Research > System Plant Physiology


The Systems Plant Physiology program is developing crops with enhanced nutritional qualities and identifying new methods to improve environmental attributes. This program focuses on plant biology and its integrations with micro and macro environments, utilizing physiological, molecular, or metabolic traits to understand associated biological processes. Our broad goal is developing crop varieties with enhanced crop productivity, nutritional qualities and tolerance to abiotic stresses for greater adaptability. The critical areas of research we focus on are:

      • Nitrogen use efficiency, nitrogen sensing, transport and assimilation
  • Molecular and genetic aspects of plant metabolism

Advancing the Sustainability Practices of Organic Vegetable Production

Poor productivity of organic crops is in part attributed to the lack of nutrient management strategy, a lack of genetics designed for optimal utilization of resources, and ineffective methods to enhance nutrient uptake.  To improve yield stability, we are investigating biochemical aspects of nutrient uptake, their interactions with soil microbiomes and evaluation of nutraceutical potential of organic vegetables for human consumption and processing.

Enhancing the Nutraceutical Potential of Plants

Non-protein amino acid “citrulline” is universal in animals, plants, bacteria, and fungi. It has extensive clinical and therapeutic implications for human and animal health. We focus on many intriguing aspects of its metabolism; such as synthesis, regulation, long-distance transport, its role as an N-carrier, and as an osmolyte using molecular and metabolic cues. We are using Arabidopsis and watermelon systems to characterize citrulline metabolism.

Photo of Spinach

Enhancing the nutrient use efficiency of plants

The leaching of excessive nitrogenous fertilizers applied to commercial crops leads to environmental problems. To understand the dynamics of nutrient use efficiency we are using cutting-edge tools in genomics to identify spinach genotypes efficient in nutrient uptake, assimilation, utilization. We are using natural variation as a tool to identify the genetic variation for the anti-microbial compounds in spinach and variation in the indigenous microbiota for it’s effectiveness against food-borne pathogens.

Dr. Vijay Joshi

Associate Professor of Systems Plant Physiology


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Team Members

Dhivya Thenappan – Postdoctoral Research Associate

Dalton Thompson – Research Technician I



Past Members

Moazzameh Ramezani – Postdoctoral Research Associate

Amit Kumar Mishra  – Postdoctoral Research Associate

Photo of Amit Mishra

Qiushuo Song, – MS Student  (Kudos to Ms. Qiushuo Song on her graduation)

Matté Moreno – Non-Affiliated Student Assistant


Publications(* corresponding author)

