Leon Kochian

Plant Sciences

• Ph.D. (Plant Physiology), University of California, Davis, U.S.A.
• B.A. (Botany), University of California, Berkeley, U.S.A.

Our research program focuses on the molecular physiology and genetics of plant mineral nutrition and root biology with emphasis on plant responses to abiotic stresses in the soil.

Currently, the lab is focusing on three major research areas:

1. How do crop plants adapt to low availability of mineral nutrients and water in the soil? To identify the mechanisms and underlying genes for tolerance to low nutrient availability, we are developing high throughput root phenotyping platforms to quantify root structure, architecture and function. Quantitative descriptors of root architecture and function are mined via whole genome analyses in order to identify genes and markers underlying these traits for developing crops with improved root traits via molecular breeding.

An example of this type of research has involved the development of novel digital tools for imaging whole root systems of crop plant species in two- and three-dimensions, and using the quantitative data for root architecture traits in order to facilitate the genetic mapping of different components of root architecture. The goals of this research are to identify genes that contribute to root system architecture traits that facilitate the uptake of sparingly available nutrients, with a focus on N, P, K and micronutrient acquisition and water uptake under drought conditions.

2.  How do crop plants tolerate the abiotic stresses on acid soils, as these acid soils comprise up to 50% of the world’s potentially arable lands? This research involves identifying genes and the associated physiological mechanisms that confer tolerance to a major stress on acid soils, aluminum (Al) toxicity. We have cloned a number of Al tolerance genes in the cereal crops sorghum, maize and rice, and are studying how these genes function and are regulated. We are also investigating plant tolerance to the other primary stress on acid soils, phosphorous deficiency, with a focus on the role of root architecture in this trait (see above). Finally, we are collaborating with the Embrapa Maize and Sorghum Laboratory in Brazil and plant breeders in Africa to translate these discoveries into improved maize and sorghum yields on acid soils in Sub-Saharan Africa.

3. Research on fundamental aspects of plant mineral nutrient transport with emphasis on improving the accumulation and the availability of Fe and Zn in cereal seeds and minimizing the entry of toxic heavy metals and metalloids such as Cd and As into the food chain.

Sheng H, Gao P, Liu L, Wang S, Bakshi A, Liu L, Nguyen H, Xi L, Qin T, Xiang D, Babic V, Wen R, Quilichini T, Ren M, Datla R, Kochian L. 2025. Target of Rapamycin (TOR) signaling coordinates a balance between wheat photosynthetic performance and transpirational water conservation for improved water use efficiency and performance under drought. Curr Plant Biol https://doi.org/10.1016/j.cpb.2025.100520

Nakhforoosh A, Hallin E, Wang Z, Hogue M, Melhorn HH, Tingstad G, Kochian L. 2025. IMP²RIS, an automated plant root dosing system for in-soil visualization of symbiotic N₂ fixation in nodulated roots of soybean plants via PET imaging. Plant Phenomics 7(1), 100027

Hufnagel B, Bernardino KC, Malosetti M, de Sousa SM, Silva LA, Guimaraes CT, Coelho AM, Santos TT, Viana JH, Schaffert RH, van Eeuwijk FA, Kochian LV, Magalhaes JV. 2024. Multi-trait association mapping for phosphorous efficiency reveals flexible root architectures in sorghum. BMC Plant Biology 24: 562 – 581.

Mutsutomo Tokizawa, Takuo Enomoto, Rahul Chandnani, Javier Mora-Macías, Connor Burbridge, Alma Armenta-Medina, Yuriko Kobayashi, Yoshiharu Y Yamamoto, Hiroyuki Koyama, Leon V Kochian. 2023. The transcription factors, STOP1 and TCP20, are required for root system architecture alterations in response to nitrate deficiency. Proceedings of the National Academy of Sciences 120: e2300446120

Rahul Chandnani, Tongfei Qin, Heng Ye, Haifei Hu, Karim Panjvani, Mutsutomo Tokizawa, Javier Mora Macias, Alma Armenta Medina, Karine Bernardino, Pierre-Luc Pradier, Pankaj Banik, Ashlyn Mooney, Jurandir V. Magalhaes, Henry T. Nguyen, Leon V Kochian. 2023. Application of an Improved 2-Dimensional High-Throughput Soybean Root Phenotyping Platform to Identify Novel Genetic Variants Regulating Root Architecture Traits. Plant Phenomics 5: 0097

Mostafa S, Mondal D, Panjvani K, Kochian LI, Stavness I. 2023. Explainable deep learning in plant phenotyping. Frontiers in Artificial Intelligence 6

Tokizawa M, Enomoto T, Ito H, Liujie W, Kobayashi Y, Mora-Macias J, Dagoberto A-M, Iuchi S, Kobayashi M, Nomoto M, Tada Y, Fujita M, Shinozaki K, Koyama H^*. Kochian LV^*. 2021. High affinity promoter binding of STOP1 is essential for the early aluminum-inducible expression of novel Al resistance genes GDH1 and GDH2 in Arabidopsis. J Exp Botany 72: 2769–2789. ^*Co-corresponding authors.

