Sombir Rao

Undergraduate & Graduate Faculty

Assistant Professor of Crop Resilience to Environmental Stresses

Faculty
Sombir Rao Headshot
Contact
Email
Email
See my Google Scholar Website
Location
Paige Laboratory Room 418

Research Area: Crop Resilience to Environmental Stresses

Field of Study: Reproductive resilience, yield stability, and crop adaptation to environmental stress

The Crop Adaptomics Lab studies how crops maintain reproduction and yield as environmental conditions change. Tomato is our primary crop system, with a particular focus on the challenges of tomato production in New England, where a short growing season and abrupt temperature fluctuations can disrupt flowering, pollen function, fruit set, and yield. Our research integrates genetics, genomics, crop physiology, reproductive biology, and metabolism to understand and improve crop resilience to heat, drought, and combined stresses.

Our research spans three connected areas:

1. APOCROP: Decoding Metabolite Signals for Agronomic Gains

We investigate apocarotenoids as metabolic signals linking environmental stress with reproductive performance. We use β-cyclocitral and related metabolites to understand pollen function and develop rapid, scalable solutions for stress protection, including metabolite-based biostimulants that can be applied when environmental conditions change abruptly. This work connects metabolite signaling with practical approaches for protecting reproduction, fruit set, and yield.

2. The Reproductive Adaptome: From Gene Discovery to Yield Stability

We uncover the genes and regulatory pathways that allow flowers, pollen, ovules, and fruit set to remain functional under stress. By integrating natural genetic diversity, physiological phenotyping, transcriptomics, metabolomics, and functional genomics, we identify mechanisms that sustain reproduction and yield under heat, drought, and combined stresses. Gene editing and prime editing are used to test candidate regulators and establish their roles in reproductive resilience.

3. Predictive and Programmable Agriculture

We study fruit set as a dynamic systems-level process shaped by interactions between plant physiology and the environment. We integrate photosynthesis, water relations, carbon allocation, hormones, metabolites, environmental conditions, fruit set, and yield with quantitative modeling, artificial intelligence, and machine learning to understand and predict crop performance across environments. This work aims to connect complex physiological responses with quantitative approaches for improving crop productivity and yield stability.

By combining natural genetic diversity, multi-omics, physiological phenotyping, functional genomics, gene discovery, gene editing, and prime editing, our research connects molecular mechanisms to reproductive performance and yield and translates these discoveries into rapid, scalable, and practical strategies for more resilient crop production.

Web: Google Scholar | ORCID: 0000-0002-5955-3940 | ResearchGate | LinkedIn
Ph.D.: National Institute of Plant Genome Research (NIPGR), New Delhi, India
Postdoctoral Research: Cornell University, Ithaca, NY, USA

Publications

  1. Hazra A, Rao S, Zhou X, Christel MJ, Wrightstone E, Yang Y, Fish T, Thannhauser TW, Liu J, Mazourek M, Li L. (2025). Phytoene synthase modulates seed longevity via the action of β-carotene derived metabolites. Plant Physiology, 199(4), kiaf598.

  2. Gupta A*, Rao S*, Jha S, Ghosh D, Virmani R, Shrivastava M, Kumar A, Sahoo L, Das JR, Crespi M, Mathur S. (2025). The MIR169 module enhances biomass and yield via ARGOS in Arabidopsis and tomato. The Plant Journal, 124, e70538. Equal contribution as first author.

  3. Wrightstone E, Xu L, Rao S, Hazra A, Li L. (2025). ORANGE family proteins: multifunctional chaperones shaping plant carotenoid level, plastid development, stress tolerance, and more. Molecular Horticulture, 5, 43.

  4. Sun T, Hazra A, Lui A, Zeng S, Wang X, Rao S, Owens LA, Fei Z, Zhao Y, Mazourek M, Giovannoni JG, Li L. (2025). GLKs directly regulate carotenoid biosynthesis via interacting with GBFs in plants. New Phytologist, 246, 645–665.

  5. Rao S, O’Hanna FJ, Saar L, Hazra A, Hullihen O, Giovannoni JJ, Li L. (2024). β-Carotene and its derivatives regulate pollen fertility in tomato. Plant Physiology, 196(3), 1733–1736.

  6. Rao S, Cao H, O’Hanna FJ, Zhou X, Lui A, Wrightstone E, Fish T, Yang Y, Thannhauser T, Cheng L, Dudareva N, Li L. (2024). Nudix hydrolase 23 post-translationally regulates carotenoid biosynthesis in plants. The Plant Cell, 36(5), 1868–1891.

  7. Gupta A, Ghosh D, Rao S, Mathur S. (2024). Deciphering the role of MIR169d module under individual as well as combined drought and heat stress in Arabidopsis. Plant Physiology Reports, 1–12.

  8. Verma A, Tiwari H, Singh S, Gupta P, Rai N, Kumar Singh S, Singh BP, Rao S, Gautam V. (2023). Epigenetic manipulation for secondary metabolite activation in endophytic fungi: current progress and future directions. Mycology, 1–17.
    Corresponding author.

  9. Sun T, Wang P, Rao S, Zhou X, Wrightstone E, Lu S, Yuan H, Yang Y, Fish T, Thannhauser T, Liu J, Mazourek M, Grimm B, Li L. (2023). Co-chaperoning of chlorophyll and carotenoid biosynthesis by ORANGE family proteins in plants. Molecular Plant, 16, 1049–1066.

