Deciphering plant-fungal interactions through functional genomics and molecular genetics approaches

Grain legumes represent major food crops cultivated and consumed in India and other developing countries owing to their high nutritional value and important role in maintaining the ecosystem. Powdery mildew is one of the most devastating fungal diseases limiting legume productivity in India. These obligate biotrophs alter plant cellular architecture and metabolism to acquire nutrients via specialized feeding structures (haustoria) while limiting plant defense responses. Chemical treatments used to control the disease are neither economical nor environmentally friendly. Furthermore, despite the availability of a few powdery mildew resistant legume varieties, identity of the genes conferring resistance and knowledge of the underlying molecular events is limited.

One of our primary goals is to identify novel host processes and the underlying genes that impact powdery mildew growth without an associated yield penalty. For this, we employ functional genomics, metabolomics, cell biology and reverse genetics tools to study Medicago truncatula/pea-Erysiphe pisi interaction as a model to identify host resistance and susceptibility factors that impact powdery mildew disease progression at different infection stages. We envision that factors limiting pathogen growth at different developmental stages would be more difficult to overcome than resistance based on a single mechanism or mechanisms governed by a single gene. Our long-term goal is to utilize these genes as molecular targets to engineer durable resistance in legumes of agronomic import.

Another major area of focus is to elucidate how these obligate biotrophic fungi utilize ‘effector’ proteins to suppress host immunity and modulate host metabolism to divert nutrients from the plant to fuel growth and reproduction. For this, we utilize genomics, transcriptomics, and RNAi-based reverse genetics tools to decipher the role of candidate fungal effectors in pea powdery mildew pathogenesis. Functionally relevant pathogen effectors are then targeted for silencing using transgenic methods as well as non-transgenic, nanocarrier-based smart delivery systems.

• Dr. Ankita Alexander
  MK Bhan Fellow
  ankita.alexander@rcb.res.in
• Dr. Radheshyam Yadav
  SERB-NPDF
  radheshyam.yadav@rcb.res.in
• Dr. Shaily Tyagi
  DBT-RA
  shaily.tyagi@rcb.res.in
• Dr. Chetan Chauhan
  Research Associate
  chetan.chauhan@rcb.res.in
• Debashish Sahu
  Senior Research Fellow
  debashish.sahu@rcb.res.in
• Poonam Ray
  Junior Research Fellow
  poonam.ray@rcb.res.in
• Gulshan Thakur
  Junior Research Fellow
  gulshan.thakur@rcb.res.in
• Rabishankar Ojha
  Junior Research Fellow
  rabishankar.ojha@rcb.res.in
• Smritilekha Mukherjee
  Junior Research Fellow
  smritilekha.mukherjee@rcb.res.in
• Sumit Sagar
  Junior Research Fellow
  sumit.sagar@rcb.res.in
• AnjiNayak Eslavath
  ntegrated MSc-PhD student
  eslavath.anja@rcb.res.in

Alumni

• Rashi Gupta (Young Investigator 2015-2017) – Currently Assistant Professor at School of Allied Health Sciences and Management, Delhi Pharmaceutical Sciences and Research University, Pushp Vihar, New Delhi
• Gunjan Sharma (SERB-NPDF 2016-2018) – Currently Assistant Professor, Gujarat Biotechnology University
• Raghavendra Aminedi (Young Investigator 2017-2020) – Currently Project Scientist III at ICAR-National Bureau of Plant Genetics Resources, New Delhi
• Varsha Gupta (Junior Research Fellow 2016-2018) – Currently Senior Officer - Microbiology (R&D) at Reckitt, Gurugram, Haryana
• Divya Saxena (Junior Research Fellow 2017-2018) – Currently Computer Vision Lead at Avidtechvision, Ahmedabad, Gujarat
• Shubham Dubey (Junior Research Fellow 2019) – Currently PhD candidate at Purdue University, Indiana, USA
• Diksha Mehta (Junior Research Fellow 2019) – Currently PhD candidate at IITB-Monash Research Academy, Mumbai, Maharashtra
• Gagan Gupta (M.Sc. student Oct 2020-Sep 2021) – IRTG 2172 PRoTECT PhD scholar at Georg-August University, Goettingen, Germany & University of British Columbia Vancouver, Canada
• Megha Gupta (PhD student Aug 2014-Jan 2022) – Postdoctoral Fellow, University of Maryland College Park, USA
• Arunima Gupta (PhD student Aug 2015-Sep 2022) – Scientist R&D, Thermo Fisher Scientific
• Ankita (M.Sc. student August 2022-2023)
• Akriti Sharma (PhD student Aug 2016-May 2023)
• Aryan (M.Sc. student August 2023-2024)
• Sakshi Sharma - Currently PhD candidate at Amity University, Noida

