Sandra Gomez-Gutierrez, MPMI Assistant Feature Editor
Sushil Chhapekar is a plant molecular biologist and currently a Research Scientist at the University of Missouri, Columbia, U.S.A. His work focused on uncovering the genetic and molecular mechanisms that govern plant disease resistance and stress adaptation using advanced genetics and genomics. Inspired by Professor Henry Nguyen’s commitment to bridging biotechnology with practical outcomes for farmers, Sushil focuses on dissecting novel gene(s) and loci, unraveling new resistance mechanisms, and translating fundamental discoveries into sustainable and climate-resilient crop improvement strategies for durable resistance.
His recent MPMI publication, “Identification of Novel Genetic Resources for Broad-Based Soybean Cyst Nematode Resistance Independent of Conventional Loci,” expands the current resistance landscape by identifying previously unexplored genomic sources of SCN resistance. This work provides new avenues for breeding soybean cultivars with more durable, diverse, and long-term resistance to most damaging pathogens of the soybean crop.
What do you think is the most important or exciting finding from your paper?
The most exciting outcome of our study is the discovery of novel genetic resources that provide broad-based resistance to soybean cyst nematode (SCN) completely independent of the conventional resistance loci, such as rhg1 and Rhg4. This work expands the resistance landscape beyond the widely used sources and uncovers new alleles that can be strategically deployed to diversify the genetic base of SCN resistance. New soybean germplasms identified in this study are highly resistant to multiple nematode populations. These findings open the door to understand new genetic mechanism and breeding cultivars with more sustainable and durable resistance while reducing overreliance on a narrow set of major resistant loci.
Was there a piece of data that was particularly challenging to obtain or a part of the project that was particularly difficult?
Yes! One of the most challenging aspects of this project was identifying truly novel SCN-resistant alleles that are completely independent of the well-characterized rhg1 and Rhg4 loci. Among the thousands of USDA soybean accessions we screened, the overwhelming majority of resistant lines trace back directly or indirectly to one of these two loci. Finding the rare new accessions that carry entirely unrelated resistance alleles required extensive genotyping, haplotyping with stringent filtering, and repeated cross-validation to ensure that the signals we detected were not artifacts or masked associations with conventional resistance sources.
In parallel, generating reliable SCN phenotyping data across such a large and genetically diverse panel added an additional layer of complexity, demanding multiple inoculation cycles, strict environmental consistency, and careful integration of phenotypic and genomic evidence. Altogether, the combination of biological, computational, and experimental challenges made the identification of these novel, rhg1/Rhg4-independent alleles one of the most demanding but also most rewarding components of the study.
What research project are you most excited about right now?
I am especially excited about functionally validating the newly identified candidate genes using CRISPR-based editing and developing functional markers to support genomics-assisted breeding. These efforts aim to translate our discoveries into practical tools and deepen our understanding of the molecular mechanisms underlying plant-nematode particularly soybean-nematode interactions.
What advice would you give to starting graduate students?
As researcher I think cultivating curiosity, patience, and resilience is the key for any scientific program and project. Research rarely unfolds as planned, and setbacks are part of the learning process. Build strong foundations in experimental design, quantitative analysis, and scientific communications and pursue questions that genuinely inspire you. These are my personal thoughts, and I believe every graduate student’s voyage is unique.
Who has inspired you scientifically? Why?
I’ve been shaped greatly by the guidance of my academic advisors and postdoctoral mentors, who encouraged curiosity, scientific rigor, and the confidence to pursue challenging biological questions.
I draw particular inspiration from Jayant Naralikar, renowned astrophysicist whose clarity of thought and ability to distill complex ideas remind me to approach biological problems with analytical precision. I’m motivated by his commitment to bringing science to the masses.
I’m also deeply inspired by Barbara McClintock, most distinguished cytogeneticist. Her perseverance and intuition in genetics continue to motivate how I explore natural variation and novel mechanisms in plant biology.
Are/were you involved in other scientific/professional development activities? And how do/did these contribute to your training?
Yes. Participation in scientific meetings including ASPB, Plant and Animal Genome meetings, collaborative genomics projects, outreach initiatives like interdisciplinary plant group seminars at University of Missouri and providing training to graduate and undergraduate students have been instrumental to my development. I’m also editing and reviewing manuscripts and scientific proposals to sharpen my scientific communication skills, broaden my perspective, and strengthen my ability to work across disciplines.
What is the greatest challenge you have encountered in your career? What did you do to overcome this challenge?
One of the greatest challenges has been navigating and interpreting large, complex genomic datasets in a biologically meaningful way. I’m addressing this by investing in computational biology training, seeking guidance from experts and peers, and building collaborative networks. A willingness to continually learn new analytical approaches proved essential.
How can people find you on social media?
I am active on LinkedIn (https://www.linkedin.com/in/sushil-chhapekar-phd-2106767b/)
and X @SushilChhapekar
I welcome connections from colleagues interested in plant microbe interactions, genomics, and molecular plant pathology.
Is there anything else you would like to share in your Spotlight? If so, what is it?
I would emphasize the importance of expanding and diversifying the genetic bases of resistance in crop improvement. Our study shows that valuable resistance sources often lie outside the well-characterized loci. I am deeply grateful to my collaborators and mentors whose support was vital to this work. Additionally, thankful to Sandra Gomez-Gutierrez and Anjali Iyer-Pascuzzi for the interview invitation.
Bonus question: What’s your favorite pathogen or disease?
Soybean cyst nematode! Its complex biology, adaptability, and impact on soybean production make it both challenging and scientifically rewarding to study.
Bonus question: What’s your favorite molecular plant pathology-related article?
One particularly influential article for me is “Copy number variation of Rhg1 explains soybean cyst nematode resistance.” In Nature Genetics.
A transformative study showing that SCN resistance at Rhg1 is conferred by copy number variation spanning multiple genes; redefining how we think about resistance loci and continue to inform current approaches to resistance discovery and deployment.