1. Staff

Michael Udvardi, Ph.D. Publications

Publication List

Udvardi, M. K. (2018). 3 ways nitrogen researchers are advancing agriculture. Noble News & Views, 36 (3), 10-11.

de Bang, T. C., Lundquist, P. K., Dai, X., Boschiero, C., Zhuang, Z., Pandey-Pant, P., Torres-Jerez, I., Roy, S., Nogales, J., Veerappan, V., Dickstein, R., Udvardi, M. K., Zhao, P. X. & Scheible, W-R. (2017). Genome-wide identification of medicago peptides involved in macronutrient responses and nodulation. Plant Physiology, 175 (4), 1669-1689 doi:10.1104/pp.17.01096.

Yang, J. & Udvardi, M. K. (2017). Senescence and nitrogen use efficiency in perennial grasses for forage and biofuel production. Journal of Experimental Botany, 69 (4), 855-865 doi.org/10.1093/jxb/erx241.

Cheng, X., Krom, N., Zhang, S., Mysore, K. S., Udvardi, M. K. & Wen, J. Q. (2017). Enabling reverse genetics in medicago truncatula using high-throughput sequencing for Tnt1 flanking sequence recovery. In Wolfgang Busch (Ed.), Plant Genomics: Methods and Protocols. (pp. 25-37). Methods in Molecular Biology: Springer New York.

Hossain, M. S., Shrestha, A., Zhong, S., Miri, M., Austin, R. S., Sato, S., Ross, L., Huebert, T., Tromas, A., Torres-Jerez, I., Tang, Y., Udvardi, M. K., Murray, J. D. & Szczyglowski, K. (2016). Lotus japonicus NF-YA1 plays an essential role during nodule differentiation and targets members of the SHI/STY gene family. Molecular Plant-Microbe Interactions, 29 (12), 950-964 doi:10.1094/mpmi-10-16-0206-r.

Mus, F., Crook, M. B., Garcia , K., Garcia Costas, A., Geddes, B. A., Kouri, E. D., Paramasivan, P., Ryu, M-H, Oldroyd, G., Poole, P. S., Udvardi, M. K., Voigt, C. A., Ané, J.-M. & Peters, J. W. (2016). Symbiotic nitrogen fixation and the challenges to its extension to nonlegumes. Applied and Environmental Microbiology, 82 (13), 3698-3710 doi: 10.1128/AEM.01055-16.

Bandyopadhyay, K., Uluçay, O., Sakiroglu, M., Udvardi, M. K. & Verdier, J. (2016). Analysis of Large Seeds from Three Different Medicago truncatula Ecotypes Reveals a Potential Role of Hormonal Balance in Final Size Determination of Legume Grains. International Journal of Molecular Sciences, 17 (9), 1472 doi:10.3390/ijms17091472.

Yao, S., Jiang, C., Huang, Z., Torres-Jerez, I., Chang, J., Zhang, H., Udvardi, M. K., Liu, R. & Verdier, J. (2016). The Vigna unguiculata Gene Expression Atlas (VuGEA) from de novo assembly and quantification of RNA-seq data provides insights into seed maturation mechanisms. Plant Journal, 88 (2), 318–327 doi:10.1111/tpj.13279.

Fajardo, D. A., Ramaraj, T., Devitt, N., Tang, H., Cameron, C. T., Brummer, E. C., Town, C. D., Udvardi, M. K., Monteros, M. J., Farmer, A. D., Miller, J. R., Young, N. D. & Mudge, J. (2016). Sequencing and Genome Assembly of Cultivated Alfalfa at the Diploid Level (CADL) Medicago sativa. In International Plant and Animal Genome Conference XXIV Jan 9-13, 2016 .San Diego, California: Plant & Animal Genome.

Udvardi, M. K. (2016). Global Reprogramming of Transcription and Metabolism in Response to Drought, and Genome Wide . In International Plant and Animal Genome Conference XXIV Jan 9-13, 2016 .San Diego, California: Plant & Animal Genome.

Kryvoruchko, I., Sinharoy, S., Torres-Jerez, I., Sosso, D., Pislariu, C. I., Guan, D. G,, Murray, J. D., Benedito, V. A., Frommer, W. B. & Udvardi, M. K. (2016). MtSWEET11, a Nodule-Specific Sucrose Transporter of Medicago truncatula Root Nodules. Plant Physiology, 171 (1), 554-565 doi:10.1104/pp.15.01910.

Yang, J., Worley, E., Ma, Q., Li, J., Torres-Jerez, I., Li, G., Zhao, P. X., Xu, Y., Tang, Y. & Udvardi, M. K. (2016). Nitrogen remobilization and conservation, and underlying senescence-associated gene expression in the perennial switchgrass Panicum virgatum. New Phytologist, 211, 75-89 doi: 10.1111/nph.13898.

Sinharoy, S., Liu, C., Breakspear, A., Guan, D. G,, Shailes, S., Nakashima, J., Zhang, S., Wen, J. Q., Torres-Jerez, I., Oldroyd, G., Murray, J. & Udvardi, M. K. (2016). A Medicago truncatula Cystathionine Beta Synthase like domain-containing protein is required for rhizobial infection and symbiotic nitrogen fixation. Plant Physiology, (Epub ahead of print), doi: 10.1104/pp.15.01853.

Kalloniati, C., Krompas, P., Karalias, G., Udvardi, M. K., Rennenberg, H., Herschbach, C. & Flemetakis, E. (2015). Nitrogen-fixing nodules are an important source of reduced sulfur, which triggers global changes in sulfur metabolism in lotus japonicus. Plant Cell, 27 (9), 2384-400 doi: http:/?/?dx.?doi.?org/?10.?1105/?tpc.?15.?001.

