Profile
Rajan Sekhon
Genetics and Biochemistry
Associate Professor
AG Biotech/Biosystems Research Complex / BRC 314 [Office]
AG Biotech/Biosystems Research Complex / BRC 319A [Lab]
AG Biotech/Biosystems Research Complex / BRC 319C [Office]
AG Biotech/Biosystems Research Complex / BRC 321 [Lab]
AG Biotech/Biosystems Research Complex / BRC 342 [Lab]
Educational Background
Ph.D., Plant Biology, Pennsylvania State University, University Park, Pennsylvania, 2007
M.S., Plant Breeding, Punjab Agricultural University, Ludhiana, India, 1994
B.S., Agriculture, Punjab Agricultural University, Ludhiana, India, 1992
Profile/About Me
I am an Associate Professor of Genetics and Biochemistry at Clemson University, and my lab studies how genes, physiology, and the environment interact to shape complex traits in crops. We use field experiments, multi-omics, biomechanics, and AI-driven analytics to understand and improve traits such as leaf senescence, source–sink balance, and stalk lodging resistance in maize and sorghum. By building genome-to-phenome maps and identifying key regulatory networks, I aim to help develop more resilient, higher-yielding crop varieties while training the next generation of interdisciplinary plant scientists.
Research Interests
My research program focuses on the genetic architecture of complex agronomic traits that enhance climate resilience and yield stability in maize and sorghum. These traits are typically controlled by many small-effect loci and are dynamically shaped by internal and external signals, producing temporal and spatial phenotypes that traditional genetic and phenotyping approaches often miss. To address this, my group develops and refines field-to-lab phenotyping strategies that capture dynamic physiology and biomechanics over time, and we apply systems-scale integration of multi-omics data—transcriptomics (including tissue- and cell-specific), metabolomics, epigenomics, and high-density genomics—combined with advanced statistical genomics and AI/ML approaches to identify causal genes, regulatory networks, and deployable alleles.
One major focus of my lab is to elucidate how source–sink interactions regulate leaf senescence in maize. Senescence is a programmed developmental transition that begins with the loss of leaf function and culminates in whole-plant death, whereas delayed senescence (staygreen/stay-green) can sustain photosynthesis, improve nutrient remobilization, and confer resilience to drought, heat, and other stresses. Through time-resolved, multi-environment experiments and integrative systems genetics, we have uncovered complex regulatory modules, candidate genes, and pathways that underlie staygreen phenotypes and nutrient recycling during senescence.
A second core focus is understanding the biological, chemical, and biomechanical determinants of stalk (stem) strength and lodging resistance in maize. Stalk lodging can cause up to 25% yield loss globally and is expected to worsen with increased planting density, high nitrogen inputs, and more frequent extreme weather events. In a highly collaborative effort involving biomechanics, mathematics, materials science, and systems genetics, we are constructing genome-to-phenome maps for stalk lodging resistance that link stalk structure and mechanical properties to underlying genetic variation. These efforts provide mechanistic insight and practical targets for breeding maize ideotypes with improved standability and resilience under future climates.
Courses Taught
1. Epigenetics (GEN4600, undergraduate, 3 credits). In this course the students acquire detailed understating of various epigenetic mechanisms operating in tandem to impose epigenetic gene regulation in eukaryotes, learn the molecular basis of key epigenetic phenomena observed in animals and plants, learn the role of epigenetic mechanisms in human and animal disease, and gain valuable presentation and discussion skills.
2. Molecular and General Genetics (GEN3020, undergraduate,3 credits) - This is the flagship course for the students majoring in genetics and biochemistry in the department.
3. Senior Seminar (GEN4930, 2 credits) - In this course meant for the senior undergrads, the students learn to read and critically evaluate scientific literature, prepare and present a scientific presentation, engage in scientific discussion and critique, and learn scientific writing.
Selected Publications
* - Corresponding author
See full list here: https://scholar.google.com/citations?user=dZCATBkAAAAJ&hl=en
1. Brar MS, Kumar R, Kunduru B, McMahan CS, Tharayil-Santhakumar N, Sekhon RS* (2025). Temporal analysis of physiological phenotypes identifies novel metabolic and genetic underpinnings of senescence in maize. The Plant Cell. https://doi.org/10.1093/plcell/koaf176.
