2008 Publications

Jetty S.S. Ammiraju, Fei Lu, Abhijit Sanyal, Yeisoo Yu, Xiang Song, Ning Jiang, Ana Clara Pontaroli, Teri Rambo, Jennifer Currie, Kristi Collura, Jayson Talag, Chuanzhu Fan, Jose Luis Goicoechea, Andrea Zuccolo, JIngfeng Chen, Jeffrey L. Bennetzen, Mingsheng Chen, Scott Jackson, and Rod A. Wing Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set. The Plant Cell 2008, published online December 2008, doi: 10.1105/tpc.108.063727
Download pdf

Chuanzhu Fana, Yong Zhang, Yeisoo Yu, Steve Rounsley, Manyuan Long, and Rod A. Wing. The Subtelomere of Oryza sativa Chromosome 3 Short Arm as a Hot Bed of New Gene Origination in Rice. Molecular Plant 2008, Molecular Plant Advance Access published online on August 22, 2008, doi:10.1093/mp/ssn050
Download pdf

Andrea Zuccolo, Jetty S. S. Ammiraju, HyeRan Kim, Abhijit Sanyal, Scott Jackson and Rod A. Wing. Rapid and Differential Proliferation of the Ty3-Gypsy LTR Retrotransposon Atlantys in the Genus Oryza. Rice 2008, DOI 10.1007/s12284-008-9002-y, published: 20 May 2008.
Download pdf

Fusheng Wei and Rod A Wing. A fruitful outcome to the papaya genome project. Genome Biology 2008, 9:227, Published: 6 June 2008.
Download pdf

Douglas E. Soltis, Victor A. Albert, Jim Leebens-Mack, Jeffrey D. Palmer, Rod A. Wing, Claude W. dePamphilis, Hong Ma, John E. Carlson, Naomi Altman, Sangtae Kim, P. Kerr Wall, Andrea Zuccolo and Pamela S. Soltis. 2008. The Amborella genome: an evolutionary reference for plant biology. Genome Biology 2008, 9:402, published: 10 March 2008.
Download pdf

Jessica A. Schlueter, Jose Luis Goicoechea, Kristi Collura, Navdeep Gill, Jer-Young Lin, Yeisoo Yu, Dave Kudrna, Andrea Zuccolo, C. Eduardo Vallejos, Monica Muñoz-Torre, Matthew W. Blair, Joe Tohme, Jeff Tomkins, Phillip McClean, Rod A. Wing, Scott A. Jackson. 2008. BAC-end Sequence Analysis and a Draft Physical Map of the Common Bean (Phaseolus vulgaris L.) Genome. Tropical Plant Biol. (2008) 1:40-48, Published online: January 15, 2008.
Download pdf

Corrinne E. Grover, Yeisoo Yu, Rod A. Wing, Andrew H. Paterson, Jonathan F. Wendel. 2008. A phylogenetic analysis of indel dynamics in the cotton genus. Molecular Biology and Evolution 2008; doi: 10.1093/molbev/msn085
Download pdf

HyeRan Kim, Bonnie Hurwitz, Yeisoo Yu, Kristi Collura, Navdeep Gill, Phillip SanMiguel, James C Mullikin, Christopher Maher, William Nelson, Marina Wissotski, Michele Braidotti, David Kudrna, José Luis Goicoeche, Lincoln Stein, Doreen Ware, Scott A Jackson, Carol Soderlund and Rod A Wing. 2008. Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza. Genome Biology 2008, Volume 9, Issue 2, Article R45, published on February 28th, 2008.
Download pdf

Rice Annotation Project, Tanaka T, Antonio BA, Kikuchi S, Matsumoto T, Nagamura Y, Numa H, Sakai H, Wu J, Itoh T, Sasaki T, Aono R, Fujii Y, Habara T, Harada E, Kanno M, Kawahara Y, Kawashima H, Kubooka H, Matsuya A, Nakaoka H, Saichi N, Sanbonmatsu R, Sato Y, Shinso Y, Suzuki M, Takeda J, Tanino M, Todokoro F, Yamaguchi K, Yamamoto N, Yamasaki C, Imanishi T, Okido T, Tada M, Ikeo K, Tateno Y, Gojobori T, Lin YC, Wei FJ, Hsing YI, Zhao Q, Han B, Kramer MR, McCombie RW, Lonsdale D, O'Donovan CC, Whitfield EJ, Apweiler R, Koyanagi KO, Khurana JP, Raghuvanshi S, Singh NK, Tyagi AK, Haberer G, Fujisawa M, Hosokawa S, Ito Y, Ikawa H, Shibata M, Yamamoto M, Bruskiewich RM, Hoen DR, Bureau TE, Namiki N, Ohyanagi H, Sakai Y, Nobushima S, Sakata K, Barrero RA, Sato Y, Souvorov A, Smith-White B, Tatusova T, An S, An G, OOta S, Fuks G, Fuks G, Messing J, Christie KR, Lieberherr D, Kim H, Zuccolo A, Wing RA, Nobuta K, Green PJ, Lu C, Meyers BC, Chaparro C, Piegu B, Panaud O, Echeverria M. The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research, 2008, Vol. 36, Database issue, Published: December 17, 2007
Download pdf

2007 Publications

Drosophila 12 Genomes Consortium. 2007. Evolution of genes and genomes on the Drosophila phylogeny. Nature 450, 203-218 (8 November 2007).
Download pdf

Shaohong Qu , Aparna Desai , Rod Wing , and Venkatesan Sundaresan. 2007. A Versatile Transposon-Based Activation Tag Vector System for Functional Genomics in Cereals and Other Monocot Plants. Plant Physiology Preview, published on November 9, 2007; 10.1104/pp.107.111427
Download pdf

Jianxin Ma, Rod A. Wing, Jeffrey L. Bennetzen and Scott A. Jackson. 2007. Evolutionary History and Positional Shift of a Rice Centromere. Genetics: Published Articles Ahead of Print, published on July 29, 2007 as 10.1534/genetics.107.078709
Download pdf

