Epigenomic variations across different plant species, and especially in Wild Crops, can teach us a lot about their adaptation to all kinds of stresses induced by climate change, diseases and other hostile environments, which can be replicated for Plant Breeding and Crop Improvement.
Sunil Kumar, our next pathbreaker, PostDoc at The Niederhuth lab, works on multiple projects involving Comparative Epigenomics for applications in crop improvement using experimental and computational approaches.
Sunil talks to Shyam Krishnamurthy from The Interview Portal about changing weather patterns that makes it important to develop crop varieties that show yield stability even when grown in different environments.
For students, there is a huge potential to use the power of Biotechnology and Genomics to decode and replicate positive traits for agriculture.
Sunil, tell us about your background?
I grew up in a small town – Kargal, near Jog Falls in Shivamogga district. I did my primary education in Sharavathi Valley English Primary School – Kargal. For high school, I went to Sathya Sai Loka Seva Vidya Kendra – Alike, near Puttur, Dakshin Kannada. Throughout my primary and high school, I participated in debates and did well in sports too. As is true with most kids, I played cricket with a lot of passion and dreamt of becoming a professional cricketer.
Growing up in a small town, I had many role models to look up to and interact with every day. My primary school teachers, particularly, Gladys, Vijayanand, and my family doctor, Dr Vasundhara Hegde, inspired me with their intelligence and service. Whenever I visited our family doctor, I used to ask a lot of questions about medicines and the process of diagnosis. She always told my parents that I will become a politician or a scientist when I grow up. Both my parents did not have opportunities to study beyond Class X. However, they made sure their children got the best education even if it meant spending beyond their means.
What did you do for graduation/post graduation?
I did my Bachelor of Science (BSc) majoring in Botany, Biotechnology, and Chemistry from Sahyadri Science College, Shivamogga and my Master of Science (MSc) in Biotechnology from Kuvempu University, Shankaraghatta, Shivamogga.
What made you choose such an offbeat, unconventional and unique career?
During one of the biology lectures in pre-university college, I became fascinated with biotechnology research. I told my friends that I will study biotechnology and not engineering, as most students aspire to. My CET (Common Entrance Test for Engineering and Medicine – Karnataka) ranking was not high enough to get me a government subsidized seat in top medical colleges in Karnataka, so I decided to study BSc in Biotechnology. However, it was not until my MSc project at GKVK, University of Agricultural Science Bangalore (UAS-B) that I got my first research experience interacting with PhD students and working scientists. Those interactions strengthened my resolve to be a scientist. At UAS-B, I got to work with top plant scientists. But unfortunately, without a degree in agriculture, I could not enroll for a PhD at UAS-B. Hence i started looking for PhD abroad, and after scoring well in GRE and TOEFL, I secured a PhD position at the University of Nebraska – Lincoln.
How did you plan the steps to get into the career you wanted? Or how did you make a transition to a new career? Tell us about your career path
After my MSc, I applied for a job at the Institute of Bioinformatics and Applied Biotechnology, Bangalore. I cleared the national-level entrance examination and interviews to get the position of research assistant to work with Dr Kshitish Acharya. This job was my first introduction to biological research, and I could not have asked for a better start. Dr Acharya and his team trained me in several aspects of microarray studies (a technique used to profile expression levels of a large number of genes simultaneously). Contrary to the rigid hierarchical structure in the universities, Dr Acharya had created a refreshing work environment in our team. We were encouraged to share our ideas and comments (however naïve) freely with senior colleagues and with Dr Acharya himself. This meant we were on top of our game every day since we were expected to be part of all project discussions from the beginning. This training laid the foundation for my scientific journey. However, my inclination towards wet lab and field experiments led me to seek opportunities for plant-based research labs.
After a short time as a Junior Research Fellow at Sir MVIT College, Bangalore, I got an opportunity to work with Dr Lohithaswa HC at UAS-Bangalore. The lab was ideal for my learning since the projects had the perfect blend of bioinformatics, wet lab, and fieldwork. I was involved in two projects involving comparative genomics in legumes and disease resistance in maize. We were developing genomic resources for economically important legume crops by utilizing sequencing information from model legumes such as Medicago truncatula. The project exploited the conservation of gene coding sequences across legumes to design cross-species polymerase chain reaction (PCR) primers. These primers were designed to amplify intronic regions which are under relaxed selection and contain single nucleotide polymorphisms (SNPs) and insertions or deletions (INDeLs) that can be used as markers for cost-effective genotyping in public plant breeding programs in developing nations.
Exposure to multiple aspects of crop improvement research led me to a PhD position in Dr Sally Mackenzie laboratory at the University of Nebraska, Lincoln. My previous experience with legumes and fieldwork helped me immensely in my first PhD project, where I developed an epigenetic breeding system in soybean for higher yield and yield stability across different environments. While ‘genetics’ deals with inheritance of traits due to differences in the DNA sequence itself, ‘epigenetics’ is the inheritance of traits that is not directly due to differences in the DNA sequence; or a set of processes that effects which genes are switched-on, or “expressed”. One of the well-studied epigenetic mechanism is DNA methylation, which is the addition of a methyl group to the cytosine nucleotide. During my PhD, I was trying to understand the inheritance of artificially induced epigenetic (DNA methylation) changes across generations in soybean population. I also took many more classes than required to graduate. Through these courses, I gained valuable knowledge in molecular biology and plant breeding. Attending these classes helped me develop an interest in computational biology. I applied some aspects of this learning into my final PhD project.