1. Ray P, Chandran D (2024) Spray inoculation and image analysis-based quantification of powdery mildew disease severity on pea leaves MethodsX. 13:102980.
2. Jangid VK, Muthappa S-K, Chandran D, Sinharoy S (2023) Callus induction and efficient in vitro plant regeneration protocol for Chickpea. Plant Cell, Tissue and Organ Culture (PCTOC) 156:21 https://doi.org/10.1007/s11240-023-02633-0
3. Ray P, Sahu D, Aminedi R* and Chandran D* (2022) Concepts and considerations for enhancing RNAi efficiency in phytopathogenic fungi for RNAi-based crop protection using nanocarrier-mediated dsRNA delivery systems. Front. Fungal Bio. 3:977502. doi:10.3389/ffunb.2022.977502
4. Sharma, A., Chandran, D. Host nuclear repositioning and actin polarization towards the site of penetration precedes fungal ingress during compatible pea-powdery mildew interactions. Planta 256, 45 (2022). https://doi.org/10.1007/s00425-022-03959-3
5. Garg T, Singh Z, Chennakesavulu K, Mushahary KKK, Dwivedi AK, Varapparambathu V, Singh H, Singh RS, Sircar D, Chandran D, Prasad K, Jain M, Yadav SR (2022). Species-specific function of conserved regulators in orchestrating rice root architecture. Development. dev.200381. https://doi.org/10.1242/dev.200381
6. Gupta A#, Awasthi P#, Sharma N, Parveen S, Vats RP, Singh N, Kumar Y, Goel A* & Chandran D* (2022)Medicarpin confers powdery mildew resistance in Medicago truncatula and activates the salicylic acid signalling pathway.Molecular Plant Pathology, 23:966-983. http://dx.doi.org/10.1111/mpp.13202
7. Bisht N#, Gupta A#, Awasthi P, Goel A, Chandran D, Sharma N* & Singh N* (2022) Development of a rapid LC-MS/MS method for the simultaneous quantification of various flavonoids, isoflavonoids, and phytohormones extracted from Medicago truncatula leaves. Journal of Liquid Chromatography & Related Technologies, doi.org/10.1080/10826076.2022.2040028
8. Gupta M., Gupta A., Chandran D. (2022) Medicago truncatula as a Model to Decipher Powdery Mildew Resistance in Legumes. In: Sinharoy S., Kang Y., Benedito V. (eds) The Medicago truncatula Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-90757-0_5
9. Gupta, M, Dubey S, Jain D, and Chandran D (2021) The Medicago truncatula sugar transport protein 13 and Its Lr67res-like variant confer powdery mildew resistance in legumes via defense modulation. Plant and Cell Physiology doi.org/10.1093/pcp/pcab021
10. Garg T, Singh Z, Dwivedi AK, Varapparambathu V, Singh RS, Yadav M, Chandran D, Prasad K, Jain M, Yadav SR (2020). Genome-wide high resolution expression map and functions of key cell fate determinants reveal the dynamics of crown root development in rice. bioRxiv, doi.org/10.1101/2020.06.11.131565
11. Burman N^*, Chandran D, Khurana JP (2020) A rapid and highly efficient method for transient gene expression in rice plants. Front Plant Sci, 11:1564
12. Gupta M, Sharma G, Saxena D, Budhwar R, Vasudevan M, Gupta V, Gupta A, Gupta R, Chandran D. (2019) Dual RNA-Seq analysis of Medicago truncatula and the pea powdery mildew Erysiphe pisi uncovers distinct host transcriptional signatures during incompatible and compatible interactions and pathogen effector candidates. Genomics | 30612-3