Andrea Zuccolo, Aswathy Sebastian, Jayson Talag, Yeisoo Yu, HyeRan Kim, Kristi Collura, Dave Kudrna and Rod A. Wing. 2007. Transposable element distribution, abundance and role in genome size variation in the genus Oryza. BMC Evolutionary Biology 2007, 7:152
Download pdf

Jetty S. S. Ammiraju, Andrea Zuccolo, Yeisoo Yu, Xiang Song, Benoit Piegu, Frederic Chevalier, Jason G. Walling, Jianxin Ma, Jayson Talag, Darshan S. Brar, Phillip J. SanMiguel, Ning Jiang, Scott A. Jackson, Olivier Panaud and Rod A. Wing1. 2007. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. The Plant Journal, (2007) 52, 342-351
Download pdf

Fusheng Wei, Ed Coe, William Nelson, Arvind K. Bharti, Fred Engler, Ed Butler, HyeRan Kim, Jose Luis Goicoechea, Mingsheng Chen, Seunghee Lee, Galina Fuks, Hector Sanchez-Villeda, Steven Schroeder, Zhiwei Fang, Michael McMullen, Georgia Davis, John E. Bowers, Andrew H. Paterson, Mary Schaeffer, Jack Gardiner, Karen Cone, Joachim Messing, Carol Soderlund, Rod A. Wing. 2007. Physical and Genetic Structure of the Maize Genome Reflects Its Complex Evolutionary History. PLoS Genet 3(7): e123
Download pdf

Corrinne E. Grover1, HyeRan Kim, Rod A. Wing, Andrew H. Paterson and Jonathan F. Wendel1. 2007. Microcolinearity and genome evolution in the AdhA region of diploid and polyploid cotton (Gossypium) The Plant Journal 50: 995-1006
Download pdf

Kim, H., P. San Miguel, W. Nelson, K. Collura, M. Wissotski, J.G. Walling, J.P. Kim, S.A. Jackson, C. Soderlund, and R.A. Wing. 2007. Comparative physical mapping between O. sativa (AA genome type) and O. punctata (BB genome type) 10.1534/genetics.106.068783. Genetics: genetics.106.068783.
Download pdf

Gowda, M., R.-C. Venu, H. Li, C. Jantasuriyarat, S. Chen, M. Bellizzi, V. Pampanwar, H. Kim, R.A. Dean, E. Stahlberg, R.A. Wing, C. Soderlund, and G.-L. Wang. 2007. Magnaporthe grisea Infection Triggers RNA Variation and Antisense Transcript Expression in Rice 10.1104/pp.107.095653. Plant Physiol.: pp.107.095653.
Download pdf

Itoh, T., T. Tanaka, R.A. Barrero, C. Yamasaki, Y. Fujii, P.B. Hilton, B.A.Antonio, H. Aono, R. Apweiler, R. Bruskiewich, T. Bureau, F. Burr, A. Costade Oliveira, G. Fuks, T. Habara, G. Haberer, B. Han, E. Harada, A.T. Hiraki,H. Hirochika, D. Hoen, H. Hokari, S. Hosokawa, Y. Hsing, H. Ikawa, K. Ikeo,T. Imanishi, Y. Ito, P. Jaiswal, M. Kanno, Y. Kawahara, T. Kawamura, H.Kawashima, J.P. Khurana, S. Kikuchi, S. Komatsu, K.O. Koyanagi, H. Kubooka,D. Lieberherr, Y.C. Lin, D. Lonsdale, T. Matsumoto, A. Matsuya, W.R.McCombie, J. Messing, A. Miyao, N. Mulder, Y. Nagamura, J. Nam, N. Namiki,H. Numa, S. Nurimoto, C. O'Donovan, H. Ohyanagi, T. Okido, S. Oota, N.Osato, L.E. Palmer, F. Quetier, S. Raghuvanshi, N. Saichi, H. Sakai, Y.Sakai, K. Sakata, T. Sakurai, F. Sato, Y. Sato, H. Schoof, M. Seki, M.Shibata, Y. Shimizu, K. Shinozaki, Y. Shinso, N.K. Singh, B. Smith-White, J.Takeda, M. Tanino, T. Tatusova, S. Thongjuea, F. Todokoro, M. Tsugane, A.K.Tyagi, A. Vanavichit, A. Wang, R.A. Wing, K. Yamaguchi, M. Yamamoto, N.Yamamoto, Y. Yu, H. Zhang, Q. Zhao, K. Higo, B. Burr, T. Gojobori, and T.Sasaki. 2007. Curated genome annotation of Oryza sativa ssp. japonica andcomparative genome analysis with Arabidopsis thaliana. Genome Res 17:175-183
Download pdf

Nelson, W.M., J. Dvorak, M.C. Luo, J. Messing, R.A. Wing, and C. Soderlund. 2007. Efficacy of clone fingerprinting methodologies. Genomics 89: 160-165
Download pdf

Jung, J., S.Y. Won, S.C. Suh, H. Kim, R. Wing, Y. Jeong, I. Hwang, and M. Kim. 2007. The barley ERF-type transcription factor HvRAF confers enhanced pathogen resistance and salt tolerance in Arabidopsis. Planta 225: 575-588

Ma, J., R.A. Wing, J.L. Bennetzen, and S.A. Jackson. 2007. Plant centromereorganization: a dynamic structure with conserved functions. Trends Genet23:135-139
Download pdf

2006 Publications

Ammiraju, JS., M. Luo, J.L. Goicoechea, W. Wang, D. Kudrna, C. Mueller, J.Talag, H. Kim, N.B. Sisneros, B. Blackmon, E. Fang, J.B. Tomkins, D. Brar,D. MacKill, S. McCouch, N. Kurata, G. Lambert, D.W. Galbraith, K.Arumuganathan, K. Rao, J.G. Walling, N. Gill, Y. Yu, P. SanMiguel, C.Soderlund, S. Jackson, and R.A. Wing. 2006. The Oryza bacterial artificialchromosome library resource: construction and analysis of 12 deep-coveragelarge-insert BAC libraries that represent the 10 genome types of the genusOryza. Genome Res 16: 140-147
Download pdf

