Jianxin MaJianxin Ma

Professor of Agronomy

Department: Agronomy
Phone: 765.496.3662
Fax: 765.496.7255
Office: WSLR B018
E-mail: maj@purdue.edu
Area of Expertise: Plant Genetics and Genomics​

Curriculum Vitae​​​

Research Interests

Comparative and evolutionary genomics:  Employing a combination of comparative, computational and experimental genomics approaches to address the mechanistic basis that underlies structural and functional genomic changes in flowering plants, with an emphasis on duplication-driven and transposon-mediated gene and genome evolution.

Genetic dissection of complex traits: Employing a combination of genomics, proteomics, molecular biology and genetics approaches to dissect complex traits of agronomic importance such as soybean plant architecture, yield components, disease resistance, as well as traits underlying soybean domestication.

Genetic diversity and germplasm enhancement: Characterizing and utilizing untapped genetic diversity underlying important agronomic traits from wild soybean to develop pre-breeding lines for enhanced yield, climate-resilience, and adaptability through marker-assisted selection and genomic selection.


Liu, Y., Zhang, D., Ping, J., Li, S., Chen, Z., and Ma, J. 2016. Innovation of a Regulatory Mechanism Modulating Semi-determinate Stem Growth through Artificial Selection in Soybean. PLOS Genet., 12: e1005818.

Ping, J., Fitzgerald, J.C., Zhang, C., Lin, F., Bai, Y., Wang, D., Aggarwal, R., Rehman, M., Crasta, O., and Ma J., 2016. Identification and molecular mapping of Rps11, a novel gene conferring resistance to Phytophthora sojae in soybean, Theor. Appl. Genet. 129: 445-451.​

Sun, L., Miao, Z., Cai, C. Zhang, D., Zhao, M., Wu, Y., Zhang, X., Swarm., S.A., Zhou, L., Zhang, Z.J., Nelson, R.L., and Ma, J.* 2015. GmHs1-1, encoding a calcineurin-like protein, controls hard-seededness in soybean. Nat. Genet47: 939-943.

Zhao, M., Meyers, B.C., Cai, C., Xu, W., and Ma, J. 2015. Evolutionary Patterns and Co-evolutionary Consequences of MIRNA Genes and MicroRNA Targets Triggered by Multiple Mechanisms of Genomic Duplications in Soybean. Plant Cell, 27: 546-562

Zhao M. , Zhai J., Lin F., Li L., Cai C., Shreve J., Thimmapuram J., Hughes T.J., Meyers B.C., and Ma, J. 2015. Coordination of microRNAs, phasiRNAs, and NB-LRR genes in immune responses: insights from analyses of soybean Rps gene near-isogenic lines. Plant Genome, 8: 10.3835.
Wang, Z., Zhou, Z., Liu, Y ., Shen, Y., Liu, T., Ji, Li, Q., Wu, M., Ma, J., and Tian, Z. 2015. Functional evolution of phosphatidylethanolamine-binding proteins (PEBPs) in soybean and Arabidopsis. Plant Cell 26: 996-1008.

Li, Y., Zhou, G., Ma, J., Jiang, W., Jin, L., Zhang, Z., Guo, Y., Zhang, J., Sui, Y., … (many authors), and Qiu, L. 2014. A pan-genome of wild soybean provides insights into evolution, diversity and domestication of soybean. Nat. Biotech., 32:1045-1054.

Chalhoub, B., Denoeud, F., Liu, S., Zhou, Y., Zhao, M. Ma, J., (many others), and Wincker, P. 2014. Early allopolyploid evolution in the post-neolithic Brassica napus oilseed genome. Science, 345: 950-953.

Ping, J., Liu, Y., Sun, L., Zhao, M. Lin, F., Sui, Y., She, M., Nelson, R.L., Clemente, T., Specht, J., and Ma, J. 2014. Dt2 is an APETALA1-like MADS-domain factor gene that controls semi-determinacy in soybean. Plant Cell, 26: 2831-2842.

Cai, C. Xiao, J., Zhao, C, and Ma, J. 2014. Sequence analysis of the coat protein gene of Chinese SMV strain SC7 and comparison with those of SMV strains from the US. Chn. J. Virology 30: 489-494.

Liu, S., Liu, Y., Yang, X., Tong, C., Edwards, D., Isobel, P., Zhao, M., Ma, J., … (many authors), and Paterson, A. 2014. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat. Comm. 10.1038/ncomms4930.