13. Sharma G, Aminedi R, Saxena D, Gupta A, Banerjee P, Jain D, Chandran D (2019) Effector mining from the Erysiphe pisi haustorial transcriptome identifies novel candidates involved in pea powdery mildew pathogenesis Mol. Plant Pathol. | doi.org/10.1111/mpp.12862
14. Wildermuth MC, Steinwand MA, McRae AG, Jaenisch J, Chandran D (2017) Adapted Biotroph Manipulation of Plant Cell Ploidy. Annu Rev Phytopathol 55:564
15. Chandran D, Wildermuth MC (2016) Modulation of Host Endocycle During Plant-Biotroph Interactions. Enzymes 40:65
16. Chandran D, Scanlon MJ, Ohtsu K, Timmermans MC, Schnable PS, Wildermuth MC (2015)  Laser Microdissection-Mediated Isolation and In Vitro Transcriptional Amplification of Plant RNA. Curr Protoc Mol Biol. 112:25A.3.1
17. Chandran D (2015)  Co-option of developmentally regulated plant SWEET transporters for pathogen nutrition and abiotic stress tolerance. IUBMB Life 67:461
18. Chandran D, Rickert J, Huang Y, Steinwand M, Marr SK, Wildermuth MC. (2014) Atypical E2F Transcriptional Repressor DEL1 Acts at the Intersection of Plant Growth and Immunity by Controlling the Hormone Salicylic Acid. Cell Host & Microbe 15: 506.
19. Chandran D, Rickert J, Cherk C, Dotson B, Wildermuth MC. (2013) Host cell ploidy underlying the fungal feeding site is a determinant of powdery mildew growth and reproduction. Molecular Plant-Microbe Interactions, 26(5):537.
20. Chandran D, Hather G, Wildermuth MC. (2011) Global expression profiling of RNA from laser microdissected cells at fungal-plant interaction sites. Methods in Molecular Biology: Plant Immunity (ed. J. McDowell) 712:263.
21. Chandran D, Inada N, Wildermuth MC. (2011) Laser microdissection of plant-fungus interaction sites and isolation of RNA for downstream expression profiling. Methods in Molecular Biology: Plant Immunity (ed. J. McDowell) 712:241.
22. Ford KA, Casida JE, Chandran D, Gulevich AG, Okrent RA, Durkin KA, Sarpong R, Bunnelle EM, Wildermuth MC. (2010). Neonicotinoid insecticides induce salicylate-associated plant defense responses. Proceedings of the National Academy of Sciences USA 107:17527.
23. Chandran D, Inada N, Hather G, Kleindt CK, Wildermuth MC. (2010) Laser microdissection of Arabidopsis cells at the powdery mildew infection site reveals site-specific processes and regulators. Proceedings of the National Academy of Sciences USA107:460.
24. Chandran D, Tai YC, Hather G, Dewdney JD, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC. (2009) Temporal global expression data reveals known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis. Plant Physiology 149:1435.
25. Chandran D, Sharopova N, VandenBosch KA, Garvin DF, Samac DA. (2008) Physiological and molecular characterization of aluminum resistance in Medicago truncatula. BMC Plant Biology 8:89.
26. Chandran D, Sharopova N , Ivashuta S, VandenBosch KA, Gantt S, Samac DA. (2008) Transcriptome profiling identified novel genes associated with aluminum toxicity, resistance and tolerance in Medicago truncatula. Planta 228(1):151.
27. Chandran D, Reinders A, Ward JM. (2003) Substrate specificity of the Arabidopsis thaliana sucrose transporter AtSUC2. Journal ofBiological Chemistry. 278(45):44320.