Udall, J.A., J.M. Swanson, K. Haller, R.A. Rapp, M.E. Sparks, J. Hatfield,Y. Yu, Y. Wu, C. Dowd, A.B. Arpat, B.A. Sickler, T.A. Wilkins, J.Y. Guo,X.Y. Chen, J. Scheffler, E. Taliercio, R. Turley, H. McFadden, P. Payton, N.Klueva, R. Allen, D. Zhang, C. Haigler, C. Wilkerson, J. Suo, S.R. Schulze,M.L. Pierce, M. Essenberg, H. Kim, D.J. Llewellyn, E.S. Dennis, D. Kudrna,R. Wing, A.H. Paterson, C. Soderlund, and J.F. Wendel. 2006. A globalassembly of cotton ESTs. Genome Res 16: 441-450
Download pdf

Bruggmann, R., A.K. Bharti, H. Gundlach, J. Lai, S. Young, A.C. Pontaroli,F. Wei, G. Haberer, G. Fuks, C. Du, C. Raymond, M.C. Estep, R. Liu, J.L.Bennetzen, A.P. Chan, P.D. Rabinowicz, J. Quackenbush, W.B. Barbazuk, R.A.Wing, B. Birren, C. Nusbaum, S. Rounsley, K.F. Mayer, and J. Messing. 2006.Uneven chromosome contraction and expansion in the maize genome. Genome Res16: 1241-1251
Download pdf

Piegu, B., R. Guyot, N. Picault, A. Roulin, A. Saniyal, H. Kim, K. Collura,D.S. Brar, S. Jackson, R.A. Wing, and O. Panaud. 2006. Doubling genome sizewithout polyploidization: dynamics of retrotransposition-driven genomicexpansions in Oryza australiensis, a wild relative of rice. Genome Res 16:1262-1269
Download pdf

Hawkins, J.S., H. Kim, J.D. Nason, R.A. Wing, and J.F. Wendel. 2006.Differential lineage-specific amplification of transposable elements isresponsible for genome size variation in Gossypium. Genome Res 16: 1252-1261
Download pdf

Luo, M., H. Kim, D. Kudrna, N.B. Sisneros, S.J. Lee, C. Mueller, K. Collura,A. Zuccolo, E.B. Buckingham, S.M. Grim, K. Yanagiya, H. Inoko, T. Shiina,M.F. Flajnik, R.A. Wing, and Y. Ohta. 2006. Construction of a nurse shark(Ginglymostoma cirratum) bacterial artificial chromosome (BAC) library and apreliminary genome survey. BMC Genomics 7: 106
Download pdf

Luo, M., Y. Yu, H. Kim, D. Kudrna, Y. Itoh, R.J. Agate, E. Melamed, J.L.Goicoechea, J. Talag, C. Mueller, W. Wang, J. Currie, N.B. Sisneros, R.A.Wing, and A.P. Arnold. 2006. Utilization of a zebra finch BAC library todetermine the structure of an avian androgen receptor genomic region.Genomics 87: 181-190
Download pdf

Soderlund, C., K. Haller, V. Pampanwar, D. Ebbole, M. Farman, M.J. Orbach,G.L. Wang, R. Wing, J.R. Xu, D. Brown, T. Mitchell, and R. Dean. 2006. MGOS:A resource for studying Magnaporthe grisea and Oryza sativa interactions.Mol Plant Microbe Interact 19: 1055-1061

Gowda, M., R.C. Venu, M.B. Raghupathy, K. Nobuta, H. Li, R. Wing, E.Stahlberg, S. Couglan, C.D. Haudenschild, R. Dean, B.H. Nahm, B.C. Meyers,and G.L. Wang. 2006. Deep and comparative analysis of the mycelium andappressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, andoligoarray methods. BMC Genomics 7: 310
Download pdf

Cunningham, C., J. Hikima, M.J. Jenny, R.W. Chapman, G.C. Fang, C. Saski,M.L. Lundqvist, R.A. Wing, P.M. Cupit, P.S. Gross, G.W. Warr, and J.P.Tomkins. 2006. New resources for marine genomics: bacterial artificialchromosome libraries for the Eastern and Pacific oysters (Crassostreavirginica and C. gigas). Mar Biotechnol (NY) 8: 521-533

Hass-Jacobus, B.L., M. Futrell-Griggs, B. Abernathy, R. Westerman, J.L.Goicoechea, J. Stein, P. Klein, B. Hurwitz, B. Zhou, F. Rakhshan, A. Sanyal,N. Gill, J.Y. Lin, J.G. Walling, M.Z. Luo, J.S. Ammiraju, D. Kudrna, H.R.Kim, D. Ware, R.A. Wing, P. San Miguel, and S.A. Jackson. 2006. Integrationof hybridization-based markers (overgos) into physical maps for comparativeand evolutionary explorations in the genus Oryza and in Sorghum. BMCGenomics 7: 199
Download pdf

Yan, H., H. Ito, K. Nobuta, S. Ouyang, W. Jin, S. Tian, C. Lu, R.C. Venu,G.L. Wang, P.J. Green, R.A. Wing, C.R. Buell, B.C. Meyers, and J. Jiang.2006. Genomic and genetic characterization of rice Cen3 reveals extensivetranscription and evolutionary implications of a complex centromere. PlantCell 18: 2123-2133
Download pdf