  10. de Oliveira NT, Namorato FA, Rao S, de Souza Cardoso AA, de Rezende PM, Guilherme LRG, Liu J, Li L. (2022). Iron counteracts zinc-induced toxicity in soybeans. Plant Physiology and Biochemistry, 194, 335–344.

  11. Rao S, Gupta A, Bansal C, Sorin C, Crespi M, Mathur S. (2022). A conserved HSF:miR169 loop involved in tomato and Arabidopsis heat stress tolerance. The Plant Journal, 112(1), 7–26.

  12. Rao S, Das JR, Balyan S, Verma R, Mathur S. (2022). Cultivar-biased regulation of HSFA7 and HSFB4a govern high-temperature tolerance in tomato. Planta, 255(2).

  13. Zhou X*, Rao S*, Wrightstone E, Sun T, Lui A, Welsch R, Li L. (2022). Phytoene Synthase: The Key Rate-Limiting Enzyme of Carotenoid Biosynthesis in Plants. Frontiers in Plant Science, 13, 977.
    Equal contribution as first author.

  14. Sun T, Rao S, Zhou X, Li L. (2022). Protein–protein interaction techniques to investigate post-translational regulation of carotenogenesis. In Carotenoids: Carotenoid and Apocarotenoid Biosynthesis, Metabolic Engineering and Synthetic Biology, p. 301.

  15. Sun T, Rao S, Zhou X, Li L. (2022). Plant carotenoids: recent advances and future perspectives. Molecular Horticulture, 2(1), 1–21.

  16. Rao S, Balyan S, Jha S, Bansal C, Das RJ, Gupta A, Mathur S. (2022). An Integrated Bioinformatics and Functional Approach for miRNA Validation. In Plant Gene Silencing, pp. 253–281. Humana, New York, NY.

  17. Rao S, Das JR, Mathur S. (2021). Exploring the master regulator heat stress transcription factor HSFA1a-mediated transcriptional cascade of HSFs in the heat stress response of tomato. Journal of Plant Biochemistry and Biotechnology, 30(4), 878–888.

  18. Rao S, Balyan S, Jha S, Bansal C, Das RJ, Mathur S. (2020). Orchestration of microRNAs and transcription factors in the regulation of plant abiotic stress response. In Plant Stress Biology, pp. 251–277. Springer, Singapore.

  19. Balyan S*, Rao S*, Jha S*, Bansal C, Das RJ, Mathur S. (2020). Characterization of novel regulators for heat stress tolerance in tomato from Indian sub-continent. Plant Biotechnology Journal, 18(10), 2118–2132.
    Equal contribution as first author.

  20. Rao S, Balyan S, Jha S, Mathur S. (2020). Novel insights into expansion and functional diversification of MIR169 family in tomato. Planta, 251, 55.

  21. Paul A, Rao S, Mathur S. (2016). The α-crystallin domain containing genes: Identification, phylogeny and expression profiling in abiotic stress, phytohormone response and development in tomato (Solanum lycopersicum). Frontiers in Plant Science, 7, 246.

Honors & Awards

  • Chair, Gordon Research Seminar on Carotenoids & Apocarotenoids, 2027.
  • Sahyadri Outstanding Plant Postdoc Award, 2024, Plant Postdocs.
  • DBT-RA Fellowship, 2021, Department of Biotechnology, Government of India.
  • Best Research Paper Award, 2020, National Institute of Plant Genome Research, India.
  • DBT-Senior Research Fellowship, 2016–2018, Department of Biotechnology, Government of India.
  • DBT-Junior Research Fellowship, 2013–2015, Department of Biotechnology, Government of India.

Service & Outreach

  1. Book Editing & Guest Editorships
  • Editor, Decoding and Engineering Plant Genomes for Functional Discovery and Stress Resilience, Taylor & Francis, expected 2026.
  • Guest Editor, Journal of Visualized Experiments (JoVE), Special Issue: “Methods Collections: Current Methods to Study the Regulation of Plant Carotenogenesis.”
  • Guest Editor, Plants, Special Issue: “Carotenoids in Crop Plants: From Metabolic Regulation to Agronomic Gain,” Plant Physiology and Metabolism Section.
  1. Editorial Boards & Peer Review
  • Review Editor,Frontiers in Plant Science, 2021–present.
  • Ad hoc reviewer for New Phytologist, Plant Physiology, The Plant Journal, Plant Communications, Horticulture Research, BMC Genomics, PLOS ONE, Plant Science, Plant Physiology and Biochemistry, Journal of Plant Growth Regulation, and Journal of Biotechnology.
  1. Conference Leadership 

News and Highlights 

  1. Scientists Uncover Novel Heat Stress Controlling Pathways In Tomato https://scisoup.org/article/2020/scientists-uncover-novel-heat-stress-controlling-pathways-in-tomato.html 
  2. https://plantae.org/the_plant_cell_january24_first_authors/ 
  3. A new player in carotenoid production https://plantae.org/a-new-player-in-carotenoid-production/ 
  4. Promoting carotenoid biosynthesis in the NUD(X23) https://pmc.ncbi.nlm.nih.gov/articles/PMC11062433/
  5. Feeling the heat: discovery of a feedback loop regulating thermotolerance in tomato and Arabidopsis https://onlinelibrary.wiley.com/doi/10.1111/tpj.15978