Udvardi, M. K., Brodie, E. L., Riley, W., Kaeppler, S.M. & Lynch, J. (2015). Impacts of agricultural nitrogen on the environment and strategies to reduce these impacts. Procedia Environmental Sciences, 29, 303 doi:10.1016/j.proenv.2015.07.275.

Sinharoy, S., Kryvoruchko, I., Pislariu, C., González-Guerrero, M., Benedito, V. A. & Udvardi, M. K. (2015). Functional genomics of symbiotic nitrogen fixation in legumes with a focus on transcription factors and membrane transporters. In F. J. de Bruijn (Ed.), Biological Nitrogen Fixation. Hoboken, NJ, USA: John Wiley & Sons, Inc.

Pislariu, C., Sinharoy, S., Wen, J. Q., Murray, J., Ratet, P. & Udvardi, M. K. (2015). Retrotransposon (Tnt1)-insertion mutagenesis in medicago as a tool for genetic dissection of symbiosis in legumes, in biological nitrogen fixation. In (ed. F. J. de Bruijn), Biological Nitrogen Fixation. Hoboken, NJ, USA: John Wiley & Sons, Inc.

Breuillin-Sessoms, F., Floss, D. S., Gomez, S. K., Pumplin, N., Ding, Y., Levesque-Tremblay, L., Noar, R. D., Daniels, D. A., Bravo, A., Eaglesham, J. B., Benedito, V. A., Udvardi, M. K. & Harrison, M. J. (2015). Suppression of arbuscule degeneration in medicago truncatula phosphate transporter4 mutants is dependent on the ammonium transporter 2 family protein AMT2;3. Plant Cell, 27 (4), 1-15 doi: 10.1105/tpc.114.131144.

Kang, Y., Sakiroglu, M., Krom, N., Stanton-Geddes, J, Wang, M., Lee, Y-C, Young, N. D. & Udvardi, M. K. (2015). Genome-wide association of drought-related and biomass traits with HapMap SNPs in Medicago truncatula. Plant Cell and Environment, 38 (10), 1997-2011 doi: 10.1111/pce.12520.

Horvath, B., Domonkos, A., Kereszt, A., Szucs, S., Abraham, E., Ayaydin, F., Boka, K., Chen, Y., Chen, R., Murray, J., Udvardi, M. K., Kondorosi, E. & Kalo, P. (2015). Loss of the nodule-specific cysteine rich peptide, NCR169 abolishes symbiotic nitrogen fixation in the Medicago truncatula dnf7 mutant. PNAS (Proceedings of the National Academy of Sciences of the United States of America), 112 (49), 15232-15237 doi: 10.1073/pnas.1500777112.

Lara-Chavez, A., Lowman , S., Kim, S., Tang, Y., Zhang, J., Udvardi, M. K., Nowak, J., Flinn, B. & Mei, C. (2015). Global gene expression profiling of two switchgrass cultivars following inoculation with Burkholderia phytofirmans strain PsJN. Journal of Experimental Botany, 66 (14), 4337-4350 doi: 10.1093/jxb/erv096.

Sinharoy, S., Pislariu, C. & Udvardi, M. K. (2015). A high-throughput RNA interference (RNAi)-based approach using hairy roots for the study of plant-rhizobia interactions. In K. Mysore and M. Senthil-Kumar (Eds.), Plant Gene Silencing. (pp. 159-178). Methods in Molecular Biology. New York: Humana Press.

Wuddineh, W.A., Mazarei, M., Zhang, J., Poovaiah, C.R., Mann, D.G.J., Ziebell, A., Sykes, R., Davis, M., Udvardi, M. K. & Stewart, C.N. (2014). Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance. Plant Biotechnology Journal, 13, 636-647 doi: 10.1111/pbi.12287.

Yang, J., Worley, E., Torres-Jerez, I., Miller, R., Wang, M., Fu, C-X., Wang, Z - Y., Tang, Y. & Udvardi, M. K. (2014). PvNAC1 and PvNAC2 are associated with leaf senescence and nitrogen use efficiency in switchgrass. BioEnergy Research, 8, 868-880 doi: 10.1007/s12155-014-9566-x.

Yang, J., Worley, E. & Udvardi, M. K. (2014). A NAP-AAO3 regulatory module promotes chlorophyll degradation via ABA biosynthesis in Arabidopsis leaves. Plant Cell, 26 (12), 4862-4874 doi: http:/?/?dx.?doi.?org/?10.?1105/?tpc.?114.?13.

Tadege, M., Chen, F., Murray, J., Wen, J. Q., Ratet, P., Udvardi, M. K., Dixon, R. A. & Mysore, K. S. (2014). Control of vegetative to reproductive phase transition improves biomass yield and reduces lignin content in Medicago truncatula. BioEnergy Research, 8, 857-867 doi: 10.1007/s12155-014-9565-y.

Noguero, M., Signor, C. L., Vernoud, V., Bandyopadyay, A., Sanchez, D. H., Fu, C-X., Torres-Jerez, I., Wen, J. Q., Mysore, K. S., Gallardo, K., Udvardi, M. K., Thompson, R. D. & Verdier, J. (2014). DASH transcription factor impacts Medicago truncatula seed size by its action on embryo morphogenesis and auxin homeostasis. Plant Journal, 81 (3), 453-466 doi: 10.1111/tpj.12742.