  • Pandey J, Thompson D, Joshi M, Scheuring D, Koym J, Joshi V*, Vales M* (2023) Genetic architecture of tuber-bound free amino acids in potato and effect of growing environment on the amino acid content. Scientific Reports 13:13940. [Impact Factor: 4.6]
  • Tolley, JP, Gorman Z, Lei J, Yeo I, Nagashima Y, Joshi V, Zhu-Salzman K, Kolomiets MV, Koiwa H*(2022) Overexpression of maize ZmLOX6 in Arabidopsis thaliana enhances damage-induced pentyl leaf volatile (C5) emissions that affect plant growth and interaction with aphids, Journal of Experimental Botany.; erac522, [Impact Factor: 7.38]
  • Joshi, V*., Shi, A., Mishra, A.K. et al. Genetic dissection of nitrogen induced changes in the shoot and root biomass of spinach (2022). Sci Rep 12, 13751. [Impact Factor: 4.996]
  • Ainong Shi, Gehendra Bhattarai, Haizheng Xiong, Carlos A Avila, Chunda Feng, Bo Liu, Vijay Joshi, Larry Stein, Beiquan Mou, Lindsey J du Toit, James C Correll (2022) Genome-wide association study and genomic prediction of white rust resistance in USDA GRIN spinach germplasm, Horticulture Research, Volume 9, 2022, uhac069, [Impact Factor: 7.291]
  • Islam ASMF, Sanders D, Mishra AK, Joshi V* (2021) Genetic diversity and population structure analysis of the USDA olive germplasm using Genotyping-By-Sequencing (GBS). Genes 2021, 12, 2007. [Impact Factor: 4.096]
  • Joshi V*, Nimmakayala P, Song Q, Abburi V, Natarajan P, Levi A, Crosby K, Reddy UK* (2021) Genome-wide association study and population structure analysis of seed-bound amino acids and total protein in watermelon. PeerJ. 9: e12343.[Impact Factor: 2.98]
  • Alves FM, Joshi M, Djidonou D, Joshi V, Gomes CN, Leskovar D* (2021) Physiological and Biochemical Responses of Tomato Plants Grafted onto Solanum pennellii and Solanum peruvianum under Water-deficit Conditions. Plants, 10, 2236. [Impact Factor: 3.94]
  • Canarejo-Antamba M, Banuelos-Tavares O, Reyes-Trejo B, Espinosa-Solares T, Joshi V, Guerra- Ramirez D (2021) Comparison of nutritional and nutraceutical properties of Chenopodium quinoa cultivated in Mexico and Ecuador. Chilean Journal of Agricultural Research. 81, 04. https://doi:10.4067/S0718-58392021000400507 [Impact Factor: 1.67]
  • Joshi V*, Penalosa A, Joshi M, Rodriguez S (2021) Regulation of oxalate metabolism in spinach revealed by RNA-Seq-based transcriptomic analysis. International Journal of Molecular Sciences. 22, 5294. [Impact Factor: 5.92]
  • Awika HO, Mishra A, Gill H, DiPiazza J, Avila C, Joshi V* (2021) Selection of nitrogen responsive root architectural traits in spinach using machine learning and genetic correlations. Scientific Reports. 11, 9536. [Impact Factor: 4.38]
  • Song Q, Joshi M, Wang S, Johnson C, Joshi V* (2020) Comparative analysis of root transcriptome profiles of sesame (Sesamum indicum) in response to osmotic stress. Journal of Plant Growth Regulation. [Impact Factor: 4.17]
  • Song Q, Joshi M, Joshi V* (2020) Transcriptomic analysis of short-term salt stress response in watermelon seedlings. International Journal of Molecular Sciences 21, 6036. [Impact Factor: 5.92]
  • Song Q, Joshi M, DiPiazza J, Joshi V* (2020) Functional relevance of citrulline in the vegetative tissues of watermelon during abiotic stresses. Frontiers in Plant Science. [Impact Factor: 5.75]
  • Joshi V*, Joshi M, Penalosa A (2020) Comparative analysis of tissue-specific transcriptomic responses to nitrogen stress in spinach (Spinacia oleracea). PLOS ONE. 15, e0232011 [Impact Factor: 3.24]
  • Shi T, Joshi V, Joshi M, Vitha S, Gibbs H, Wang K, Okumoto S (2019) Broad-spectrum amino acid transporters ClAAP3 and ClAAP6 expressed in watermelon fruits. International Journal of Molecular Sciences. 20(23) pii: E5855 [Impact Factor: 5.92]
  • Awika HO, Cochran K, Joshi V, Bedre R, Mandadi KK, Avila CA (2019) Single‐marker and haplotype‐based association analysis of anthracnose (Colletotrichum dematium) resistance in spinach (Spinacia oleracea). Plant Breeding. 139 (2): 402–18 [Impact Factor: 1.83]
  • Joshi V, Shinde S, Nimmakayala P, Abburi VL, Alaparthi SB, Lopez-Ortiz C, Levi A, Panicker G, Reddy UK (2019) Haplotype networking of GWAS hits for citrulline variation associated with the domestication of watermelon. International Journal of Molecular Sciences. 20, 5392 [Impact Factor: 5.92]
  • Joshi V*, Joshi M, Silwal D, Noonan K, Rodriguez S, Penalosa A (2019) Systematized biosynthesis, and catabolism regulates citrulline accumulation in watermelon.  Phytochemistry.162: 129-140. [Impact Factor: 4.07]
  • Joshi V*, Fernie A (2017) Citrulline Metabolism in Plants. Amino Acids 49(9): 1543-1559 [Impact Factor: 3.52]
  • Huang T, Joshi V, Jander G (2014) The catabolic enzyme MGL methionine gamma-lyase limits methionine accumulation in potato tubers. Plant Biotechnology Journal. 12(7): 883-893 [Impact Factor: 9.80]
  • Adio AM, Casteel CL, De Vos Martin, Kim J, Joshi V, Li B, Juéry C, Daron J, Kliebenstein DJ, Jander G. (2011) Biosynthesis and defensive function of Nδ-acetylornithine, a jasmonate-induced Arabidopsis metabolite. Plant Cell. 23(9):3303 [Impact Factor: 11.28]
  • Jander G, Joshi V (2010) Deciphering the biosynthesis of aspartate-derived amino acids in plants: Metabolic networks and molecular mechanisms. Molecular Plant 3:54-65 [Impact Factor: 13.16]
  • Joshi V*, Joung J, Fei Z, Jander G (2009) Transcriptional regulation and synthesis of branched chain amino acids as osmolytes in plants under drought and cold stress. Amino Acids. 39(4):933-47 [Impact Factor: 3.52].
  • Joshi V, Jander G (2009) Arabidopsis thaliana methionine gamma-lyase is regulated according to isoleucine biosynthesis needs but plays a subordinate role to threonine deaminase. Plant Physiology. 151:367-378. [Impact Factor: 8.34].
  • Jander G, Joshi V (2009) Aspartate-derived amino acid biosynthesis in Arabidopsis thalianaThe Arabidopsis Book, Rockville, MD: American Society of Plant Biologists 7, e0121 Open Access.
  • Joshi V, Laubengayer K, Schauer N, Fernie A, Jander G (2006) Two Arabidopsis threonine aldolases are non-redundant and compete with threonine deaminase for a common substrate pool. Plant Cell. 18: 3564-3575. [Impact Factor: 11.28]
  • Jander G, Norris SR, Joshi V, Fraga M, Rugg A, Yu S, Li L, Last R (2004) Application of a high throughput HPLC-MS/MS assay to Arabidopsis mutant screening; evidence that threonine aldolase plays a role in seed nutritional quality. Plant Journal. 39 (3) 465-475. [Impact Factor: 6.42].
  • Telang M, Srinivasan A, Patankar A, Harsulkar A, Joshi V, Damle A, Deshpande V, Sainani M, Ranjekar P, Gupta G, Birah A, Rani S, Kachole M, Giri A, Gupta V (2003) Bitter gourd proteinase inhibitors: potential growth inhibitors of Helicoverpa armigera and Spodoptera lituraPhytochemistry. 63(6) 643-652 [Impact Factor: 4.07].
  • Joshi V*, Ugale SD (2002) Involvement of higher order gene interactions addressing complex polygenetically controlled the inheritance of downy mildew (Sclerospora graminicola S), resistance in pearl millet (Pennisetum glaucum). Euphytica. 127(2): 149-161 [Impact Factor: 1.90]


  • Grant #1