Lin, F., Zhao, M., Baumann, D.D., Ping, J., Sun, L., Liu, Y., Zhang, Biao, Tang, Z., Hughes, E., Doerge, .W., Hughes, T.J., and Ma, J.  2014. Molecular response to the pathogen Phytophthora sojae among ten soybean near isogenic lines revealed by comparative transcriptomics. BMC Genomics 15: 18.

Zhao, M., Du, J., Lin, F., Tong, C., Yu, J., Huang, S. Wang, X. Liu, S., Ma, J. 2013. Shifts in evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous retrotransposons and relics of a whole genome triplication. Plant J. 76: 211-222.​

Zhao, M., Du, J., Lin, F., Tong, C., Yu, J., Huang, S. Wang, X. Liu, S. Ma, J. 2013. Shifts in evolutionary rate and intensity of purifying selection between two Brassica genomes revealed by analyses of orthologous retrotransposons and relics of a whole genome triplication. Plant J. 10.1111/tpj.12291.

Zhao, M., Zhang, B., Liu, S.-Y., and Ma, J. 2013. Transposon expression and potential effect on gene regulation in the Brassica rapa and Brassica oleracea genomes. Hereditas 35: 1014-1022.

Zhao, M., and Ma, J. 2013. Co-evolution of plant LTR-retrotransposons and their host genomes. Protein Cell 4: 493-501.

Motamayor. J.C., Mockaitis, K., Schmutz, J., Haiminen, N., Livingstone, D. 3rd, Cornejo, O., Findley, S.D., Zheng, P., Utro, F., Royaert, S., Saski, C., Jenkins, J., Podicheti, R., Zhao, M., Scheffler, B.E., Stack, J.C., Feltus, F.A., Mustiga, G.M., Amores, F., Phillips, W., Marelli, J.P., May, G.D., Shapiro, H., Ma, J., Bustamante, C.D., Schnell, R.J., Main, D., Gilbert, D., Parida, L., Kuhn, D.N. 2013. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol. 14: R53.

Lin, F., Zhao, M., Ping, J., Johnson, A., Zhang, B., Abney, T.S., Hughes, T.J., and Ma, J. 2013. Molecular mapping of two genes conferring resistance to Phytophthora sojae in a soybean landrace PI 567139B. Theor. Appl. Genet. 126: 2177-2185.

Li, Y.H., Zhao, S.C., Ma, J.X., Li, D., Yan, L., Li, J., Qi, X.T., Guo, X.S., Zhang, L., He, W.M., Chang, R.Z., Liang, Q.S., Guo, Y., Ye, C., Wang, X.B., Tao, Y., Guan, R.X., Wang, J.Y., Liu, Y.L., Jin, L.G., Zhang, X.Q., Liu, Z.X., Zhang, L.J., Chen, J., Wang, K.J., Nielsen, R., Li, R.Q., Chen, P.Y., Li, W.B., Reif, J.C., Purugganan, M., Wang, J., Zhang, M.C., Wang, J., Qiu, L.J. 2013. Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics 14: 579.

Ma, J., 2013. Retrotransposons. In: Stanley, M., and Kelly, H., (eds). Brenner’s Encyclopedia of Genetics, 2nd edition, Vol. 6., San Diego, Academic Press, p. 208-210.

Yin, H., Liu, J., Xu, Y., Liu, X., Zhang, S., Ma, J., Du, J. 2013. TARE1, a mutated copia-Like LTR retrotransposon followed by recent massive amplification in tomato. PLoS One 8: e68587.

Tian, Z., Zhao, M., She, M., Du, J., Cannon, S.B., Liu, X., Xu, X., Qi, X., Li, M.W., Lam, H.M., and Ma, J. 2012. Genome-wide characterization of nonreference transposons reveals evolutionary propensities of transposons in soybean. Plant Cell. 24: 4422-4436.

