Contact Information:

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:

·        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

·       Ma, J., SanMiguel, P.J., Lai, J., Messing, J., and Bennetzen, J.L. 2005. DNA rearrangements in the orthologous Orp regions of the maize, rice and sorghum genomes. Genetics, 170: 1209-1220

·       Emberton, J.*, Ma, J.*, Yuan, Y., and Bennetzen, J.L. 2005. Consrtuction of HypoMethylated Partial Restriction (HMPR) librariy and it application in sequencing maize genes. Genome Res. 15: 1441-1446 (*co-first authorship)

·        Bennetzen, J.L., Ma, J., and Devos, K.M. 2005. Mechanisms of recent genome size variation in flowering plants. Annals Bot. 95: 127-132

·        Ma, J., and Bennetzen, J.L. 2004. Recent rapid growth and divergence of the rice nucleotide genomes. Proc. Natl. Acad. Sci. USA 101: 12404-12410

·        Ma, J., Devos, K.M., and Bennetzen, J.L. 2004. Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res.14: 860-869

·        Swigonova, Z., Lai, J., Ma, J., Ramakrishna, R., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. Close split of the maize and sorghum progenitors. Genome Res. 14: 1916-1923

·       Lai, J., Ma, J., Swigonova, Z., Ramakrishna, W., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. Gene loss and movement in the maize genome. Genome Res. 14: 1924-1931

·       Bennetzen, J.L., Coleman, C., Liu, R., Ma, J., and Ramakrishna, W. 2004. Consistent over-estimation of gene number in complex plant genomes. Curr. Opin. Plant Biol. 7: 732-736

·        Swigonova, Z., Lai, J., Ma, J., Ramakrishna, R., Llaca, V., Bennetzen, J.L., and Messing, J. 2004. On the tetraploid origin of maize genome. Comp. Funct. Genomics. 5: 281-284

·        Bennetzen, J.L., and Ma, J. 2003. The genetic colinearity of rice and other cereals based on gnomic sequence analysis. Curr. Opin. Plant Biol., 6:  128-133

·       Wang, L., Ma, J., Zhou, R., Wang, X., and Jia, J. 2002. Molecular tagging of the yellow rust resistance gene Yr10 in common wheat, P.I.178383 (Triticum aestivum L.). Euphytica 124: 71-73

·        Ramakrishna, W., Ma, J., SanMiguel, P., Emberton, J., Dubcovsky, J., Shiloff, B.A., Jiang, Z., Rostoks N., Busso, C.S., Matthew, O., Linton, E., Kleinhofs, A., Devos, K.M., Messing, J., and Bennetzen, J.L. 2002. Frequent genic rearrangements in two regions of grass genomes identified by comparative sequence analysis. Comp. Funct. Genomics, 3:165-166

·       Rostoks, N., Park, Y.-J., Ramakrishna, W., Ma, J., Druka, A., Shiloff, B.A., SanMiguel, P.J., Jiang, Z., Brueggeman, R., Sandhu, D., Gill, K., Bennetzen, J.L., and Kleinhofs, A. 2002. Genomic sequencing reveals gene content, genomic organization, and recombination relationships in barley. Funct. Integr. Genomics, 10: 1007-1014

·       Ma, J., Zhou, R., Dong, Y., and Jia J.  2001. Chromosomal location and detection of a yellow rust resistance gene in common wheat transferred from Triticum tugidum L. using microsatellite markers. Euphytica, 120: 219-226

·       Ma, J., Zhou, R., Dong, Y., and Jia J. 2000. Control and inheritance of resistance to yellow rust in Triticum aestivum-Lophopyrum elongatum chromosomal substitution lines. Euphytica, 111:57-60

·       Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Chromosomal location of yellow rust resistance gene in Triticum aestivum-Lophopyrum elongatum substitution lines. Chn. Sci. Bull., 44: 65-69

·       Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Molecular mapping of yellow rust resistance genes of wheat. Biotech. Bull., 24: 1-6

·       Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Genetic stability and transmission of chromosome 6V from H. villosa through gametes in wheat background. Chn. J. Genetics, 26: 384-390

·       Ma, J., Zhou, R., Dong, Y., and Jia J. 1999. Molecular mapping of a novel yellow rust resistance gene of wheat using microsatellite markers. Chn. Sci. Bull., 44: 1513-1517

·       Ma, J., Zhou, R., and Jia, J. 1997. Identification of wheat-Haynaldia villosa substitution line conferring resistance to powdery mildew using GISH and RFLP markers. Chn. J. Genetics 24: 309-314
 

Most Recent Talks:

·        Ma, J. Utilization of transposon-based genomics tools for crop improvement. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China, May 23, 2007

·        Ma, J. Exploration of transposon-based genomics tools for crop translational genomics. Purdue Agronomy Departmental Seminar. West Lafayette, IN, Feb. 12, 2007

·        Ma, J.  Comparative sequence analysis of Orp regions of five Oryza species. 3nd Annual Oryza Map Alignment Project Advisory Committee Meeting.  Narbonne, France. Oct. 18, 2006

·        Ma, J. Comparative analysis of Cen8 regions of rice and related wild rice species. 3nd Annual Oryza Map Alignment Project Advisory Committee Meeting.  Narbonne, France. Oct. 18, 2006

·        Ma, J.  Shift and evolutionary history of a rice centromere revealed by physical anchoring orthologs in related Oryza genomes. Genomes, Evolution, & Bioinformatics Conference, Tempe, AZ, May 24-28, 2006

·         Ma, J.  Recombination and rearrangement of centromeric DNA in rice. Purdue Agronomy Departmental Seminar. West Lafayette, IN, Feb. 27, 2006

·        Ma, J. Evolutionary dynamics of a rice centromere revealed by physical anchoring orthologs in related Oryza genomes. Genomes International Plant & Animal Genome Conference XIV, San Diego, Ca, Jan. 12-16, 2006. 

·        Ma J. Aggressive accumulation of LTR-retrotransposons and genic rearrangement prompt the diversification of two genomic regions of rice and its close relatives. 5^th International Symposium of Rice Functional Genomics, Epochal Tsukuba, Japan, Oct. 15-17, 2007
 

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

Awards:

·      National One-Hundred Outstanding Doctoral Dissertations, by National Council and Department of Education of China, 2001

·        Excellent Research Paper, by Beijing Genetics Society, 1999

·        Doctoral Graduate with the Most Distinction, by CAAS, 1999

·        Excellent Master/Doctoral Dissertation, by CAAS, 1996/1999
 

Education:

MS/Ph.D., CAAS, Beijing, 1996/1999
 

Date joined staff:  June 2006

Last updated:  March, 2008