Adema, C.M., Luo, M.Z., Hanelt, B., Hertel, L.A., Marshall, J.J., Zhang,S.M., DeJong, R.J., Kim, H.R., Kudrna, D., Wing, R.A., Soderlund, C.,Knight, M., Lewis, F.A., Caldeira, R.L., Jannotti-Passos, L.K., Carvalho,O.d.S., Loker, E.S. 2006. A BAC library for Biomphalaria glabrata,intermediate snail host of Schistosoma mansoni. Mem Inst Oswaldo Cruz, Riode Janeiro, Vol. 101 (Suppl. 1): 167-177
Download pdf

Lin, Y.R., T.Y. Chow, M. Luo, D. Kudrna, C.C. Lin, R.A. Wing and Y.C. Hsing.(2006). Two highly representiative rice BAC libraries of Japonica cv Tainung67 suitable for rice structural and functional genomic research. PlantScience

2005 Publications

The International Rice Genome Sequencing Project Project. (2005). The Map Based Sequence of the Rice Genome. Nature 436:793-800.
Download pdf

The Rice Chromosome 3 Sequencing Consortium (R. Buell, W.R. McCombie & R. Wing - Corresponding Authors). (2005). Sequence, Annotation, and Analysis of Synteny Between Rice Chromosome 3 and Diverged Grass Species. Genome Res 15:1-10.
Download pdf

Ammiraju, J.S.S., Y Yu, M. Luo, D. Kudrna, H.R. Kim, J. Goicoechea, Y. Katayose, T. Matsumoto, J. Wu, T. Sasaki, R.A. Wing. (2005). Random sheared fosmid library as a new genomic tool to accelerate complete finishing of rice (Oryza sativa spp. Japonica cv Nipponbare) genome sequence: sequencing of gap specific fosmid clones uncovers new euchromatic portions of the genome. Theor Appl Genet 111:1596-1607
Download pdf

The Rice Chromosomes 11 and 12 Sequencing Consortium. (2005) The Sequence of Rice Chromosomes 11 and 12, rich in disease resistance genes and recent duplications. BMC Biology 3:20-37.
Download pdf

Yang, T.-J., Y. Yu, S.-B. Chang, H.d. Jong, C.-S. Oh, S.-N. Ahn, E. Fang, and R.A. Wing. (2005). Toward closing rice telomere gaps: mapping and sequence characterization of rice subtelomere regions. Theor Appl Genet 111:467-78
Download pdf

Yang, T.-J., S. Lee, S.-B. Chang, Y. Yu, H.d. Jong, and R.A. Wing. (2005). In-depth sequence analysis of the tomato chromosome 12 centromere: identification of a large CAA block and characterization of a species-specific pericentromere retrotranposons. Chromosoma 114:103-117.
Download pdf

Wing, R.A., J.S.S. Ammiraju, M. Luo, H.R. Kim, Y. Yu, D. Kudrna, J.L. Goicoechea, W. Wang, W. Nelson, K. Rao, C. Soderlund, D. Brar, D.J. Mackill, B. Han, L. Stein, P. SanMiguel, and S. Jackson. (2005). The Oryza Map Alignment Project: The Golden Path to Unlocking the Genetic Potential of Wild Rice Species. Plant Molecular Biology 59:53-62.
Download pdf

Bowers, J.E., M.A. Arias, R. Asher, J.A. Avise, R.T. Ball, G.A. Brewer, R.W. Buss, A.H. Chen, T.M. Edwards, J.C. Estill, H.E. Exum, V.H. Goff, K.L. Herrick, C.L. Steele, S. Karunakaran, G.K. Lafayette, C. Lemke, B.S. Marler, S.L. Masters, J.M. McMillan, L.K. Nelson, G.A. Newsome, C.C. Nwakanma, R.N. Odeh, C.A. Phelps, E.A. Rarick, C.J. Rogers, S.P. Ryan, K.A. Slaughter, C.A. Soderlund, H. Tang, R.A. Wing, and A.H. Paterson. 2005. Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses. Proc Natl Acad Sci U S A 102:13206-13211.
Download pdf

Haberer, G., S. Young, A.K. Bharti, H. Gundlach, C. Raymond, G. Fuks, E. Butler, R.A. Wing, S. Rounsley, B. Birren, C. Nusbaum, K.F. Mayer, and J. Messing. 2005. Structure and architecture of the maize genome. Plant Physiol 139:1612-1624.

Pratt, L.H., C. Liang, M. Shah, F. Sun, H. Wang, S.P. Reid, A.R. Gingle, A.H. Paterson, R. Wing, R. Dean, R. Klein, H.T. Nguyen, H.M. Ma, X. Zhao, D.T. Morishige, J.E. Mullet, and M.M. Cordonnier-Pratt. 2005. Sorghum expressed sequence tags identify signature genes for drought, pathogenesis, and skotomorphogenesis from a milestone set of 16,801 unique transcripts. Plant Physiol 139: 869-884.
Download pdf

Nelson, W.M., A.K. Bharti, E. Butler, F. Wei, G. Fuks, H. Kim, R.A. Wing, J. Messing, and C. Soderlund. (2005). Whole-Genome Validation of High-Information-Content Fingerprinting. Plant Physiol 139: 27-38.
Download pdf

Kumar, C.S., R.A. Wing, and V. Sundaresan. (2005). Efficient insertional mutagenesis in rice using maize En/Spm elements. The Plant Journal 139: 27-38.
Download pdf

Wang, W., M. Tanurdzic, M. Luo, N. Sisneros, H.R. Kim, J.K. Weng, D. Kudrna, C. Mueller, K. Arumuganathan, J. Carlson, C. Chapple, C. de Pamphilis, D. Mandoli, J. Tomkins, R.A. Wing, and J.A. Banks. 2005. Construction of a bacterial artificial chromosome library from the spikemoss Selaginella moellendorffii: a new resource for plant comparative genomics. BMC Plant Biol 5:10-18.
Download pdf