2. Kunduru B, Bokros NT, Tabaracci K, Kumar R, Brar MS, Stubbs CJ, Oduntan Y, DeKold J, Bishop R, Woomer J, Verges V, McDonald AG, McMahan CS, DeBolt S, Robertson DJ, Sekhon RS* (2025). High density phenotypic map of natural variation for intermediate phenotypes associated with stalk lodging resistance in maize. Scientific Data. https://doi.org/10.1038/s41597-025-06008-2.
3. Brar MS, De Souza A, Ghai A, Ferreira JF, Sandhu D, Sekhon RS* (2025). Untargeted metabolomics reveals key metabolites and genes underlying salinity tolerance mechanisms in maize. The Plant Genome. https://doi.org/10.1002/tpg2.70102.
4. e Silva CM, Kunduru B, Bokros N, Tabaracci K, Oduntan Y, Brar MS, Kumar R, Stubbs CJ, Nardino M, McMahan CS, DeBolt S, Robertson DJ, Sekhon RS*, Morota G* (2025). Genomic prediction of stalk lodging resistance and the associated intermediate phenotypes in maize using whole-genome resequence and multi-environmental data. The Plant Genome. https://doi.org/10.1002/tpg2.70125.
5. Kunduru B, Kumar R, Brar MS, Stubbs CJ, Tabaracci K, Bokros N, Bridges WC, Cook DD, DeBolt S, McMahan CS, Robertson DJ, Sekhon RS* (2023). Unveiling the phenotypic landscape of stalk lodging resistance in diverse maize hybrids. Field Crops Research. https://doi.org/10.1016/j.fcr.2023.109168.
6. Kumar R, Brar MS, Kunduru B, Ackerman, AJ, Yang Y, Luo F, Saski CA, Bridges WC, de Leon N, McMahan CS, Kaeppler SM, Sekhon RS* (2023). Genetic architecture of source-sink regulated senescence in maize. Plant Physiology. https://doi.org/10.1093/plphys/kiad460.
7. Kumar R, Gyawali A, Morrison GD, Saski CA, Robertson DJ, Cook DD, Tharayil N, Schaefer RJ, Beissinger TM, Sekhon RS* (2021). Genetic architecture of maize rind strength revealed by the analysis of divergently selected populations. Plant & Cell Physiology. https://doi.org/10.1093/pcp/pcab059.
8. Sekhon RS*, Joyner CS, Ackerman AJ, McMahan CS, Cook DD, Robertson DJ (2020). Stalk bending strength is strongly associated with maize stalk lodging incidence across multiple environments. Field Crops Research. https://doi.org/10.1016/j.fcr.2020.107737.
9. Sekhon RS*, Saski C, Kumar R, Flinn B, Luo F, Beissinger TM, Ackerman AJ, Breitzman MW, Bridges WC, de Leon N, Kaeppler SM (2019). Integrated genome-scale analysis identifies novel genes and networks underlying senescence in maize. The Plant Cell. https://doi.org/10.1105/tpc.18.00930. (selected as the issue highlight and accompanied a commentary by the Plant Cell editorial staff).
10. Kumar R, Bishop E, Bridges, WC, Tharayil, N, Sekhon, RS* (2019). Sugar partitioning and source-sink interaction are key determinants of leaf senescence in maize. Plant, Cell & Environment. https://doi.org/10.1111/pce.13599.
Memberships
Crop Science Society of America
American Society of Plant Biologists
American Association for the Advancement of Science
Outreach
• Associate editor of Crop Science
• Served on four USDA-NIFA grant review panels
• Served on NSF-GRPF panels and several NSF ad-hoc review assignments
• Reviewed over 60 manuscripts mostly for society journals including ASPB (Plant Cell, Plant Physiology), CSSA (Crop Science, Plant Genome), and GSA (Genetics, G3)
• Trained over 60 undergrad students to nurture their interest in STEM fields
• Member of the departmental executive committee for three years
• Research adviser to VPR, Clemson University