Verdier, J., Bandyopadyay, A. & Udvardi, M. K. (2014). A tutorial on lotus japonicus transcriptomic tools. In Tabatam, S., Stougaard, J. (Eds.), The Lotus japonicus Genome. (pp. 183-199). Heidelberg, Germany: Springer Berlin Heidelberg.

Guefrachi, I., Nagymihaly, M., Pislariu, C., Van de Velde, W., Ratet, P., Mars, M., Udvardi, M. K., Kondorosi, E., Mergaert, P. & Alunni, B. (2014). Extreme specificity of NCR gene expression in Medicago truncatula. BMC Genomics, 15, 712 doi:10.1186/1471-2164-15-712.

Bahulikar, R. A., Torres-Jerez, I., Worley, E., Craven, K. D. & Udvardi, M. K. (2014). Diversity of nitrogen-fixing bacteria associated with switchgrass in the native tall-grass prairie of northern Oklahoma. Applied and Environmental Microbiology, 80 (18), 5636-5643 doi: 10.1128/AEM.02091-14.

Veerappan, V., Kadel, K., Alexis, N., Scott, A., Kryvoruchko, I., Sinharoy, S., Taylor, M., Udvardi, M. K. & Dickstein, R. (2014). Keel petal incision: a simple and efficient method for genetic crossing in Medicago truncatula. Plant Methods, 10 (11), eCollection doi: 10.1186/1746-4811-10-11.

Zhang, J., Cruz de Carvalho, M. H., Torres-Jerez, I., Kang, Y., Allen, S. N., Huhman, D. V., Tang, Y., Murray, J., Sumner, L. W. & Udvardi, M. K. (2014). Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after rewatering. Plant Cell and Environment, 37 (11), 2553-2576 doi: 10.1111/pce.12328.

Gallego-Giraldo, L., Bhattarai, K., Pislariu, C., Nakashima, J., Jikumaru, Y., Kamiya, Y., Udvardi, M. K., Monteros, M. J. & Dixon, A. (2014). Lignin modification leads to increased nodule numbers in alfalfa (Medicagosativa L.). Plant Physiology, 164 (3), 1139-14150 doi:http:/?/?dx.?doi.?org/?10.?1104/?pp.?113.?2324.

Dai, X., Sinharoy, S., Udvardi, M. K. & Zhao, P. X. (2013). PlantTFcat: an online plant transcription factor and transcriptional regulator categorization and analysis tool. BMC Bioinformatics, 14 (321), doi: 10.1186/1471-2105-14-321.

Cheng, X., Wang, M., Lee, H-K., Tadege, M., Ratet, P., Udvardi, M. K., Mysore, K. S. & Wen, J. Q. (2013). An efficient reverse genetics platform in the model legume Medicago truncatula. New Phytologist, 201 (3), 1065-1076 doi: 10.1111/nph.12575.

Sinharoy, S., Torres-Jerez, I., Bandyopadhyay, K., Kereszt, A., Pislariu, C., Nakashima, J., Benedito, V. A., Kondorosi, E. & Udvardi, M. K. (2013). The C2H2 transcription factor Regulator of Symbiosome Differentiation represses transcription of the secretory pathway gene VAMP721a and promotes symbiosome development in medicago truncatula. Plant Cell, 25 (8), 3584-3601 doi: 10.1105/tpc.113.114017.

Verdier, J., Lalanne, D., Pelletier, S., Torres-Jerez, I., Righetti, K., Bandyopadhyay, K., Laprince, O., Chatelain, E., Vu, B. L., Gouzy, J., Gamas, P., Udvardi, M. K. & Buitink, J. (2013). A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds. Plant Physiology, 163 (2), 757-774 doi: 10.1104/pp.113.222380.

Wang, M., Verdier, J., Benedito, V. A., Tang, Y., Murray, J., Ge, Y., Becker, J., Carvalho, H., Rogers, C., Udvardi, M. K. & He, J. (2013). LegumeGRN: A gene regulatory network prediction server for functional and comparative studies. PLoS ONE, 8 (7), e67434 doi:10.1371/journal.pone.0067434.

Pérez-Delgado, C. M., Garcia-Calderon, M., Sánchez, D. H., Udvardi, M. K., Kopa, K., Marquez, A. J. & Betti, M. (2013). Transcriptomic and metabolic changes associated to photorespiratory ammonium accumulation in the model legume Lotus japonicus. Plant Physiology, 162 (4), 1834-1848 doi:10.1104/pp.113.217216.

Udvardi, M. K. & Poole, P. S. (2013). Transport and Metabolism in Legume-Rhizobia Symbioses. Annual Review of Plant Biology, 64, 781-805 doi:10.1146/annurev-arplant-050312-120235.

Guan, D. G,, Stacey, N. S., Liu, C., Wen, J. Q., Mysore, K. S., Torres-Jerez, I., Vernie´, T., Tadege, M., Zhou, C., Wang, Z - Y., Udvardi, M. K., Oldroyd, G. & Murray, J. (2013). Rhizobial infection is associated with the development of peripheral vasculature in nodules of Medicago truncatula. Plant Physiology, 162, 107-115 doi: 10.1104/pp.113.215111.

Bourcy, M., Brocard, L., Pislariu, C., Cosson, V., Mergaert, P., Tadege, M., Mysore, K. S., Udvardi, M. K., Gourion, B. & Ratet, P. (2013). Medicago truncatula DNF2 is a PI-PLC-XD-containing protein required for bacteroid persistence and prevention of nodule early senescence and defense-like reactions. New Phytologist, 197 (4), 1250-1261 doi:10.1111/nph.12091.