Horn, R., A.C. Lecouls, A. Callahan, A. Dandekar, L. Garay, P. McCord, W. Howad, H. Chan, I. Verde, D. Main, S. Jung, L. Georgi, S. Forrest, J. Mook, T. Zhebentyayeva, Y. Yu, H.R. Kim, C. Jesudurai, B. Sosinski, P. Arus, V. Baird, D. Parfitt, G. Reighard, R. Scorza, J. Tomkins, R. Wing, and A.G. Abbott. (2005). Candidate gene database and transcript map for peach, a model species for fruit trees. Theor Appl Genet 110:1419-1428.
Download pdf

Chetchawan, J., M. Gowda, K. Haller, J. Hatfield, G. Lu, E. Stahlberg, B. Zhou, H. Li, H. Kim, Y. Yu, R.A. Dean, R.A. Wing, C. Soderlund, and G.L. Wang. (2005). Large-scale identification of expressed sequence tags involved in rice and rice blast fungus interaction. Plant Physiol 138: 105-115.
Download pdf

2004 Publications

Messing, J., A.K. Bharti, W.M. Karlowski, H. Gundlach, H.R. Kim, Y. Yu, F. Wei, G. Fuks, C.A. Soderlund, K.F. Mayer, and R.A. Wing. (2004). Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A 101: 14349-14354.

Singh, N.K., S. Raghuvanshi, S.K. Srivastava, A. Gaur, A.K. Pal, V. Dalal, A. Singh, I.A. Ghazi, A. Bhargav, M. Yadav, A. Dixit, K. Batra, K. Gaikwad, T.R. Sharma, A. Mohanty, A.K. Bharti, A. Kapur, V. Gupta, D. Kumar, S. Vij, R. Vydianathan, P. Khurana, S. Sharma, W.R. McCombie, J. Messing, R. Wing, T. Sasaki, T. Mohapatra, J.P. Khurana, and A.K. Tyagi. (2004). Sequence analysis of the long arm of rice chromosome 11 for rice-wheat synteny. Funct Integr Genomics 4: 102-117.

Tomkins, J., M. Fregene, D. Main, H. Kim, R. Wing, and J. Tohme. (2004). Bacterial artificial chromosome (BAC) library resource for positional cloning of pest and disease resistance genes in cassava (Manihot esculenta Crantz). Plant Mol Biol 56: 555-561.

Hamblin, M.T., S.E. Mitchell, G.M. White, J. Gallego, R. Kukatla, R.A. Wing, A.H. Paterson, and S. Kresovich. (2004). Comparative population genetics of the panicoid grasses: sequence polymorphism, linkage disequilibrium and selection in a diverse sample of sorghum bicolor. Genetics 167: 471-483.

Grover, C.E., H. Kim, R.A. Wing, A.H. Paterson, and J.F. Wendel. (2004). Incongruent patterns of local and global genome size evolution in cotton. Genome Res 14: 1474-1482.

Thon, M.R., S.L. Martin, S. Goff, R.A. Wing and R.A. Dean. (2004). BAC end sequences and a physical map reveal transposable element content and clustering patterns in the genome of Magnaporthe grisea. Fungal Genetics and Biology 41:657-666.

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.

Zhang, Y., Y. Huang, L. Zhang, Y.L., T. Lu, Y. Lu, Q. Feng, Q. Zhao, Z. Cheng, Y. Xue, R.A. Wing, and B. Han. (2004). Structural features of the rice chromosome 4 centromere. Nucl. Acids Res. 32:2023-2030.

Gardmer. K., S. Schroeder, M.L. Polacco, H. Sanchez-Villeda, Z. Fang, M. Morgante, T. andewe, K. Fengler, F. Useche, M. Hanafey, S. Tingey, H. Chou, R.A. Wing, C. Soderlund, E.H. Coe (2004). Anchoring 9,371 Maize expressed sequence tagged unigenes to the bacterial artificial chromosome contig map by two-dimensional overgo hybridization. Plant Physiology 134:1317-1326.

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.

2003 Publications

Meizhong Luo and Rod A. Wing. 2008. An Improved Method for Plant BAC Library Construction. Methods in Molecular Biology, vol. 236: Plant Functional Genomics: Methods and Protocols. 2008.
Download pdf

Rong, J., , C. Abbey, J.E. Bowers, C.L. Brubaker, C. Chang, P.W. Chee, T.A. Delmonte, X. Ding2, J.J. Garza, B.S. Marler, C. Park, G.J. Pierce, K.M. Rainey, V.K. Rastogi, S.R. Schulze, N.L. Trolinder, J.F. Wendel, T.A. Wilkins, T.D. Williams-Coplin, R.A. Wing, R.J. Wright, X. Zhao, L. Zhu, A.H. Paterson. (2003). A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389-417.

The Rice Chromosome 10 Sequencing Consortium. In-Depth View of Structure, Activity, and Evolution of Rice Chromosome 10 Science.2003;1566-1569.

Georgi LL, Wang Y, Reighard GL, Mao L, Wing RA, Abbott AG. Comparison of peach and Arabidopsis genomic sequences: fragmentary conservation of gene neighborhoods. Genome. 2003 Apr;46(2):268-76.

Senchina DS, Alvarez I, Cronn RC, Liu B, Rong J, Noyes RD, Paterson AH, Wing RA, Wilkins TA, Wendel JF. Rate variation among nuclear genes and the age of polyploidy in gossypium. Mol Biol Evol. 2003 Apr;20(4):633-43.

2002 Publications
Cone KC, McMullen MD, Bi IV, Davis GL, Yim YS, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH Jr. Genetic,
physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol. 2002 Dec;130(4):1598-605.

Cheng Z, Buell CR, Wing RA, Jiang J. Resolution of fluorescence in-situ hybridization mapping on rice mitotic prometaphase chromosomes, meiotic pachytene chromosomes and extended DNA fibers. Chromosome Res. 2002;10(5):379-87.

Wei F, Wing RA, Wise RP. Genome dynamics and evolution of the Mla (powdery mildew) resistance locus in barley. Plant Cell. 2002 Aug;14(8):1903-17.

