Jianxin Ma

Jianxin Ma
Professor of Agronomy
Department of Agronomy, Center for Plant Biology
Phone: 765.496.3662
Fax: 765.496.7255
Office: WSLR B018
Email: 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.


Publications

Ren, B., Wang, X., Duan, J., and Ma, J.* 2019. Rhizobial tRNA-derived small RNAs are signal molecules regulating plant nodulation. Science, 10.1126/science.aav8907.

Zhang, D., Wang, X., Li, S., Wang, C., Gosney, M., Mickelbart, M., and Ma, J.* 2019. A post-domestication mutation Dt2 triggers systemic modification of divergent and convergent pathways modulating multiple agronomic traits in soybean. Mol. Plants. https://doi.org/10.1016/j.molp.2019.05.010

Wang, X., Chen, L. and Ma, J.*, 2019. Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication. Genome Biol., 20, 22.

Swarm, S.A., Sun, L., Wang, X., Wang, W., Brown, P.J., Ma, J.* and Nelson, R.L.*, 2019. Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations. Theor. Appl. Genet. 1-15.

Taylor, M.S., Tornqvist, C.E., Zhao, X., Grabowski, P., Doerge, R., Ma, J., Volenec, J., Evans, J., Ramstein, G., Sanciangco, M. and Buell, C.R., Casler, M.D., and Jiang, Y.*, 2018. Genome-Wide Association Study in Pseudo-F2 Populations of Switchgrass Identifies Genetic Loci Affecting Heading and Anthesis Dates. Front. Plant Sci. 9: 1250.

Zeng, A., Chen, P.*, Korth, K.L., Ping, J., Thomas, J., Wu, C., Srivastava, S., Pereira, A., Hancock, F., Brye, K., and Ma, J. 2018.RNA sequencing analysis of salt tolerance in soybean (Glycine max). Genomics. doi: 10.1016/j.ygeno.2018.03.020.

Li, S., Ding, Y., Zhang, D., Wang, X., Tang, X., Dai, D., Jin, H., Lee, S.H., Cai, C. and Ma*, J. 2018. Parallel domestication with a broad mutational spectrum of determinate stem growth habit in leguminous crops. Plant Journal doi: 10.1111/tpj.14066.
Zhang, D., Sun, L., Li, S., Wang, W., Ding, Y., Swarm, S.A.,, Li, L. Wang, X., Tang, X., Zhang, Z., Tian, Z., Brown, P.J., Cai, C., Nelson, R.L., and Ma., J. 2018. Elevation of soybean seed oil content through selection for seed coat shininess. Nature Plants, 4: 30-35. 

Zhao, M., Zhang, B., Lisch, D., and Ma, J. 2017. Patterns and Consequences of Subgenome Differentiation Provide Insights into the Nature of Paleopolyploidy in Plants. Plant Cell ,29: 2974-2994​.

Zhao M, and Ma, J. 2017. Transposable Elements of Brassica, In: The Brassica Genomes, eds. Wang, X., and Liu S. Springer, Wiley-Blackwell, Taylor and Francis. (in press).

Zhang, D., Zhao, M., Li, S., Sun, L., Wang, W., Cai, C., Dierking, E.C. and Ma, J. 2017. Plasticity and innovation of regulatory mechanisms underlying seed oil content mediated by duplicated genes in the palaeopolyploid soybean. Plant J., 90, pp.1120-1133. ​

Zhao, M, and Ma, J. 2017. Transposable elements. In: H.T. Nguyen and M.K. Bhattacharyya (eds.), The Soybean Genome, Springer International Publishing, pp171-181.

Gao, J., Yang, S., Cheng, W., Fu, Y., Leng, J., Yuan, X., Jiang, N., Ma, J., and Feng, X., 2017. GmILPA1, Encoding an anaphase-promoting complex-like protein, affects leaf petiole angle. Plant Physiol., 174: 1167-1176.

Li, L., Lin, F., Wang, W., Ping, J., Fitzgerald, J.C., Zhao, M., Li, S., Sun, L., Cai, C., and Ma, J. 2016. Fine mapping and candidate gene analysis of two loci conferring resistance to Phytophthora sojae in soybean. Theor. Appl. Genet.129: 2379-2386.​

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. Genet. 47: 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.


News Releases

http://www.purdue.edu/newsroom/releases/2014/Q3/gene-discovery-could-lead-to-better-soybean-varieties-for-northern-united-states.html

http://www.purdue.edu/newsroom/research/2010/100426MaSoybean.html

http://www.purdue.edu/newsroom/research/2010/100113JacksonSoybean.html

http://www.purdue.edu/newsroom/releases/2013/Q3/researchers-discover-genes-resistant-to-soybean-pathogen.html​

http://www.purdue.edu/newsroom/releases/2015/Q2/researchers-identify-gene-that-controls-soybean-seed-permeability,-calcium-content.html​

http://www.genetics-gsa.org/media/releases/GSA_PR_20140918_G3_editors.html​

https://www.purdue.edu/newsroom/releases/2018/Q4/purdue-agriculture-professor-named-aaas-fellow.html


Teaching

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

Elected Fellow, the American Association for the Advancement of Science (AAAS)
Purdue Agricultural Research Award (2016)
University Senator (2015-)
University Faculty Scholar (2012-2017). Purdue University
Seeds for Success (2009, 2012). Purdue University

Other Activities

Editorial Boards: G3: Genes, Genomes, Genetics (2014 - )                                                                                                                                                                             Journal of Integrative Agriculture (2017 - )                                                                                                                                                                                                         Molecular Breeding (2018 - )                                                                                                                                                                                                                                 The Crop Journal (2013 - )                                                                                                                                                                                                                                     The Plant Genome (2018 - )                                                                                                                                                                                                                                   The Plant Journal (2019 - )       


Education

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

Date joined staff:  June 2006 ​​​​​​​​​​​

Department of Agronomy, 915 West State Street, West Lafayette, IN 47907-2053 USA, (765) 494-4773

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