Joachim Messing University Professor and Director Waksman Institute Rutgers University Busch Campus Piscataway. NJ 08854-8020 (732) 445-4256 FAX - 5735 messing@waksman.rutgers.edu Visit the Messing Lab

Molecular and genetic mechanisms of agronomically important quantitative traits. Molecular biology of plant development. Regulation of gene expression in higher plants. Plant genomics. Bioinformatics.

Twenty-five years ago. we developed a method called shotgun DNA sequencing. which has been used to sequence the genomes of microorganisms. animals. and plants. Recently. in collaboration with other laboratories we have sequenced the entire rice genome as a reference for gene discovery and organization in cereal species. Cereals are part of the grass family and some of its members provide the major food supply on earth. One interesting feature of the genomes of different cereal species is the enormous size variation. which is in part due to differential retro-transpositions and up to some degree due to gene amplification. An example of differential gene amplification is the seed storage protein genes in maize. From a practical point of view. the amino acid composition of the mature seed is controlled by the accumulation of the differentially expressed storage proteins. which therefore regulate nitrogen deposition in the seed and serve as a major renewable energy resource on earth. Interestingly. gene amplification results in differential regulation of individual gene members. providing new clues of plant chromosomal organization and functionalization.

Selected Publications

Rotter D, Bharti AK, Li HM, Luo C, Bonos SA, Bughrara S, Jung G, Messing J, Meyer WA, Rudd S, Warnke SE, Belanger FC. (2007) Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses. Mol Genet Genomics. May 12; [Epub ahead of print]

Settles AM, Holding DR, Tan BC, Latshaw SP, Liu J, Suzuki M, Li L, O'brien BA, Fajardo DS, Wroclawska E, Tseung CW, Lai J, Hunter CT 3rd, Avigne WT, Baier J, Messing J, Hannah LC, Koch KE, Becraft PW, Larkins BA, McCarty DR. (2007) Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics. 8(1):116.

Rice Annotation Project; Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, Sasaki T. (2007) Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Res. 17(2):175-83.

Xu JH, Messing J. (2006) Maize haplotype with a helitron-amplified cytidine deaminase gene copy. BMC Genet. 7:52.

Nelson WM, Dvorak J, Luo MC, Messing J, Wing RA, Soderlund C. (2007) Efficacy of clone fingerprinting methodologies. Genomics. 89(1):160-5.

Du C, Swigonova Z, Messing J. (2006) Retrotranspositions in orthologous regions of closely related grass species. BMC Evol Biol. 6:62.

Bruggmann R, Bharti AK, Gundlach H, Lai J, Young S, Pontaroli AC, Wei F, Haberer G, Fuks G, Du C, Raymond C, Estep MC, Liu R, Bennetzen JL, Chan AP, Rabinowicz PD, Quackenbush J, Barbazuk WB, Wing RA, Birren B, Nusbaum C, Rounsley S, Mayer KF, Messing J. (2006) Uneven chromosome contraction and expansion in the maize genome. Genome Res. 16(10):1241-51.

Messing J. Dooner HK. (2006) Organization and variability of the maize genome. Curr Opin Plant Biol. 9(2):157-63.

Haberer G. Young S. Bharti AK. Gundlach H. Raymond C. Fuks G. Butler E. Wing RA. Rounsley S. Birren B. Nusbaum C. Mayer KF. Messing J. (2005) Structure and architecture of the maize genome. Plant Physiol. 139(4):1612-24.

McCarty DR. Settles AM. Suzuki M. Tan BC. Latshaw S. Porch T. Robin K. Baier J. Avigne W. Lai J. Messing J. Koch KE. Hannah LC. (2005) Steady-state transposon mutagenesis in inbred maize. Plant J. 44(1):52-61.

Nelson WM. Bharti AK. Butler E. Wei F. Fuks G. Kim H. Wing RA. Messing J. Soderlund C. (2005) Whole-genome validation of high-information-content fingerprinting. Plant Physiol. 139(1):27-38.

Lai. J.. Li. Y.. Messing. J.. and Dooner. H. (2005). Gene movement by Helitrons contributes to the haplotype variability of maize. Proc. Natl. Acad. Sci. USA. 102:968-973.

Swigonová. Z.. Bennetzen. J.L.. and Messing. J. 2005. Structure and evolution of the r/b chromosomal regions in rice. maize. and sorghum. Genetics 169:891-906.

Song. R.. Segal. G. and Messing. J. (2004). Expression of the sorghum ten-member kafirin gene cluster in maize endosperm. Nucl. Acids Res. 32:e189.

Messing. J.. Bharti. A.K.. Karlowski. W.M.. Gundlach. H.. Kim. H.-R.. Yu. Y.. Wei. F.. Fuks. G.. Soderlund. C.A.. Mayer. K.F.X.. and Wing. R.D. (2004). Sequence Composition and Genome Organization of Maize. Proc. Natl. Acad. Sci. USA. 101:14349-14354.

Lai. J.. Dey. N.. Kim. C-S.. Bharti. A.K.. Rudd. S.. Mayer. K.F.X. Larkins. B.A.. Becraft. P.. and Messing J. 2004. Characterization of the maize endosperm transcriptome and its comparison to the rice genome. Genome Res. 14:1932-1937.

Lai. J.. Ma. J.. Swigonová. Z.. Ramakrishna. W.. Linton. E.. Llaca. V.. Tanyolac. B. Park. Y-J.. Jeong. O-Y.. Bennetzen. J.L.. and Messing. J. 2004. Gene loss and movement in the maize genome. Genome Res. 14:1924-1931.

Swigonová. Z.. Lai. J.. Ma. J.. Ramakrishna. W.. Llaca. V.. Bennetzen. J.L.. and Messing. J. 2004. Close split of maize and sorghum genome progenitors. Genome Res. 14:1916-1923.

Clark. RM. Linton. E. Messing. J. and Doebley. JF (2004). Pattern of diversity in the genomic region near the domestication gene tb1. Proc Natl Acad Sci USA 101:700-707.

Hamada. S.. Ishiyama. K.. Salkulsingharoj. C.. Choi. S-B.. Wu. Y.. Wang. C.. Singh. S.. Kawai. N.. Messing. J.. and Okita. T.W. (2003). Multiple RNA Transport Pathways to the Cortical Region in Developing Rice Endosperm. Plant Cell 15:2265-2272.

Segal. G.. Song. R.. and Messing. J. (2003). A New Opaque Variant of Maize by a Single Dominant RNAi-Inducing Transgene. Genetics 165:387-397.

Song. R. and Messing. J. (2003). Gene expression of a gene family in maize based on non-collinear haplotypes. Proc. Natl. Acad. Sci. USA 100:9055-9060.

The Rice Chromosome 10 Sequencing Consortium (2003). In-depth view of structure. activity. and evolution of rice chromosome 10. Science 300:1566-1569.

Song. R. and Messing. J. (2002). Contiguous genomic DNA sequence comprising the 19-kDa-zein gene family from Zea mays. Plant Physiol. 130:1626-1635.

Song. R.. Llaca. V.. and Messing. J. (2002). Mosaic organization of orthologous sequences in grass genomes. Genome Research 12:1549-1555.

Park. W.. Li. J.. Song. R.. Messing. J.. and Chen. X. (2002). CARPEL FACTORY. a dicer homolog. and HEN1. a novel protein. act in microRNA metabolism in Arabidopsis thaliana. Current Biol. 12:1484-1495.

Lai. J.. and Messing. J. (2002). Increasing maize seed methionine by mRNA stability. The Plant Journal 30:395-402.