Jiang N, Bao Z, Temnykh S, Cheng Z, Jiang J, Wing RA, McCouch SR, Wessler SR. Dasheng: a recently amplified nonautonomous long terminal repeat element that is a major component of pericentromeric regions in rice. Genetics. 2002 Jul;161(3):1293-305.

Zhao Q, Zhang Y, Cheng Z, Chen M, Wang S, Feng Q, Huang Y, Li Y, Tang Y, Zhou B, Chen Z, Yu S, Zhu J, Hu X, Mu J, Ying K, Hao P, Zhang L, Lu Y, Zhang LS, Liu Y, Yu Z, Fan D, Weng Q, Chen L, Lu T, Liu X, Jia P, Sun
T, Wu Y, Zhang Y, Lu Y, Li C, Wang R, Lei H, Li T, Hu H, Wu M, Zhang R, Guan J, Zhu J, Fu G, Gu M, Hong G, Xue Y, Wing R, Jiang J, Han B. A fine physical map of the rice chromosome 4. Genome Res. 2002 May;12(5):817-23.

Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T,
Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T,
Oliphant A, Briggs S. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science. 2002 Apr 5;296(5565):92-100.

Wechter WP, Begum D, Presting G, Kim JJ, Wing RA, Kluepfel DA.Physical mapping, BAC-end sequence analysis, and marker tagging of the soilborne nematicidal bacterium, Pseudomonas synxantha BG33R. OMICS. 2002;6(1):11-21.

Roche D, Conner A, Budiman A, Frisch D, Wing R, Hanna W, Ozias-Akins P. Construction of BAC libraries from two apomictic grasses to study the microcolinearity of their apospory-specific genomic regions. Theor Appl Genet. 2002 Apr;104(5):804-812.

Coe E, Cone K, McMullen M, Chen SS, Davis G, Gardiner J, Liscum E, Polacco M, Paterson A, Sanchez-Villeda H, Soderlund C, Wing R. Access to the maize genome: an integrated physical and genetic map. Plant Physiol. 2002 Jan;128(1):9-12.

Martin SL, Blackmon BP, Rajagopalan R, Houfek TD, Sceeles RG, Denn SO, Mitchell TK, Brown DE, Wing RA, Dean RA. MagnaportheDB: a federated solution for integrating physical and genetic map data with BAC end derived sequences for the rice blast fungus Magnaporthe grisea. Nucleic Acids Res. 2002 Jan 1;30(1):121-4.

Mingsheng Chen, Gernot Presting, W. Brad Barbazuk, Jose Luis Goicoechea, Barbara Blackmon, Guangchen Fang, Hyeran Kim, David Frisch, Yeisoo Yu, Shouhong Sun, Stephanie Higingbottom, John Phimphilai, Dao Phimphilai, Scheen Thurmond, Brian Gaudette, Ping Li, Jingdong Liu, Jamie Hatfield, Dorrie Main, Kasey Farrar, Caroline Henderson, Laura Barnett, Ravi Costa, Brian Williams, Suzanne Walser, Michael Atkins, Caroline Hall, Muhammad A. Budiman, Jeffery P. Tomkins, Meizhong Luo, Ian Bancroft, Jerome Salse, Farid Regad, Trilochan Mohapatra, Nagendra K. Singh, Akhilesh K. Tyagi, Carol Soderlund, Ralph A. Dean, and Rod A. Wing. An Integrated Physical and Genetic Map of the Rice Genome. The Plant Cell, Vol. 14, 537-545, March 2002, www.plantcell.org 2002 American Society of Plant Biologists.

2001 Publications

Mao, L., D. Begum, S.A. Goff, R.A. Wing. 2001. Sequence and Analysis of the Tomato JOINTLESS Locus. Plant Physiology: 126:1331-1340.

Cheng, Z., G. Presting, C.R. Buell, R.A. Wing, and J. Jiang. 2001. High resolution pachytene chromosome mapping of bacterial artificial chromosomes anchored by genetic markers reveals the centromere location and the distribution of genetic recombination along chromosome 10 of rice. Genetics: 157: 1749-1757

Luo, M., Y.H. Wang, D. Frisch, T. Joobeur, R.A. Wing and R.A. Dean. 2001. Melon BAC library construction using improved methods and identification of clones linked to the locus conferring resistance to melon Fusarium Wilt (Fom-2). Genome: 44:154-162

Draye, X, Y-R Lin, X-Y. Qian, J.E. Bowers, G.B. Burrow, P.L. Morrell, D.G. Peterson, G.G. Presting, S-X. Ren, R.A. Wing, and A.H. Paterson. 2001. Toward Integration of Comaprative Genetic Physical, Diversity, and Cytomolecular maps for Grasses and Grains, Using the Sorghum Genome as a Foundation. Plant Physiology: 125:1325-1341.

Tomkins, J.P., T.C. Wood, L.S. Barnes, A. Westman, R.A. Wing. 2001. Evaluation of genetic variation in the daylily (Hemerocallis spp.) using AFLP markers. Theoretical and Applied Genetics 102: 489-496.

2000 Publications
Wang, W., W. Zhai, M. Luo, G. Jiang, X. Chen, X. Li, R.A. Wing, L. Zhu. 2000. Chromosome Landing at the Bacterial Blight Resistance Gene Xa4 Locus Using a Deep Coverage Rice BAC Library. Mol Gen Genet, 265:118-125.

Mao, L., D. Begum, H.W. Chuang, M.H. 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.

Yu, Y., J.P. Tomkins, R. Waugh, D.A. Frisch, D. Kudrna, A. Kleinhofs, R.S. Brueggeman, G.J. Muehlbauer, R.P. Wise, and R.A. Wing. 2000. A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theoretical and Applied Genetics 101:1093-1099.