Yusaku Uga, Ithipong Assaranurak, Yuka Kitomi, Brandon G. Larson, Eric J. Craft, Jon E. Shaff, Susan R. McCouch, Leon V. Kochian. 2018. Genomic regions responsible for seminal and crown root lengths identified by 2D & 3D root system image analysis. BMC Genomics 19: 273-284.

Wang Y, Li R, Li D, Jia X, Zhou D, Li J, Ly SM, Hou S, Huang Y, Kochian LV, Liu J. 2017. NIP1;2 is a plasma membrane-localized transporter mediating aluminum uptake, translocation, and tolerance in Arabidopsis. Proc Natl Acad Sci USA 114: 5047-5052

Zhang Z, Zheng Y, Ham B-K, Chen J, Yoshida A, Kochian LV, Fei Z, Lucas WJ. 2016. Vascular-mediated signalling involved in early phosphate stress response in plants. Nature Plants 2: 16033.

Piñeros MA, Larson BG, Shaff JE, Schneider DJ, Falcão AX, Yuan L, Clark RT, Craft EJ, Davis TW, Pradier PL, Shaw NM, Assaranurak I, McCouch SR, Sturrock C, Bennett M, Kochian LV. 2016. Evolving technologies for growing, imaging, and analyzing 3D root system architecture of crop plants. J Integrative Plant Biol 58: 230–241.

Carvalho, G., Schaffert, R.E., Malosetti, M., Viana, J.H.M., Menezes, C.B., Silva, L.A., Guimaraes, C.T., Coelho, A.M., Kochian, L.V., van Eeuwijk, F.A. and Magalhaes, J.V. 2016. Back to acid soil fields: the citrate transporter SbMATE is a major asset for sustainable grain yield for sorghum cultivated on acid soils. G3: Genes| Genomes| Genetics, 6: 497-484.

Kochian LV, Piñeros MA, Liu J, Magalhaes JV. 2015. Plant adaptation to acid soils: The molecular basis for crop aluminum resistance. Annual Review of Plant Biology 66: 571-598.

Hufnagel B, de Sousa SM, Assis L, Guimaraes CT, Leiser W, Azevedo GC, Negri B, Larson BG, Shaff JE, Pastina MM, Barros BA, Weltzien E, Rattunde FFW, Viana JH, Clark RT, Falcão A, Gazaffi R, Garcia AAF, Schaffert RE, Kochian LV, Magalhaes JV. 2014. Duplicate and conquer: Multiple homologs of PHOSPHORUS-STARVATION TOLERANCE1 enhance phosphorus acquisition and sorghum performance on low-phosphorus soils. Plant Physiol 166: 159-167.

Schroeder JI, Delhaize E, Frommer WB, Guerinot ML, Harrison MJ, Herrera-Estrella L, Horie T, Kochian LV, Munns R, Nishizawa NK, Tsay Y-F, Sanders D. 2013. Using membrane transporters to improve crops for sustainable food production. Nature 497: 60 - 66.

Maron LG, Guimarães CT, Kirst M, Albert PS, Birchler JA, Bradbury P, Buckler ES, Coluccio AE, Danilova TV, Kudrna D, Magalhaes JV, Piñeros MA, Schatz MC, Wing R, Kochian LV. 2013. Aluminum tolerance is associated with higher MATE1 gene copy-number in maize. Proc Natl Acad Sci USA 110: 5241-5246.

• Fellow, Royal Society of Canada, 2025
• Canada Excellence Research Chair in Global Food Security, 2016-2025
• Arrell Global Food Innovation Award, recognizing global excellence in food innovation and community impact ($100,000 prize), 2019
• USDA-Agricultural Research Service (ARS) Scientist Hall of Fame, 2016
• Fellow of the American Association for the Advancement of Science (AAAS), 2008
• Fellow of the American Society of Plant Physiology, 2007
• USDA-Agricultural Research Service (ARS) National Scientist of the Year, 1999

• PLSC 898 Plant roots: The Hidden Half