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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Research Project #424765

Research Project: Genomic and Genetic Analysis of Crop Adaptation to Soil Abiotic Stresses

Location: Plant, Soil and Nutrition Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

AhFRDL1-mediated citrate secretion contributes to adaptation to iron deficiency and aluminum stress in peanuts Reprint Icon - (Peer Reviewed Journal)
Qui, W., Wang, N., Dai, J., Wang, T., Kochian, L.V., Liu, J., Zuo, Y. 2019. AhFRDL1-mediated citrate secretion contributes to adaptation to iron deficiency and aluminum stress in peanuts. Journal of Experimental Botany. 70(10):2873-2886. https://doi.org/10.1093/jxb/erz089.

Adaption of roots to nitrogen deficiency revealed by 3D quantification and proteomic analysis Reprint Icon - (Peer Reviewed Journal)
Qin, L., Walk, T., Han, P., Liyu, C., Sheng, Z., Li, Y., Hu, X., Xie, L., Yang, Y., Liu, J., Lu, X., Yu, C., Tian, J., Shaff, J., Kochian, L.V., Liao, X., Liao, H. 2018. Adaption of roots to nitrogen deficiency revealed by 3D quantification and proteomic analysis. Plant Physiology. 179:329-347. https://doi.org/10.1104/pp.18.00716.

Association of proteomics changes with Al-sensitive root zones in switchgrass Reprint Icon - (Peer Reviewed Journal)
Rangu, M., Ye, Z., Bhatti, S., Zhou, S., Fish, T., Yang, Y., Thannhauser, T.W. 2018. Association of proteomics changes with Al-sensitive root zones in switchgrass. Proteomes. 6(2). https://doi.org/10.3390/proteomes6020015.

Aluminum-activated root malate and citrate exudation is independent of NIP1;2-facilitated root-cell-wall aluminum removal in Arabidopsis Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Cai, Y., Cao, Y., Liu, J. 2018. Aluminum-activated root malate and citrate exudation is independent of NIP1;2-facilitated root-cell-wall aluminum removal in Arabidopsis. Plant Signaling and Behavior. 13(1). https://doi.org/10.1080/15592324.2017.1422469.

Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter from Sorghum bicolor Reprint Icon - (Peer Reviewed Journal)
Doshim, R., McGrath, A., Pineros, M., Szewczyk, P., Garza, D., Kochian, L., Chang, G. 2017. Functional characterization and discovery of modulators of SbMATE, the agronomically important aluminium tolerance transporter from Sorghum bicolor. Scientific Reports. 7(17996). https://doi.org/10.1038/s41598-017-18146-8.

Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits - (Peer Reviewed Journal)
Huang, B., Routaboul, J., Liu, M., Mohamed, Z., Vrebalov, J., Giovannoni, J.J., Bouzayen, M. 2017. Overexpression of the class D MADS-box gene Sl-AGL11 impacts fleshy tissue differentiation and structure in tomato fruits. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erx303.

Identification and characterization of suppressor mutants of stop1 Reprint Icon - (Peer Reviewed Journal)
Jiang, F., Wang, T., Wang, Y., Kochian, L., Chen, F., Liu, J. 2017. Identification and characterization of suppressor mutants of stop1. Biomed Central (BMC) Plant Biology. 17:128. https://doi.org/10.1186/s12870-017-1079-2.

Genome structure of bacillus cereus tsu1 and genes involved in cellulose degradation and poly-3-hydroxybutyrate synthesis Reprint Icon - (Peer Reviewed Journal)
Li, H., Zhou, S., Johnson, T., Vercruysse, K., Lizhi, O., Ranganathan, P., Phambu, N., Ropelewski, A., Thannhauser, T.W. 2017. Genome structure of bacillus cereus tsu1 and genes involved in cellulose degradation and poly-3-hydroxybutyrate synthesis. International Journal of Polymer Science. https://doi.org/10.1155/2017/6192924.

Proteins in phytohormone signaling pathways for abiotic stress in plants - (Book / Chapter)
Sangireddy, S., Ye, Z., Bhatti, S., Pei, X., Barozai, M., Thannhauser, T.W., Zhou, S. 2017. Proteins in phytohormone signaling pathways for abiotic stress in plants. In: Pandey, P.K., editor. Mechanism of Plant Hormone Signaling Under Stress. Hoboken, New Jersey:John Wiley & Sons, Inc. p.187-198.