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

Zhang, H-B., M.A. Budiman and R.A. Wing. 2000. Genetic mapping of jointless-2, a locus controlling tomato pedicel abscission zone structure, using RAPD and RFLP analysis. Theoretical and Applied Genetics 100:1183-1189.

Budiman, M.A., L. Mao, T. Wood and R.A. Wing. 2000. A Deep-Coverage Tomato BAC Library and Prospects Toward Development of an STC Framework for Genome Sequencing. Genome Research 10:129-136.

Choi, S.D., D. Begum, H. Hoshinsky, D.W. Ow and R.A. Wing. 2000. A new approach for the indentification and cloning of gene: the pBACwich system using Cre/lox site-specific recombination. Nucleic Acids Research 28: i - vii.

Lin, Y., X. Draye, X. Qian, S. Ren, L. Zhu, J.P. Tomkins, R.A. Wing, Z. Li, andH. Paterson. 2000. Locus-specific contig assembly in highly-duplicated genomes using the BAC-RF method. Nucleic Acids Research Vol 28, article e23.

Peterson D.G., J.P. Tomkins, D.A. Frisch, R.A. Wing, A.H. Paterson. 2000. Construction of plant bacterial artificial chromosome (BAC) libraries: An illustrated guide. J. Agric. Genomics, 5: (www.ncgr.org/research/jag).

Yuan, Q., F. Liang, J. Hsiao, V. Zismann, M.I. Benito, J. Quackenbush, R.A. Wing, and R. Buell. 2000. Anchoring of Rice BAC clones to the Rice Genetic Map in silico. Nucl. Acids. Res Vol. 28: 3636-3641.

Druka, A., D. Kudrna, F. Han, A. Kilian, B. Steffenson, D. Frisch, J. Tomkins, R.A. Wing and A. Kleinhofs. 2000. Physical mapping of the barley stem rust resistance gene rpg4. Molecular and General Genetics 264:283-290.

1999 Publications
Budiman, M.A., J.P. Tomkins, D.A. Frisch, R.A. Wing, and A.H. Patterson. 1999. Construction of a deep-coverage BAC Library from Lycopersicon esculentum cv. Heinz 1706. Tomato Genetics Cooperative Report: 49:9.

Lijavetzky D., G. Muzzi, T. Wicker, B. Keller, R.A. Wing and J. Dubcovsky. 1999. Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42: 1176-1182.

Wei F., K. Gobelman-Werner, S.M. Morroll, J Kurth, L. Mao, R.A. Wing, D. Leister, P. Schulze-Lefert, and R.P. Wise. 1999. The Mla (powdery mildew) resistance cluster is associated with three NBS-LRR gene families and suppressed recombination within a 240-kb DNA interval on chromosome 5S (1HS) of barley. Genetics 153: 1929-1948.

Tomkins, J.P., H. Miller-Smith, M. Sasinowski, S. Choi, H. Sasinowska, M.F. Verce, D.L. Freedman, R.A. Dean and R.A. Wing. 1999. Physical map and gene survey of the Ochrobactrum anthropi genome using bacterial artificial chromosome contigs. Microbial and Comparative Genomics: 4:203-217.

Tomkins, J.P., R. Mahalingham, H. Miller-Smith, J.L. Goicoechea, H.T. Knapp, and R.A. Wing. 1999. A soybean bacterial artificial chromosome library for PI 437654 and the identification of clones associated with cyst nematode resistance. Plant Mol. Biol. 41:25-32.

Tomkins, J.P., Y. Yu, H. Miller-Smith, D.A. Frisch, S. Woo, and R.A. Wing. 1999. A bacterial artificial chromosome library for sugarcane. Theoretical and Applied Genetics: 99:419-424.

1998 Publications
Zwick, M.S., M.N.I. Faridid, R.A. Wing, G.E. Hart, J. Dong, D.M. Stelly and H.J. Price. 1998. Physical mapping of the liguleless linkage group using rice RFLP-selected sorghum bacterial artificial chromosome (BACs). Genetics 148:1983-1992.

Huang, Y.F., W.R. Jordan, R.A. Wing and P.W. Morgan. 1998. Gene expression induced by physical impedance in maize roots. Plant Mol. Biol. 37:921-930.

M.I.Gomes, M.N. Islam-Faridi, M.S. Zwick, D.G. Czeschin Jr., G. E. Hart, R.A. Wing, D.M. Stelly, and H.J. Price. 1998. Tetraploid Nature of Sorghum bicolor (L.) Moench. Jor. Of Heredity 89:188-190.

1997 Publications
Chen, M., Pl SanMiguel, A.X. de Oliveria, S.S. Woo, H. Zhang, R.A. Wing, and J.L. Bennetzen. 1997. Microcolinearity in sh2-homologous regions of the maize, rice and sorghum genomes. Proc. Natl. Acad. Sci. (USA) 94:3431-3435.

Zhang, H.B., and R.A. Wing. 1997. Physical mapping of the rice genome with BACs. Plant Mol. Biol. 35:115-127.

Gomez, M.I., M. Islam-Faradi, S.S. Woo, K.F. Schertz, D. Czeschin, M.S. Zwick, R.A. Wing, D.M. Stelly and H.J. Price. 1997. FISH of maize sh-2 selected sorghum BAC to chromosomes of Sorghum bicolor. Genome 40:475-478.

Zhu, H., S. Choi, A.K. Johnston, R.A. Wing and R.A. Dean. 1997. Construction, characterization and application of a bacterial artificial chromosome (BAC) library from Magnaporthe grisea. Fungal Genetics and Biology. 21:337-347.

Zwick, M.S., R.E. Hanson, T.D. McKnight, M.N.I.Faridi, D.M. Stelly, R.A. Wing and H.J. Price. 1997. A rapid procedure for the isolation of Cot-1 DNA from plants. Genome 40:138-142.