Du, J., Tian, Z., Sui, Y., Zhao, M., Song, Q., Cannon, S.B., Cregan, P., and Ma, J. 2012. Pericentromeric effects shape the patterns of divergence, retention, and expression of duplicated genes in the palaeopolyploid soybean (Glycine max (L.). Plant Cell 24: 21-32 

Zhuang, X., Köllner, T., Zhao, N., Li, G., Jiang, Y., Zhu, L., Ma, J. Degenhardt, J. Chen, F.  2012. Dynamic evolution of herbivore-induced sesquiterpene biosynthesis in sorghum and related grass crops. Plant J. 69: 70-80

Li, X., Zhu, C., Lin, Z., Wu, Y., Zhang, D., Ma, J., Song, W., Bai., G., Muehlbauer, G., Scanlon, M., Zhang., M., and Yu,, J. 2011. Conservative boundaries of chromosome size variation in Eukaryotes. Mol. Bio. Evol. 28: 1901-1911

Tian, Z., Yu.Y., Lin, F., Yu, Y.-S., SanMiguel, P., Wing, R.A., McCouch, S., Ma, J.*, and Jackson, S.A.* 2011. Exceptional lability of a genomic complex of rice and its close relatives. BMC Genomics, 12: 142 (*co-corresponding)

Kim, M.Y., Lee, S., Van, K., Kim, T.-H., Jeong, S.-C., Choi, I.-Y., Kim. D.-S., Lee, Y.-S., Park, D., Ma, J., Kim, W.-Y., Kim., B., Park, S., Lee, K.-A., Kim, D.-H., Kim, K.-H., Shin, J.-H., Jang, T.-E., Kim, K.D., Liu, W.X., Chaisan, T., Kang, Y.J., Lee, Y.-H., Kim, K.-H., Moon, J.-K., Schmutz, J., Jackson, S., Bhak, J., and Lee., S.-H. 2010. Whole-genome sequencing and intensive analysis of the undomesticated soybean (Glycine soja Sieb. and Zucc.) genome. Proc. Natl. Acad. Sci. USA 107: 22032-22037

Sanyal, A., Jetty, A.S.S., Lu, F., Yu, Y. Rambo, T., Currie, J., Kollura, K., Kim, H.R., Chen, J., Ma, J..SanMiguel, P., Chen, M., Wing, R.A., Jackson, S.A. 2010. Orthologous comparisons of the Hd1 region across genera reveal Hd1 gene lability within diploid Oryza species and Ddsruptions to microsynteny in sorghum Mol. Bio. Evol. 27: 2487-2506

Du, J., Tian, Z., Christian, H., Laten, H., Jackson, S., Cannon, S., Shoemaker, R.C., and Ma, J. 2010. Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: new insights from genome-wide analysis and multi-specific comparison. The Plant Journal 63: 584-598

Findley, S.D., Cannon, S., Varala, K., Du, J., Ma, J., Hudson, M., Birchler, J., and Stacey, G. 2010. A soybean paint-by-numbers kit: a fluorescence in situ hybridization karyotyping system. Genetics 185: 727-744.

Tian, Z., Wang, X., Lee, R., Li, Y., Specht, J., Nelson, R., McClean, P., Qiu, L., and Ma, J. 2010. Artificial selection for determinate growth habit in soybean. Proc. Natl. Acad. Sci. USA 107: 8563-8568.

The International Brachypodium Initiative. 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763-768

Du, J., Grant, D., Tian, Z., Nelson, R.T., Zhu, L., Shoemaker, R.C.,  and Ma, J. 2010. SoyTEdb: a comprehensive database of transposable elements in the soybean genome. BMC Genomics 11: 113

Schmutz, J., Cannon, S.B., Schlueter, J., Ma, J. ... Du, J., Tian, Z., Zhu. L. ... (many others), Rokhsar, D., R.C. Shoemaker, R.C., Jackson, S.A.. 2010. Genome sequence of the paleopolyploid soybean (Glycine max (L.) Merr.). Nature 463: 178-183.

Du, J., Tian, Z., Schmutz, J., Bowen, N.J., Shoemaker, R.C., and Ma, J. 2010. Bifurcation and enhancement of autonomous-nonautonomous retrotransposon partnership through LTR swapping in soybean. The Plant Cell. 22: 48-61

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. 19:2221-2230.

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. pp395-410.

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. 60:805-819.

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 2:211-223.

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. 151:1167-1174.

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.  60:820-831.

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., 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

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AGRY 320 Genetics
AGRY 480 Plant Genetics

Professional Experiences

Professor, Dept. of Agronomy, Purdue Univeristy, 08/2015 -
Associate Professor, Dept. of Agronomy, Purdue University, 08/2011 to 08/2015
Assistant Professor, Dept. of Agronomy, Purdue University, 08/2007 to 08/2011
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 & Honors

Purdue Agricultural Research Award (2016)
University Senator (2015-)
University Faculty Scholar (2012-2017). Purdue University
Seeds for Success (2009, 2012). Purdue University


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

Date joined staff:  June 2006 ​​