My group has a broad research interest in the area of structural and functional genomics of crop plants which can be divided into 6 research areas: 1) BAC library construction center; 2) BAC/EST resource center; 3) DNA sequencing center; 4) Physical mapping center; 5) Finishing and Annotation center; and 6) Functional and comparative genomics center.

1) BAC library construction center (Group Leader: Dr. Meizhong Luo). The focus of this center is to construct and characterize high-quality, large-insert, deep-coverage BAC libraries. These libraries serve as entry points into various structural and functional genomics projects within my group and in collaboration with other groups at UA and across the world. Our focus is primarily with agricultural systems but we can make libraries for any organism/tissue that is required.

2) BAC/EST resource center (Group Leader: Mr. Dave Kudrna). The focus of this center is to archive and distribute genomic resources at an affordable price to the scientific community. Here, we deposit all BAC libraries that we construct as well as all cDNA libraries that we sequence. We also provide a service to the community by archiving and distributing genomic resources generated by other groups.

3) DNA sequencing and fingerprinting center (Group Leader: Dr. HyeRan Kim). The center runs a medium throughput DNA sequencing and fingerprinting facility and specializes in BAC end sequencing, BAC shotgun sequencing, EST sequencing and BAC fingerprinting. The center can process 30,720 sequencing lanes/week and 7,680 fingerprints/week with success rates in the low 90s. Major center projects include: sequencing the short arms of rice chromosomes 10 and 3; rice, cotton, citrus and peach EST sequencing; and generation of 2,000,000 BAC end sequences and 1,000,000 fingerprints from 12 wild rice BAC libraries.

4) Physical mapping center (Group Leader: Mr. Dave Kudrna). This center is responsible for building BAC-based physical maps for genomes, chromosomes and genomic regions using AGCoL software FPC. Our two major projects are to develop a sequence ready map for maize and to construct and physical maps of 12 wild rice species.

5) Finishing and Annotation center (Group Leader: Dr Yeisoo Yu). The focus of this center is to finish BAC clones that have been shotgun sequenced in the DNA sequencing center. Once a clone is in a single contig and has an error rate of less than 1 in 10,000 nucleotides, the sequence is then annotated us Apollo software. Major projects include: finishing and annotating the rice genome (chromosomes 10, 3, 4, 5 and 9).

6) Functional and comparative genomics center (Group Leader: Dr. Rod A. Wing). This group has two major research thrusts. The first is comparative genomics. Our biggest project is the Oryza Map Alignment Project (www.OMAP.org ) with the objective to align the physical maps of 12 wild rice species to the sequenced rice genome. We hope to use OMAP to help us to understand how a genus evolves at the whole genome level and what evolutionary processes that have occurred during the domestication of rice.

Our second thrust is in the molecular dissection of the development of the formation of abscission zones using the tomato jointless and jointless-2 genes as a model system.
In addition, the entire AGI is gearing up to play a major role in the maize genome sequencing project with our collaborators at Cold Spring Harbor Laboratory. Given our track record with the International Rice Genome Sequencing Project and our creation of a sequence ready map of the maize genome we feel we will be highly competitive.

Dietrich, F.S., S. Voegeli, S. Brachat, A. Lerch, K. Gates, S. Steiner, C. Mohr, R. Pöhlmann, P. Luedi, S. Choi, R.A. Wing, A. Flavier, T.D. Gaffney and P. Philippsen. (2004). The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science 304:304-307.

Close, T.J., S. Wanamaker, R.A. Caldo, S.M. Turner, D.A. Ashlock, J.A. Dickerson, R.A. Wing, G.J. Muehlbauer, A. Kleinhofs, and R.P. Wise. (2004). A new resource for cereal genomics: 22k barley GeneChip comes of age. Plant Physiology 134:960-968.

Budiman, M.A., S-B. Chang, S. Lee, T.J. Yang, H-B. Zhang, H. de Jong and R.A. Wing (2004). Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theo Appl Genet 108:190-196.