1996 Publications
Vielle-Calzada, J.P., M.L. Nuccio, M.A. Budiman, T.L. Thomas, B.L. Burson, M.A. Hussey, and R.A. Wing. 1996. Comparative gene expression in sexual and apomictic ovaries of Pennisetum cilare (L.) Link. Plant Mol. Biol. 32:1085-1092.

Zhang, H.B., S.D. Choi, S.S. Woo, Z.K. Li, and R.A. Wing. 1996. Construction and characterization of two rice bacterial artificial chromosome libraries from the parents of a permanent recombinant inbred mapping population. Molecular Breeding 2:11-24.

Avramova, Z.A., Thikhonov, P. San Miguel, H.K. Jin, C. Liu, S.S. Woo, R.A. Wing and J. Bennetzen. 1996. Gene identification in a complex chromosomal continuum by local cross-referencing. Plant J. 10:1163-1168.

Jiang, J., S. Nasuda, F. Dong, C.W. Scherrer, R.A. Wing, B.S. Gill, and D.C. Ward. 1996. A conserved repetitive DNA element located in the centromeres of cereal chromosomes. Proc. Natl. Acad. Sci. (USA) 93:14210-14213.

1995 Publications
Zhang, H.B., X.P. Zhao, A.H. Patterson, and R.A. Wing. 1995. Prepartation of megabase DNA from plant nuclei. The Plant Journal 7:175-184.

Choi, S.D., R. Creelman, J. Mullet, and R.A. Wing. 1995. Construction and characterization of a bacterial artificial chromosome library form Arabidopsis thaliana. Weeds World. 2:17-20.

Zhao, X.P., R.A. Wing and A.H. Patterson. 1995. Cloning and characterization of the major repeated DNA sequences in cotton (Gossypium L). Genome 38:1177-1188.

Woo, S.S., V.K. Rastogi, H.B. Zhang, A.H. Patterson, K. Schertz, and R.A. Wing. 1995. Isolation of sorghum megabase-size DNA and applications for physical mapping and bacterial and yeast artificial chromosome library construction. Plant Mol. Biol. Rep. 13:82-94.

Cai, L., J.F. Taylor, R.A. Wing, D.S. Gallagher, S.S. Woo, and S.K. Davis. 1995. Construction and characterization of a bovine bacterial artificial library. Genomics 29:413-425.

Hanson, R.E., M. Zwick, S.D. Choi, M.N. Islam-Faridi, T.D. Mcknight, R.A. Wing, H.J. Price and D.M. Stelly. 1995. Fluorescent in situ hybridization of a bacterial artificial chromosome produces a noval plant molecular cytogenetic marker. Genome 38:646-651.

1994 Publications
Woo, S.S., J. Jiang, B.S. Gill, A.H. Patterson, and R.A. Wing. 1994. Construction and characterization of a bacterial artificial chromosome library for Sorghum bicolor. Nucleic Acids Res. 22:4922-4931.

Wing, R.A., H.B. Zhang and S. Tanksley. 1994. Map-based cloning in crop plants: Tomato as a model system. I. Genetic and physical mapping of jointless. Mol. Gen. Genet. 242:681-688.

Zhang, H.B., G.B. Martin, S.D. Tanksley, and R.A. Wing. 1994. Map-based cloning in crop plants. Tomato as a model system. II. Isolation and characterization of a set of overlapping YACs that encompass the jointless locus. Mol. Gen. Genet. 244:613-621.

Chittenden, L.M., K.F. Schertz, Y.R. Lin, R.A. Wing, and A.H. Patterson. 1994. RFLP mapping of a cross between Sorghum Bicolor and. S.propinquum, suitable for high-density mapping, suggests ancestral duplication of Sorghum chromosomes. Theor. Appl. Genet. 87:925-933.

1993 Publications
Wing, R.A., V. Rastogi, H. Zhang, A. Paterson, and S.D. Tanksley. 1993. An improved method of plant megabase DNA isolation in agarose microbeads suitable for physical mapping and YAC cloning. The Plant Journal 4:893-898.

Paterson, A and R.A. Wing. 1993. Genome mapping in plants. Current Opinion in Biotechnology 4: 147.

1992 Publications
Tanksley, S.D., M.W. Ganal, J.C. Prince, M.C. deVicente, MW. Bonierbale, P. Broun, T.M. Fulton, J.J. Giovannoni, S. Grandillo, G.B. Martin, R. Messequer, J.C. Miller, L. Miller, A.H. Paterson, O. Pineda, M.S. Roeder, R.A. Wing, W. Wu, N.D. Young. 1992. High-density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160.

1991 Publications
Wing, R.A., J.J. Giovannoni, M. Ganal, and S.D. Tanksley. 1991. Isolation of molecular markers from specific chromosomal intervals using DNA pools from existing mapping populations. Nucleic Acids Research 23: 6553-6558.

Twell, D., J. Yamaguchi, R.A. Wing, J. Ushiba, and S. McCormick. 1991. Promoter analysis of three genes that are coordinately expressed during pollen development reveals pollen-specific enhancer sequences and shared regulatory elements. Genes and Development. 5:496-507.

1990 Publications
Wing, R.A., J. Yamaguchi, S. Larabell, V. Ursin, and S. McCormick. 1990. Molecular and genetic characterization of two pollen-expressed cDNAs that have sequence similarities to pectate lyases of the plant pathogen Erwinia. Plant Molecular Biology 14:17-28.

1989 Publications
Deng, X.W., R.A. Wing, and W. Gruissem. 1989. The chloroplast genome exists in multimeric forms. Proc. Natl. Acad. Sci. 86:4156-4160.

Twell, D., R.A. Wing, J. Yamaguchi and S. McCormick. 1989. Isolation and expression of a floral specific gene from tomato. Mol. Gen. Genet. 217:240-245.

1988 Publications
Matoba, S., J. Fukayama, R.A. Wing, and D.M. Ogrydziak. 1988. Intracellular precursors and secretion of the alkaline extracellular protease of Yarrowia lipolytica. Mol. And Cell Biol. 8:4904-4916.