Verdier, J., Torres-Jerez, I., Wang, M., Andriankaja, A., Allen, S. N., He, J., Tang, Y., Murray, J. & Udvardi, M. K. (2013). Establishment of the Lotus japonicus Gene Expression Atlas (LjGEA) and its use to explore legume seed maturation. Plant Journal, 74 (2), 351-362 doi: 10.1111/tpj.12119.

Zhang, J., Lee, Y., Torres-Jerez, I., Wang, M., Yin, Y., Chou, W-C., He, J., Shen, H., Srivastava, A. C., Pennacchio, C., Lindquist, E., Grimwood, J., Schmutz, J., Xu, Y., Sharma, M., Sharma, R., Bartley, L.E., Ronald, P., Saha, M. C., Dixon, R. A., Tang, Y. & Udvardi, M. K. (2013). Development of an integrated transcript sequence database and a gene expression atlas for gene discovery and analysis in switchgrass (Panicum virgatum L.). Plant Journal, 74, 160-173 doi:10.1111/tpj.12104.

Wen, J. Q., Cheng, X., Wang, M., Mysore, K. S. & Udvardi, M. K. (2013). Development and application of Medicago truncatula mutant resources. In International Plant & Animal Genome Conference Proceedings XXI January 12-16, 2013 .San Diego, California: Plant & Animal Genome.

Pislariu, C., Sinharoy, S., Kryvoruchko, I., Torres-Jerez, I., Wen, J. Q., Wang, M., Krom, N., Cheng, X., Nakashima, J., Zhang, S., Taylor, M., Tang, Y., Blancaflor, E. B., Chen, F., Mysore, K. S., Benedito, V. A., Murray, J., Oldroyd, G., Ratet, P. & Udvardi, M. K. (2013). Functional genomics of symbiotic nitrogen fixation in Medicago truncatula. In International Plant & Animal Genome Conference Proceedings XXI January 12-16, 2013 .San Diego, California: Plant & Animal Genome.

Udvardi, M. K. (2013). Development and use of tools for switchgrass functional genomics. In International Plant & Animal Genome Proceedings XXI January 12-16, 2013 .San Diego, California: Plant & Animal Genome.

Dai, X., Sinharoy, S., Udvardi, M. K. & Zhao, P. X. (2013). PlantTFcat: An online plant transcription factor and transcriptional regulator categorization and analysis tool . In International Plant & Animal Genome Conference Proceedings XXI January 12-16, 2013 .San Deigo, California: Plant & Animal Genome.

Kang, Y. & Udvardi, M. K. (2012). Global regulation of reactive oxygen species scavenging genes in alfalfa root and shoot under gradual drought stress and recovery. Plant Signaling & Behavior, 7 (5), 539-543.

Verdier, J., Benedito, V. A. & Udvardi, M. K. (2012). The Medicago truncatula Gene Expression Atlas (Mtgea): A Tool for Legume Seed Biology and Biotechnology . In Ganesh Kumar Agrawal and Randeep Rakwal, Seed development : OMICS technologies toward improvement of seed quality and crop yield. (pp. 111-128). Dordrecht: Springer.

Verdier, J., Zhao, J., Dixon, R. A. & Udvardi, M. K. (2012). Methods and compositions for regulating production of proanthosyanidins. 20120278914.

Xu, B., Sathitsuksanoh, N., Tang, Y., Udvardi, M. K., Zhang, J., Shen, Z., Balota, M., Harich, K., Zhang, P.Y-H. & Zhao, B. (2012). Overexpression of AtLOV1 in Switchgrass Alters Plant Architecture, Lignin Content, and Flowering Time. PLoS ONE, 7 (12), 10.1371/journal.pone.0047399.

Balestrini, R., Ott, T., Güther, M., Bonfante, P., Udvardi, M. K. & De Tullio, M.C. (2012). Ascorbate oxidase: The unexpected involvement of a ‘wasteful enzyme’ in the symbioses with nitrogen-fixing bacteria and arbuscular mycorrhizal fungi. Plant Physiology Biochemistry, 59, 71-79 doi.org/10.1016/j.plaphy.2012.07.006.

Pislariu, C., Murray, J., Wen, J. Q., Cosson, V., Duvvuru Muni , R. R., Wang, M., Benedito, V. A., Andriankaja, A., Cheng, X., Torres-Jerez, I., Mondy, S., Zhang, S., Taylor, M., Tadege, M., Ratet, P., Mysore, K. S., Chen, R. & Udvardi, M. K. (2012). A Medicago truncatula tobacco-retrotransposon (Tnt1)-insertion mutant collection with defects in nodule development and symbiotic nitrogen fixation. Plant Physiology, 159 (4), 1686-1699 doi:10.1104/pp.112.197061.

Verdier, J., Zhao, J., Torres-Jerez, I., Ge, S., Liu, C., He, X-Z., Mysore, K. S., Dixon, R. A. & Udvardi, M. K. (2012). MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula. PNAS (Proceedings of the National Academy of Sciences of the United States of America), 109 (5), 1766–1771 doi:10.1073/pnas.1120916109.

Udvardi, M. K. (2012). Medicago systems genomics. In International Plant & Animal Genome Proceedings XX January 14-18, 2012 .San Diego, California: Plant & Animal Genome.