The Rice Chromosome 10 Sequencing Consortium: Yu, Y., T. Rambo, J. Currie, C. Saski, H.R. Kim, K. Collura, S. Thompson, J. Simmons, T.J. Yang, G.N. Park, A.J. Patel, S. Thurmond, D. Henry, R. Oates, M. Palmer, G. Pries, J. Gibson, H. Anderson, M. Paradkar, L. Crane, J. Dale, M.B. Carver, T. Wood, D. Frisch, F. Engler, C. Soderlund, L.E. Palmer, L. Tetylman, L. Nascimento, M. de la Bastide, L. Spiegel, D. Ware, A. O'Shaughnessy, S. Dike, N. Dedhia, R. Preston, E. Huang, K. Ferraro, K. Kuit, B. Miller, T. Zutavern, F. Katzenberger, S. Muller, V. Balija, R.A. Martienssen, L. Stein, P. Minx, D. Johnson, H. Cordum, E. Mardis, Z. Cheng, J. Jiang, R. Wilson, W.R. McCombie, Q Yuan, S Ouyang, JL, K.M. Jones, K Gansberger, K Moffat, J Hill, T Tsitrin, L Overton, J Bera, M Kim, S Jin, L Tallon, A Ciecko, G Pai, S.V. Aken, T Utterback, S Reidmuller, J Bormann, T Feldblyum, J Hsiao, V Zismann, S Blunt, A de Vazeilles, T Shaffer, H Koo, B Suh, Q Yang, B Haas, J Peterson, M. Pertea, N. Volfovsky, J. Wortman, O. White, S.L. Salzberg, C.M. Fraser, and C.R. Buell, J. Messing, R. Song, G. Fuks, V. Llaca, S. Kovchak, and S. Young, J.E. Bowers and A.H. Paterson, M.A. Johns and L. Mao, H. Pan, R.A. Dean and R.A. Wing. (2003). In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300:1566-1569.

Chen M, Presting G, Barbazuk WB, Goicoechea JL, Blackmon B, Fang G, Kim HR, Frisch DA, Yu Y, Higingbottom S, Phimphilai K, Phimphilai S, Thurmond S, Gaudette B, Li P, Liu J, Hatfield J, Main D, Sun S, Farrar K, Henderson C, Barnett L, Costa R, Williams B, Walser S, Atkins M, Hall C, Bancroft I, Salse J, Regad F, Mohapatra T, Singh NK, Tyagi AK, Soderlund C, Dean RA & R.A. Wing (2002). An Integrated Physical and Genetic Map of the Rice Genome. The Plant Cell 14:537-545.

Goff, S.A., D. Ricke, R. Wang, G. Presting, D. Lan, M. Dunn, J. Glazebrook, H. Varma, D. Hadley, D Hutchison, A Sessions, C Martin, F Katagiri, P Oeller, B.M. Lange, T Moughamer, Y Xia, P Budworth, J Zhong, T Miguel, CB Ho, U Paszkowski, S Zhang, M Colbert, W Sun, L Chen, B Cooper, S Park, W Kimmerly, T.C. Wood , L. Mao, P. Quail, R.A. Wing, R. Dean, Y. Yu, S. Briggs, A. Zharkikh, R. Shen, A. Oliphant, S. Sahasrabudhe, A. Thomas, R. Cannings, A Gutin, D Pruss, J Reid, S Tavtigian, J Mitchell, G Eldredge, T Scholl, RM Miller, S Bhatnagar, N Adey, T Rubano, N Tusneem, R Robinson, J Feldhaus, T Macalma (2002). Draft Sequence of the Rice Genome. Science 296:92-100.

Wei, F., R.A. Wing and R.P. Wise (2002). Genome dynamics and evolution of the Mla (Powdery Mildew) resistance locus in barley. Plant Cell 14:1903-1917.

Cheng Z., Buell CR, R.A. Wing, Gu M, Jiang J. (2001) Toward a Cytological Characterization of the Rice Genome. Genome Research, 11, 2133-2141.

Publications Continued:
Mao, L., D. Begum, H.W. Chuang, M.A. Budiman, E.J. Szymkowiak, E.E. Irish and R.A. Wing. 2000. JOINTLESS is a MADS-box gene controlling tomato flower abscission zone development. Nature: 406:910-913.

Mao, L., T.C. Wood, Y.Yu, M.A. Budiman, S.S. Woo, M. Sasinowski, G. Presting, D. Frisch, S. Goff, R.A. Dean, and R.A. Wing. 2000. Rice Transposable Elements: A Survey of 73,000 Sequence-Tagged-Connectors. Genome Research: 10:982-990.