Effects of Al3+ and La3+ trivalent metal ions on tomato fruit proteomes - (Peer Reviewed Journal)
Sangireddy, S., Okekeogbu, I., Ye, Z., Zhou, S., Howe, K.J., Fish, T., Thannhauser, T.W. 2017. Effects of Al3+ and La3+ trivalent metal ions on tomato fruit proteomes. Proteomes. 5(1):7. doi:10.3390/proteomoes5010007.

Loss-of-function mutation of the calcium sensor CBL1 increases aluminum sensitivity in Arabidopsis Reprint Icon - (Peer Reviewed Journal)
Ligaba, A., Fei, Z., Liu, J., Xu, Y., Jia, X., Shaff, J., Lee, S., Luan, S., Kudla, J., Kochian, L.V., Pineros, M. 2017. Loss-of-function mutation of the calcium sensor CBL1 increases aluminum sensitivity in Arabidopsis. New Phytologist. 214(2):830-841. https://doi.org/10.1111/nph.14420.

Quantitative iTRAQ proteomics revealed possible roles for antioxidant proteins in sorghum aluminum tolerance Reprint Icon - (Peer Reviewed Journal)
Zhou, D., Yang, Y., Zhang, J., Jiang, F., Jia, X., Craft, E.J., Thannhauser, T.W., Kochian, L.V., Liu, J. 2017. Quantitative iTRAQ proteomics revealed possible roles for antioxidant proteins in sorghum aluminum tolerance. Frontiers in Plant Science. 7:2043. https://doi.org/10.3389/fpls.2016.02043.

The ALMT family of organic acid transporters in plants and their involvement in detoxification and nutrient security Reprint Icon - (Review Article)
Sharma, T., Dreyer, I., Kochian, L.V., Pineros, M. 2016. The ALMT family of organic acid transporters in plants and their involvement in detoxification and nutrient security. Frontiers in Plant Science. 7(1488). https://doi.org/10.3389/fpls.2016.01488.

An Arabidopsis ABC transporter mediates phosphate deficiency-induced remodeling of root architecture by modulating iron homeostasis in roots Reprint Icon - (Peer Reviewed Journal)
Dong, J., Pineros, M., Li, X., Yang, H., Liu, Y., Murphy, A., Kochian, L.V., Liu, D. 2017. An Arabidopsis ABC transporter mediates phosphate deficiency-induced remodeling of root architecture by modulating iron homeostasis in roots. Molecular Plant. 10(2):244-259. https://doi.org/10.1016/j.molp.2016.11.001.

Redefining ‘stress resistance gene’, and why it matters Reprint Icon - (Review Article)
Maron, L., Pineros, M., Kochian, L.V., Mccouch, S. 2016. Redefining ‘stress resistance gene’, and why it matters. Journal of Experimental Botany. 67(19):5588-5591. https://doi.org/10.1093/jxb/erw323.

The raf-like kinase ILK1 and the high affinity K+ transporter HAK5 are required for innate immunity and abiotic stress response - (Peer Reviewed Journal)
Brauer, E.K., Ahsan, N., Dale, R., Kato, N., Coluccio, A.E., Pineros, M., Kochian, L.V., Thelen, J.J., Popescu, S. 2016. The raf-like kinase ILK1 and the high affinity K+ transporter HAK5 are required for innate immunity and abiotic stress response. Plant Physiology. doi: 10.1104/pp.16.00035.

Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor - (Peer Reviewed Journal)
Martin, L., Scherwood, R., Nicklay, J., Yang, Y., Muratore, S., Anderson, E., Thannhauser, T.W., Rose, J., Zhang, S. 2016. Application of wide selected-ion monitoring data-independent acquisition to identify tomato fruit proteins regulated by the CUTIN DEFICIENT2 transcription factor. Proteomics. 16:2081-2094.

Proteome modification in tomato plants upon long-term aluminum treatment - (Peer Reviewed Journal)
Zhou, S., Okekeogbu, I., Sangireddy, S., Yi, Z., Hui, L., Bhatti, S., Hui, D., Yang, Y., Howe, K.J., Fish, T., Thannhauser, T.W. 2016. Proteome modification in tomato plants upon long-term aluminum treatment. Journal of Proteome Research. 15:1670-1684.