Young, N. D. , Debellé, F., Oldroyd, G., Geurts, R., Cannon, S. B. , Udvardi, M. K., Benedito, V. A., Mayer, K.F.X., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D. R. , Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Murray, J., Naoumkina, M., Rosen, B., Silverstein, K.A.T., Tang, H., Rombauts, S., Zhao, P. X., Zhou, P., Barbe, V., Bardou, P., Bechner, M., Bellec, A., Berger, A., Bergès, H., Bidwell, T. G., Bisseling, T., Choisne, N., Couloux, A., Denny, R., Deshpande, S., Dai, X., Doyle, J.J., Dudez, A-M., Farmer, A. D., Fouteau, S., Franken, C., Gibelin, C., Gish, J., Goldstein, S., González, A.J., Green, P.J., Hallab, A., Hartog, M., Hua, A., Humphray, S.J., Jeong, D-H., Jing, Y., Jöcker, A., Kenton, S., Kim, D-J., Klee, K., Lai, H., Lang, C., Lin, S., Macmil, S.L., Magdelenat, G., Matthews, L., McCorrison, J., Monaghan, E.L., Mun, J-H., Najar, F.Z. , Nicholson, C., Noirot, C., O’Bleness, M., Paule, C.R., Poulain, J., Prion, F., Qin, B., Qu, C., Retzel, E. F. , Riddle, C., Sallet, E., Samain, S., Samson, N., Sanders, I., Saurat, O., Scarpelli, C., Schiex, T., Segurens, B., Severin, A.J., Sherrier, D. J., Shi, R., Sims, S., Singer, S.R. , Sinharoy, S. , Sterck, L., Viollet, A., Wang, B-B., Wang, K., Wang, M., Wang, X-H., Warfsmann, J., Weissenbach, J., White, D.D., White, J. D., Wiley, G. B., Wincker, P., Xing, Y., Yang, L., Yao, Z., Ying, F., Zhai, J., Zhou, L., Zuber, A., Dénarié, J., Dixon, R. A., May, G. D., Schwartz, D.C., Rogers, J., Quétier, F., Town, C. D., & Roe, B. A. (2011). The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, November 16, Published online doi:10.1038/nature10625.

Kang, Y., Han, Y., Torres-Jerez, I., Wang, M., Tang, Y., Monteros, M. J., & Udvardi, M. K. (2011). System responses to long-term drought and re-watering of two contrasting alfalfa varieties. Plant Journal, August, doi:10.1111/j.1365-313X.2011.04738.x.

Sanchez, D.H., Schwabe, F., Erban, A., Udvardi, M. K., & Kopka, J. (2011). Comparative metabolomics of drought acclimation in model and forage legumes. Plant Cell and Environment, September, doi:10.1111/j.1365-3040.2011.02423.x.

Sanchez, D.H., Pieckenstain, F. L. , Erban, A., Escaray, F., Kraemer, P.M., Udvardi, M. K., & Kopa, K. (2011). Comparative ionomics and metabolomics in extremophile and glycophytic Lotus species under salt stress challenge the metabolic pre-adaptation hypothesis. Plant Cell and Environment, 34, 605-617 doi/10.1111/j.1365-3040.2010.02266.

Zhou, C. , Han, L., Pislariu, C., Nakashima, J., Fu, C-X., Jiang, Q., Quan, L., Blancaflor, E. B., Tang, Y., Bouton, J. H., Udvardi, M. K., Xia, G., & Wang, Z - Y. (2011). From model to crop: identification of a STAY-GREEN gene from the model legume Medicago truncatula and effective use of gene in improving quality of alfalfa (M. sativa). Plant Physiology, 157 (3), 1483–1496 doi:10.1104/pp.111.185140.

Han, Y., Kang, Y., Torres-Jerez, I., Cheung, F., Town, C. D., Zhao, P. X., Udvardi, M. K., & Monteros, M. J. (2011). Genome-wide SNP discovery in tetraploid alfalfa using 454 sequencing and high resolution melting analysis. Genomics, 12 (350), doi:10.1186/1471-2164-12-350.

Murray, J., Reddy, R., Duvvuru Muni , R. R., Torres-Jerez, I., Tang, Y., Allen, S. N., Andriankaja, M., Li, G., Laxmi, A., Cheng, X., Wen, J. Q., Vaughn, D., Schultze, M., Sun, J., Charpentier, M., Oldroyd, G., Tadege, M., Ratet, P., Mysore, K. S., Chen, R. & Udvardi, M. K. (2011). Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula . Plant Journal, 65 (2), 244-252 doi:10.1111/j.1365-313X.2010.04415.x.

Sanchez, D.H., Pieckenstain, F. L., Szymanski, J., Erban, A., Bromke, M., Hannah, M., Kraemer, P.M., Kopka, J. & Udvardi, M. K. (2011). Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics. PLoS ONE, 6 (2), e17094 doi:10.1371/journal.pone.0017094.

Tsikou, D., Stedel, C., Kouri, E. D., Udvardi, M. K., Wang, T. L. , Katinakis, P., Labrou, N. E., & Flemetakis, E. (2011). Characterization of two novel nodule-enhanced a-type carbonic anhydrases from Lotus japonicus. BBA - Biochimica et Biophysica Acta - Proteins and Proteomics, 1814 (4), 496-504 doi:10.1016/j.bbapap.2011.01.007.

Fotelli, M. N., Tsikou, D., Kolliopoulou, A., Aivalakis, G., Katinakis, P., Udvardi, M. K., Rennenberg, H., & Flemetakis, E. (2011). Nodulation enhances dark CO2 fixation and recycling in the model legume Lotus japonicus. Journal of Experimental Botany, February 9, doi:10.1093/jxb/err009.

