Research Interests:
My research has been directed toward understanding the nature, timing, mechanisms and biological outcomes of genome evolution in flowering plants, and development and use of high throughput genomics tools for characterization of natural variation that leads to genomic, transcriptomic and phenotypic diversification of plant species. We use a combination of comparative, computational and experimental genomics approaches to analyze the ever-increasing databases of genomic sequences from multiple plant species to address the mechanistic basis that underlies structural and functional genomic changes, with an emphasis on transposable element-mediated gene and genome evolution. We currently have been developing new genomics tools in soybean to facilitate the translation of basic findings into tangible application for germplasm enhancement.

Our main research areas include: Comparative, structural and functional genomics of grass and legume species; Translational genomics for crop improvement; Transposable element and genome evolution; Centromere structure and evolution; and DNA recombination, methylation and epigenomics.

Currently, we have graduate student positions available. Please contact Jianxin Ma (maj@purdue.edu) directly for information on the assistantships and other potential openings in my program.

Publications:
Du, J., Tian, Z., Schmutz, J., Bowen, N.J., Shoemaker, R.C., and Ma, J. 2009. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean. The Plant Cell. (in press) 

Tian, Z., Rizzon, C., Du, J., Liu, Z., Bennetzen, J.L., Gaut, B., Jackson, S.A.,and Ma, J. 2009. Do genetic recombination and gene density shape the pattern of DNA elimination in rice LTR-retrotransposons?. Genome Res. (in press).

Ma, J. Jackson, S.A., Cannon, S. and Shoemaker, R.C., 2009. Comparative genomics of soybean. In, Bilyeu, K., Ratnaparkhe, M.B., and Kole, C. (ed.), Genetics, Genomics and Breeding in Soybean, Science Publisher, Inc. (in press).

Wu, J.*, Fujisawa, M.*, Tian, Z.*, Yamagata, H., Kamiya, K., Shibata, M., Hosokawa, S., Ito, Y., Hamada, M., Katagiri, S., Kurita, K., Yamamoto, M., Kikuta, A., Machita, K., Karasawa, W., Kanamori, H., Namiki, N., Mizuno, H., Ma, J., Sasaki T., Matsumoto T., 2009. Comparative analysis of complete orthologous centromeres from two subspecies of rice reveals rapid variation of centromere organization and structure. Plant J. (in press, * equal contribution).

Joseph, B., Schlueter, J.A., Du, J., Graham, M.A., Ma, J. and Shoemaker, R.C. 2009. Retrotransposons in the intergenic regions of syntenic blocks between soybean and medicago truncatula and their contribution to local genome evolution. The Plant Genome (in press).

Gill, N., Findley, S., Walling, J.G., Ma, J., Stacey, G, Doyle, J.J., and Jackson, S.A. 2009. Molecular and chromosomal evidence for allopolyploidy in soybean, Glycine max (L.) Merr. Plant Physiol. (in press).

Gao, D., Gill, N., Kim, H-R., Walling, J., Zhang, W., Fan, C., Yu, Y., Ma, J. SanMiguel, P, Jiang, N., Cheng, Z., Wing, R., Jiang, J., Jackson, S.A. 2009. A lineage-specific centromere retrotransposon in Oryza brachyantha. Plant J.  (in press).

Nelson, W.*, Luo, M.*, Ma, J.*, Estep, M,, Estill, J., He, R., Talag, J., Sisneros, N., Kudrna, D., Kim, H., Ammiraju, J.S., Collura, K., Bharti, A.K., Messing, J., Wing, R.A., SanMiguel, P., Bennetzen, J.L., Soderlund, C. 2008. Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. BMC Genomics 9:621 (*equal contribution)

Ma, J., Wing, R.A., Bennetzen, J.L., and Jackson, S.A. 2007. Evolutionary history and positional shift of a rice centromere. Genetics, 177: 1217-1220.

Jetty, S.S.A., Zuccolo, A., Yu, Y., Song, X., Peigu, B., Chevalier, F., Walling, J.G., Ma., J., Talag, J., Brar, D.S., SanMiguel, P.J., Jinag, N., Jackson, S.A., Panaud, O., and Wing, R.A. 2007. Evolutionary dynamics of an ancient retrotransposon family provides insights into evolution of genome size in the genus Oryza. Plant J. 52: 342-351.

Liu, R., Vitte, C., Ma, J., Mahama, A., Dhliwayo, T., Lee M., and Bennetzen, J.L. 2007. A GeneTrek analysis of the maize genome. Proc. Natl. Acad. Sci. USA 104:11844-11849 

Ma, J., Wing, R.A., Bennetzen, J.L. and Jackson, S.A. 2007. Plant centromere organization:  conserved functions within a dynamic structure. Trends Genet. 23: 134-139

Wing, R.A., Kim, H.R., Goicoechea, J.L., Yu, Y., Kudrna, D.,  Zuccolo, A., Jetty, S.S.A., Luo, M., Nelson, W., Ma, J., SanMiguel, P., Hurwitz, B., Ware, D., Brar, D., Mackill, D., Soderlund, C., Stein, L., and Jackson, S.A. 2006. Resource for comparative genome studies within Oryza. In Upadhyaya, N.M. (ed.) Rice Functional Genomics. Springer (395-410)

Ma, J., Wing, R.A., Bennetzen, J.L. and Jackson, S.A. 2006. Plant Centromere Organization:  Conserved Functions, Dynamic Structure. Trends Genet. (in press)

Ma, J., and Jackson, S.A. 2006. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. Genome Res. 16: 251-259

Ma, J., and Bennetzen, J.L. 2006. Recombination, rearrangement, reshuffling and divergence in a centromeric region of rice.  Proc. Natl. Acad. Sci. USA 103: 383-388

Bennetzen, J.L., Liu, R., Ma, J., and Pontaroli, A. 2005. Maize genome structure and rearrangement. Maydica 50: 387-392

Devos, K.M., Ma, J., Pontaroli, A., Pratt, L., and Bennetzen, J.L. 2005. Analysis and physical mapping of randomly chosen BAC clones from hexaploid bread wheat.  Proc. Natl. Acad. Sci. USA 102: 19243-19248

More publications

Teaching:
AGRY 320 Genetics

Professional Experiences:
Assistant Professor, Dept. of Agronomy, Purdue University, 08/2007 -
Research Assistant Professor, Dept. of Agronomy, Purdue University, 06/2006 to 08/2007
Research Geneticist, Dept. of Agronomy, Purdue University, 06/2005 to 05/2006
Assistant Research Scientist/Postdoctoral Associate, Dept. of Genetics, University of Georgia, 08/2003 to 06/2005
Postdoctoral Associate, Dept. of Biological Sciences, Purdue University, 04/2000 to 08/2003
Assistant Professor, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China, 08/1999 to 04/2000

Education:
MS/Ph.D., CAAS, Beijing, 1996/1999

Date joined staff:  June 2006