Plant vasculature-mediated signaling involved in early phosphate stress response - (Peer Reviewed Journal)
Zhang, Z., Zheng, Y., Ham, B., Chen, J., Yoshida, A., Kochian, L.V., Fei, Z., Lucas, B. 2016. Plant vasculature-mediated signaling involved in early phosphate stress response. Nature Plants. doi: 10.1038/nplants.2016.33.

Advances and considerations in technologies for growing, imaging, and analyzing 3-D root system architecture - (Peer Reviewed Journal)
Pineros, M., Larson, B., Shaff, J., Schneider, D.J., Falcao, A., Lixing, Y., Clark, R.T., Craft, E.J., Davis, T.W., Pradier, P., Liu, J., Assaranurak, I., Susan, M., Sturrock, C., Bennett, M., Kochian, L.V. 2016. Advances and considerations in technologies for growing, imaging, and analyzing 3-D root system architecture. Journal of Integrative Plant Biology. 58(3):230-241.

How high do ion fluxes go? A re-evaluation of the two-mechanism model of K+ 2 transport in plant roots - (Peer Reviewed Journal)
Coskun, D., Britto, D.T., Kochian, L.V., Kronzucker, H.J. 2015. How high do ion fluxes go? A re-evaluation of the two-mechanism model of K+ 2 transport in plant roots. Plant Science. 243:96-104.

Duplicate and conquer: multiple homologs of phosphorus-starvation tolerance 1 enhance phosphorus acquisition and sorghum performance on low-P soils - (Peer Reviewed Journal)
Hufnagel, B., De Sousa, S.M., Assis, L., Guimaraes, C.T., Leiser, W., Corradi, G., Negri, B., Larson, B.G., Shaff, J.E., Pastina, M., Barros, B.A., Weltzien, E., Rattunde, H.W., Viana, J.H., Clark, R.T., Falcao, A., Gazaffi, R., Garcia, A.F., Schaffert, R.E., Kochian, L.V., Magalhaes, J.V. 2014. Duplicate and conquer: multiple homologs of phosphorus-starvation tolerance 1 enhance phosphorus acquisition and sorghum performance on low-P soils. Plant Physiology. 166(2):659-677.

Plant adaptation to acid soils: the molecular basis for crop aluminum resistance - (Review Article)
Kochian, L.V., Pineros, M., Liu, J., Magalhaes, J. 2015. Plant adaptation to acid soils: the molecular basis for crop aluminum resistance. Annual Reviews of Plant Biology. 66:571-598. DOI: 10.1146/annualrev-arplant-043014-114822.

OPT3 is a phloem-specific iron transporter that is essential for systemic iron signaling and redistribution of iron and cadmium in arabidopsis - (Peer Reviewed Journal)
Zhiyang, Z., Gayomba, S.R., Jung, H., Vimalakumar, N.K., Pineros, M., Rutzke, M., Danku, J., Lahner, B., Punshon, T., Guerinot, M., Salt, D.D., Kochian, L.V., Vatamaniuk, O.K. 2014. OPT3 is a phloem-specific iron transporter that is essential for systemic iron signaling and redistribution of iron and cadmium in arabidopsis. The Plant Cell. DOI: http:dx.doi.org/10.1105/tpc.114.123737.

Natural variation underlies alterations in NRAT1 expression and function that play a key role in rice aluminum tolerance - (Peer Reviewed Journal)
Li, J., Liu, J., Dong, D., Jia, X., Mccouch, S., Kochian, L.V. 2014. Natural variation underlies alterations in NRAT1 expression and function that play a key role in rice aluminum tolerance. Proceedings of the National Academy of Sciences. 111(17):6503-6508.

Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance - (Peer Reviewed Journal)
Lyi, J., Liu, J., Dong, D., Jia, X., Mccouch, S., Kochian, L.V. 2014. Natural variation underlies alterations in Nramp aluminum transporter (NRAT1) expression and function that play a key role in rice aluminum tolerance. Proceedings of the National Academy of Sciences. 111(17):6503-6508.

Effect of aluminum treatment on proteomes of radicles of seeds derived from Al-treated tomato plants - (Peer Reviewed Journal)
Okekeogbu, I., Ye, Z., Sangireddy, S.R., Li, H., Bhatti, S., Zhou, S., Howe, K.J., Fish, T., Yang, Y., Thannhauser, T.W. 2014. Effect of aluminum treatment on proteomes of radicles of seeds derived from Al-treated tomato plants. Proteomes. 2(2):169-190.