Udvardi, M. K., Pislariu, C., Valentine, A. J. , Kryvoruchko, I., Sinharoy, S. , Wang, M., Duvvuru Muni , R. R., Torres-Jerez, I., Taylor, M. , Zhang, S. , Cheng, X., Wen, J. Q., He, J., Dai, X., Zhao, P. X., Tang, Y., Chen, R., Mysore, K. S., Ratet, P., Benedito, V. A., Oldroyd, G., & Murray, J. (2011). Functional genomics of medicago nodule development and differentiation (abstract). In International Plant & Animal Genomes XIX Conference .Town & Country Convention Center San Diego, CA: Plant & Animal Genomes.

Kalliampakou, K. I. , Kouri, E. D., Boleti, H., Pavli, O., Maurousset, L., Udvardi, M. K., Katinakis, P., Lemoine, R., & Flemetakis, E. (2011). Cloning and functional characterization of LjPLT4, a plasma membrane xylitol H+- symporter from Lotus japonicus. Molecular Membrane Biology , 28 (1), 1-13 DOI:10.3109/09687688.2010.500626.

Becana, M., Matamoros, M. , Udvardi, M. K., & Dalton, D. A. (2010). Recent insights into antioxidant defenses of legume root nodules. New Phytologist, 188 (4), 960-976 DOI:10.1111/j.1469-8137.2010.03512.x.

Diaz, P., Betti, M., Sanchez, D.H., Udvardi, M. K., Monza, J. , & Marquez, A. J. (2010). Deficiency in plastidic glutamine synthetase alters proline metabolism and transcriptomic response in Lotus japonicus under drought stress. New Phytologist, , DOI: 10.1111/j.1469-8137.2010.03440.x.

Goodrich-Blair, H., Ané, J.-M., Bever, J. D. , Bordenstein, S., Bright, M., Chaston, J.M, Clay, K., Currie, C.R., Douglas, A.E., Gerardo, N., Harrison, M. J., Ley, R.E., McFall-Ngai , M., Mukherjee, A., Rader, B., Raffa, K. F. , Ruby, E. G. , Saffo, M. B., Selosse, M-A., Sonnenburg, J. L. , Stock, S. P. , Suen, G. , Turnau, K., Udvardi, M. K., Visick , K.L., & Weis, V. M. (2010). Symbiosis research, technology, and education(abstract). In Proceedings of the 6th International Symbiosis Society Congress ..

Barrero, J. M., Millar, A.A., Griffiths, J. , Czechowski, T., Scheible, W-R., Udvardi, M. K., Reid, J. B., Ross, J. J. , Jacobsen, J. V. , & Gubler, F. (2010). Gene expression profiling identifies two regulatory genes controlling dormancy and ABA sensitivity in Arabidopsis seeds. Plant Journal, 61, 611-622 DOI:10.1111/j.1365-313X.2009.04088.x.

Ghimire, S. R. , Craven, K. D., Chaluvadi, S. R., Bennetzen, J., Worley, D. S., Yang, J., Udvardi, M. K., & Keller, M. (2010). Enhanced quality, value, yield, carbon capture and sustainability of switchgrass biomass by the improvement of root, microbe and soil interactions (abstract). In 2010 APS Annual Meeting Dallas, Texas (pp. S40). .

Gao, L-L., Kamphuis, L. G., Kakar, K., Edwards, O. R. , Udvardi, M. K., & Singh, K. B. (2010). Identification of potential early regulators of aphid resistance in Medicago truncatula via transcription factor expression profiling. New Phytologist, 186, 980-994 DOI: 10.1111/j.1469-8137.2010.03229.x .

Sanchez, D.H., Szymanski, J., Erban, A., Udvardi, M. K., & Kopka, J. (2010). Mining for robust transcriptional and metabolic responses to long-term salt stress: a case study on the model legume Lotus japonicus. Plant Cell and Environment, 33 (4), 468-480 DOI: 10.1111/j.1365-3040.2009.02047.x .

Wang, M., Benedito, V. A., Zhao, P. X., & Udvardi, M. K. (2010). Inferring large-scale gene regulatory networks using a low-order constraint-based algorithm. Molecular Biosystems, 6 (6), 988-998 DOI: 10.1039/b917571g.

Lefebvre, B., Timmers, T., Mbengue, M., Moreau, S., Hervé, C., Tóth, K., Bittencourt-Silvestre, J., Klaus, D., Deslandes, L., Godiard, L., Murray, J., Udvardi, M. K., Raffaele, S., Mongrand, S., Cullimore, J., Gamas, P., Niebel, A., & Ott, T. (2010). A remorin protein interacts with symbiotic receptors and regulates bacterial infection. Proceedings of the National Academy of Sciences of the United States of America, 107 (5), 2343-2348 DOI:10.1073/pnas.0913320107.

Benedito, V. A., Li, H., Dai, X., Wandrey, M., He, J., Kaundal, R., Torres-Jerez, I., Gomez, S. K. , Harrison, M. J., Tang, Y., Zhao, P. X., & Udvardi, M. K. (2010). Genomic inventory and transcriptional analysis of Medicago truncatula transporters. Plant Physiology, 152, 1716-1730 DOI: 10.1104/pp.109.148684.

Li, H., Benedito, V. A., Udvardi, M. K., & Zhao, P. X. (2009). TransportTP: A two-phase classification approach for membrane transporter prediction and characterization. BMC Bioinformatics, 10 (418), DOI:10.1186/1471-2105-10-418.

