustered in more distal regions of the chromosomes. From our physical map, we were also able to establish the location of group 2 chromosome re-arrangements. This information will be of value to wheat geneticists in map-based cloning of expressed sequences located on wheat homoeologous group 2 chromosomes.

Technical Abstract: The large and complex hexaploid wheat genome offers many challenges for wheat genomic research. Expressed sequence tags (ESTs) facilitate the analysis of gene-coding regions, and provide a rich source of molecular markers for mapping and comparison with model organisms. The objectives of this study were to construct a high-density EST chromosome deletion map of wheat homoeologous group 2 chromosomes to assess the distribution of loci, construct a consensus map of group 2 ESTs, investigate disruptions in synteny, examine patterns of duplication, and assess the co-linearity of ESTs assigned to the group 2 consensus map with rice. A total of 2600 EST loci generated from 1110 ESTs were mapped to group 2 chromosomes by Southern hybridization onto wheat aneuploid and deletion stocks. A consensus map of 553 ESTs mapping to more than one group 2 chromosome was constructed. Chi-square analysis of EST distributions revealed regions of high gene density in distal bins, and low gene density in proximal bins. Additionally, highly-dense, interstitial gene islands flanked by relatively gene-poor regions on both the short and long arms were discovered. These islands contain a large number of ESTs with BLAST matches to closely neighboring rice BACs. The map locations of three ESTs indicated the presence of a small pericentric inversion on chromosome 2B. Approximately one-third of the 1110 ESTs had at least one locus that mapped to another homoeologous group in addition to group 2. No pattern of duplication to a particular group or bin was found. Expressed sequence tags were assigned to putative orders within consensus bins by comparison with BAC/PAC clones of the co-linear rice chromosomes. Wheat chromosome group 2 has good co-linearity with rice chromosomes 4 and 7.