Root and shoot transcriptome analysis of two ecotypes of Noccaea caerulescens uncovers the role of NcNramp1 in Cd hyperaccumulation - (Peer Reviewed Journal)
Milner, M., Mitani-Ueno, N., Yamaji, N., Yokosho, K., Craft, E.J., Fei, Z., Ebbs, S., Ma, J., Kochian, L.V. 2014. Root and shoot transcriptome analysis of two ecotypes of Noccaea caerulescens uncovers the role of NcNramp1 in Cd hyperaccumulation. Plant Journal. 78:398-410.

Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan - (Peer Reviewed Journal)
Guimaraes, C.T., Simoes, C.C., Lyza, M.G., Pastina, M.M., Magalhaes, J.V., Vasconcellos, R., Guimaraes, L., Lana, U., Tinoco, C., Noda, R.W., Jardim-Belicuas, S.N., Parentoni, S.N., Alves, V., Kochian, L.V. 2014. Genetic dissection of Al tolerance QTLs in the maize genome by high density SNP scan. Biomed Central (BMC) Genomics. 15:153. DOI:10.1186/1471-2164-15-153.

Phosphate transporters OsPHT1;9 and OsPHT1;10 are involved in phosphate uptake in rice - (Peer Reviewed Journal)
Wang, X., Wang, Z., Pineros, M., Wang, Z., Wang, W., Li, C., Wu, Z., Kochian, L.V., Wu, P. 2014. Phosphate transporters OsPHT1;9 and OsPHT1;10 are involved in phosphate uptake in rice. Plant Cell and Environment. 37(5):1159-1170. DOI: 10.1111/pce.201437.issue-5/issuetoc.

The role of aluminum sensing and signaling in plant aluminum resistance Reprint Icon - (Review Article)
Liu, J., Pineros, M., Kochian, L.V. 2014. The role of aluminum sensing and signaling in plant aluminum resistance. Journal of Integrative Plant Biology. 56(3):221-230. DOI: 10.1111/jipb.12162

Identification of a novel pathway involving a GATA transcription factor in yeast and possibly plant Zn uptake and homeostasis Reprint Icon - (Peer Reviewed Journal)
Milner, M., Pence, N., Liu, J., Kochian, L.V. 2014. Identification of a novel pathway involving a GATA transcription factor in yeast and possibly plant Zn uptake and homeostasis. Journal of Integrative Plant Biology. 56(3):271-280. DOI: 10.1111/jipb.12169.

Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB - (Peer Reviewed Journal)
Caniato, F.F., Hamlin, M.T., Guimaraes, C.T., Zhang, Z., Schaffert, R.E., Kochian, L.V., Magalhaes, J.V. 2014. Association mapping provides insights into the origin and the fine structure of the sorghum aluminum tolerance locus, AltSB. PLoS One. 9(1):e87438.

Physiological and molecular analysis of selected Kenyan maize lines for aluminum tolerance - (Peer Reviewed Journal)
Matonyei, T., Cheprot, R., Liu, J., Pineros, M., Shaff, J., Gudo, S., Were, B., Magalhaes, J., Kochian, L.V. 2014. Physiological and molecular analysis of selected Kenyan maize lines for aluminum tolerance. Plant Journal. 377:357-367.

Functional, structural and phylogenetic analysis of domains underlying the Al-sensitivity of the aluminium-activated malate/anion transporter, TaALMT1 Reprint Icon - (Peer Reviewed Journal)
Ligaba, A., Dreyer, I., Margaryan, A., Schneider, D.J., Kochian, L.V., Pineros, M. 2013. Functional, structural and phylogenetic analysis of domains underlying the Al-sensitivity of the aluminium-activated malate/anion transporter, TaALMT1. Plant Journal. 76(6):766-780. DOI: 10.1111/tpj.12332

Phylogenetic relationship among Kenyan sorghum germplasms based on aluminum tolerance - (Peer Reviewed Journal)
Cheprot, R.K., Matonyei, T.K., Liu, J., Were, B.A., Dangasuk, G.O., Onkware, A.O., Ouma, E.O., Gudo, S., Kochian, L.V. 2013. Phylogenetic relationship among Kenyan sorghum germplasms based on aluminum tolerance. African Journal of Biotechnology. 12(22):3528-3536.