Hernandez, G., Valdes-Lopez, O., Ramirez, M., Goffard, N., Weiller, G., Aparicio-Fabre, R., Fuentes, S. I. , Erban, A., Kopka, J., Udvardi, M. K., & Vance, C.P. (2009). Global changes in the transcript and metabolic profiles during symbiotic nitrogen fixation in phosphorus-stressed common bean plants. Plant Physiology, 151 (3), 1221-1238 DOI:10.1104/pp.109.143842.

Hogslund, N., Radutoiu, S., Krusell, L., Voroshilova, V., Hannah, M., Goffard, N., Sanchez, D.H., Lippold, F., Ott, T., Sato, S., Tabata, S., Liboriussen, P., Lohmann, G., Schauser, L., Weiller, G., Udvardi, M. K. & Stougaard, J. (2009). Dissection of symbiosis and organ development by integrated transcriptome analysis of Lotus japonicus mutant and wild-type plants. PLoS ONE, 4 (8), e6556 doi:10.1371/journal.pone.0006556.

Libault, M., Joshi, T., Benedito, V. A., Xu, D. , Udvardi, M. K., & Stacey, G. (2009). Legume transcription factor genes: what makes legumes so special? Plant Physiology, 151, 991-1001 DOI:10.1104/pp.109.144105.

Kouri, E. D., Labrou, N. E., Garbis, S. D., Kalliampakou, K. I. , Stedel, C., Dimou, M., Udvardi, M. K., & Flemetakis, M. (2009). Molecular and biochemical characterization of the parvulin-type PPIases in Lotus japonicus. Plant Physiology, 150 (3), 1160-1173 DOI:10.1104/pp.108.132415 .

Van der Ent, S., Van Hulten, M., Pozo, M. J. , Czechowski, T., Udvardi, M. K., Pieterse, C. M. , & Ton, J. (2009). Priming of plant innate immunity by rhizobacteria and B-aminobutyric acid: differences and similarities in regulation. New Phytologist, 183, 419–431 DOI: 10.1111/j.1469-8137.2009.02851.x.

Ott, T., Sullivan, J., James, E. K., Flemetakis, M., Gunthur, C., Gibon, Y., Ronson, C., & Udvardi, M. K. (2009). Absence of symbiotic leghemoglobins alters bacteroid and plant cell differentiation during development of Lotus japonicus root nodules. Molecular Plant-Microbe Interactions, 22 (7), 800-808 DOI:10.1094/MPMI-22-7-0800.

Guether, M., Balestrini, R., Hannah, M., He, J., Udvardi, M. K., & Bonfante, P. (2009). Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus. New Phytologist, 182, 200-212 DOI:10.1111/j.1469-8137.2008.02725.x.

Gruber, V., Blanchet, S., Diet, A., Zahaf, O., Boulem, A., Kakar, K., Alunni, B., Udvardi, M. K., Frugier, F., & Crespi, M. (2009). Identification of transcription factors involved in root apex responses to salt stress in Medicago truncatula. Molecular Genetics and Genomics, 281 (1), 55-66 DOI:10.1007/s00438-008-0392-8.

Udvardi, M. K. (2009). Gene atlas project looks to identify gene function. Ag News and Views, 27 (7), 7.

Andreadeli, A., Flemetakis, M., Axarli, I., Dimou, M., Udvardi, M. K., Katinakis, P., & Labrou, N. E. (2009). Cloning and characterization of Lotus japonicus formate dehydrogenase: A possible correlation with hypoxia. BBA - Biochimica et Biophysica Acta - Proteins and Proteomics, 1794 (6), 976-984 DOI:10.1016/j.bbapap.2009.02.009.

Gutjahr, C., Novero, M., Guether, M., Montanari, O., Udvardi, M. K., & Bonfante, P. (2009). Presymbiotic factors released by the arbuscular mycorrhizal fungus Gigaspora margarita induce starch accumulation in Lotus japonicus roots. New Phytologist, 183 (1), 53-61, DOI:10.1111/j.1469-8137.2009.02871.x.

Young, N. D., & Udvardi, M. K. (2009). Translating Medicago truncatula genomics to crop legumes. Current Opinion in Plant Biology, 12 (2), 193-201 DOI:10.1016/j.pbi.2008.11.005.

Lippold, F., Sanchez, D.H., Musialak, M., Schlereth, A, Scheible, W-R., Hincha, D. K., & Udvardi, M. K. (2009). AtMyb41 regulates transcriptional and metabolic responses to osmotic stress in Arabidopsis thaliana. Plant Physiology, 149 (4), 1761-1772 DOI:10.1104/pp.108.134874.

Gomez, S. K. , Javot, H. , Deewatthanawong, P., Torres-Jerez, I., Tang, Y., Blancaflor, E. B., Udvardi, M. K., & Harrison, M. J. (2009). Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis. BMC Plant Biology, 9 (10), DOI:10.1186/1471-2229-9-10.

Udvardi, M. K., Czechowski, T., & Scheible, W-R. (2008). Eleven golden rules of quantitative RT-PCR. Plant Cell, 20 (7), 1736-1737 DOI:10.1105/tpc.108.061143.

Rogato, A., D'Apuzzo, E., Barbulova, A., Omrane, S., Stedel, C., Simon-Rosin, U., Katinakis, P., Flemetakis, M., Udvardi, M. K., & Chiurazzi, M. (2008). Tissue-specific down-regulation of LjAMT1;1 compromises nodule function and enhances nodulation in Lotus japonicus. Plant Molecular Biology, 68, 585-595 DOI:10.1007/s11103-008-9394-5.

Kakar, K., Wandrey, M., Czechowski, T., Gaertner, T., Scheible, W-R., Stitt, M., Torres-Jerez, I., Xiao, X., Redman, J., Wu, H., Cheung, F., Town, C. D., & Udvardi, M. K. (2008). A community resource for high-throughput quantitative RT-PCR analysis of transcription factor gene expression in Medicago truncatula. Plant Methods, 4 (18), 1-12 DOI:10.1186/1746-4811-4-18.

Verdier, J., Kakar, K., Gallardo, K., Le Signor, C., Aubert, G., Schlereth, A, Town, C. D., Udvardi, M. K., & Thompson, R. D. (2008). Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling. Plant Molecular Biology, 67 (6), 567-580 DOI:10.1007/s11103-008-9320-x.

Ruffel, S., Freixes, S., Balzergue, S., Tillard, P., Jeudy, C., Martin-Magniette, M. L., van der Merwe, M. J., Kakar, K., Gouzy, J., Fernie, A. R., Udvardi, M. K., Salon, C., Gojon, A., & Lepetit, A. (2008). Systemic signaling of the plant nitrogen status triggers specific transcriptome responses depending on the N source in Medicago truncatula. Plant Physiology, 146 (4), 2020-2035 DOI:107.115667v1.

Benedito, V. A., Torres-Jerez, I., Murray, J., Andriankaja, A., Allen, N. S., Kakar, K., Wandrey, M., Verdier, J., Zuber, H., Ott, T., Moreau, S., Niebel, A., Frickey, T., Weiller, G., He, J., Dai, X., Zhao, P. X., Tang, Y., & Udvardi, M. K. (2008). A gene expression atlas of the model legume Medicago truncatula. Plant Journal, 55 (3), 504-513 DOI:10.111/j.1365-313X.2008.03519.x.

Sanchez, D.H., Siahpoosh, M. R., Roessner-Tunali, U., Udvardi, M. K., & Kopka, J. (2008). Plant metabolomics reveals conserved and divergent metabolic responses to salinity. Physiologia Plantarum, 132 (2), 209-219 DOI:10.1111/j.1399-3054.2007.00993.x.

Sanchez, D.H., Lippold, F., Redestig, H., Hannah, M., Erban, A., Kramer, K., Kopka, J., & Udvardi, M. K. (2008). Integrative functional genomics of salt acclimatization in the model legume Lotus japonicus. Plant Journal, 53 (6), 973-987 DOI:10.1111/j.1365-313X.2007.03381.x.

Frickey, T., Benedito, V. A., Udvardi, M. K., & Weiller, G. (2008). AffyTrees: Facilitating comparative analysis of Affymetrix plant microarray chips. Plant Physiology, 146, 377-386 DOI:10.1104/pp.107.109603.

D'Antuono, A.L., Ott, T., Krusell, L., Voroshilova, V., Ugalde, R.A., Udvardi, M. K., & Lepek, V.C. (2008). Defects in rhizobial cyclic glucan and lipopolysaccharide synthesis alter legume gene expression during nodule development. MPMI - Molecular Plant-Microbe Interactions, 21 (1), 50-60 DOI:10.1094/MPMI -21-1-0050.

Libault, M., Wan, J., Czechowski, T., Udvardi, M. K., & Stacey, G. (2007). Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. Molecular Plant-Microbe Interactions, 20, 900-911.

Udvardi, M. K., Kakar, K., Wandrey, M., Montanari, O., Murray, J., Andriankaja, A., Zhang, J., Benedito, V. A., Hofer, J., Cheung, F., & Town, C.D. (2007). Legume transcription factors: Global regulators of plant development and response to the environment. Plant Physiology, 144, 538-549.

Hernandez, G., Ramirez, M., Valdes-Lopez, O., Tesfaye, M., Graham, M. A., Czechowski, T., Schlereth, A, Wandrey, M., Erban, A., Cheung, F., Wu, H., Lara, M., Kopka, J., Udvardi, M. K., Vance, C.P., & Town, C.D. (2007). Phosphorus stress in common bean: Root transcript and metabolic responses. Plant Physiology, 144, 752-767.

Morcuende, R., Bari, R, Gibon, Y., Zheng, W., Datt Pant, B., Blasing, O., Usadel, B., Czechowski, T., Udvardi, M. K., Stitt, M., & Scheible, W-R. (2007). Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorous. Plant Cell and Environment, 30, 85-112.

Gunther, C., Schlereth, A, Udvardi, M. K., & Ott, T. (2007). Metabolism of reactive oxygen species is attenuated in leghemoglobin-deficient nodules of Lotus japonicus. MPMI - Molecular Plant-Microbe Interactions, 20 (12), 1596-1603.

Benedito, V. A., Dai, X., He, J., Zhao, P. X., & Udvardi, M. K. (2006). Functional genomics of plant transporters in legume nodules. Functional Plant Biology, 33, 731-736.

Wood, C. C., Porée, F., Dreyer, I., Koehler, G. J., & Udvardi, M. K. (2006). Mechanisms of ammonium transport, accumulation, and retention in ooyctes and yeast cells expressing Arabidopsis. FEBS Letters, 580 (16), 3931-3936.

Domoney, C., Duc, G., Ellis, J. S., Ferrandiz, C., Firnhaber, C., Gallardo, K., Mayer, K., Thompson, R. D., Udvardi, M. K., & Salon, C. (2006). Genetic and genomic analysis of legume flowers and seeds. Current Opinion in Plant Biology, 9 (April), 133-141.