After finishing my Ph.D., I briefly worked with Dr James Schnable, a world expert in comparative genomics. During my short time at the Schnable lab, I was exposed to comparative transcriptomics and phenomics in maize, and the Python programming language. Taking multiple computational biology courses and exposure to comparative genomics in the Schnable lab set me up for my postdoc with Dr Chad Niederhuth at Michigan State University.
How did you get your first break?
I consider every opportunity I got as a break. During my MSc project, I had developed a good relationship with senior researchers in the lab. These researchers were not directly involved with my training. However, I volunteered to help them with their research so that I can learn from them. A couple of years later, one such mentor introduced me to Dr Lohithaswa, who was then looking for a research associate. Dr Lohithaswa decided to give me a chance to work with him just after talking to me for a couple of minutes. That was my first break into plant molecular breeding. Later, I got a PhD position at the University of Nebraska-Lincoln based on my GRE scores and previous research experience. However, I had never imagined getting into such a good lab and PhD program without having published research papers from my MSc. Thus, I consider that to be an even bigger break.
Luck also favored me when I was transitioning from my PhD into a postdoc position. For my postdoc, I wanted to join a lab where I would have opportunities to improve my computational skills and know how to establish a new lab. While I was looking for postdoc positions, I was active on Twitter making connections with plant scientists throughout the USA. Networking on twitter paid off and I contacted Dr Chad Niederhuth via twitter replying to his post advertising a postdoc position in his lab to work on comparative epigenomics. Dr Niederhuth had recently completed his postdoc and was starting his own group at Michigan State University. Since the lab was opening after a few months, I had to find a short-term place to work in the interim. Many suggested I will have to lie about my intentions to join a lab for such a short time. However, I booked an appointment to meet with Dr James Schnable and asked him if I could join his lab for five months to learn comparative genomics. I was fully prepared for a ‘NO’ since my joining his lab to learn would not benefit the lab much, and training someone for such a short time is usually considered unproductive. However, to my surprise, halfway through our meeting, Dr Schnable asked me to go meet the HR, so they can process paperwork for me to join his lab. I was beyond thrilled, and as it turns out, joining the Schnable lab was one of the best decisions of my career.
Each of these events has had a significant impact on my career. I am grateful for all my mentors who took a chance on me and gave me these breaks that have continued to shape my career.
What were the challenges? How did you address them?
Challenge #1: One of the significant challenges, particularly in the earlier stages of our career, is to get guidance and mentoring to help navigate towards our goals. During my MSc, I was aspiring to go abroad for further education, but I didn’t know anyone doing their PhD outside India or even how to apply for one. It was not until I joined UAS-B that I came to know about GRE and TOEFL exams. I also reached out to professors from other institutes in India to learn more about the process of applying abroad. Eventually, their guidance helped me in this regard. Expanding your network is crucial when you are planning to explore opportunities beyond what is considered normal.
Challenge #2: Foreign researchers in the USA usually face a lack of sense of belonging to the community in their labs/departments. During my Ph.D., I volunteered for the departmental graduate student association. I made friends who came from various parts of the world. By the end of my Ph.D., I had made so many good friends and got the opportunity to develop my leadership skills as president of the organization.
Where do you work now? Tell us what you do
As a postdoc in the Niederhuth lab, I’m working on multiple projects involving comparative epigenomics for applications in crop improvement. Niederhuth lab studies the function and evolution of plant genomes using experimental and computational approaches. Unlike epigenetics, epigenomics is the study of the complete set of modifications on the genetic material that form the chromatin without considering its inheritance. One of the advantages of working in this lab is the enormous opportunities to learn new things. I have standardized a range of cutting-edge protocols ranging from high-quality DNA extraction for long-read sequencing, RNA-seq library, methylome library, and Fluorescence-Activated Nuclei Sorting, followed by Assay for Transposase-Accessible Chromatin (FANS-ATAC-seq). My previous lab experiences and regular help/input from Dr Niederhuth were instrumental in getting these protocols working in the lab. For the computational aspects, I am continually learning through weekly meetings with Dr Niederhuth and taking online courses through Coursera.
A typical workday in the lab includes taking care of the plants in the growth chamber and greenhouses, extracting nuclei from plant samples, and preparing libraries for sequencing. A large part of my work also involves looking at sequencing results on the university’s computer cluster. I analyze gene expression, chromatin accessibility, and DNA methylation levels in different samples. Once the data starts making sense, I use visualization tools to plot graphs and figures and write papers for publications in scientific journals.
As a scientist, you do not make discoveries every day. Most of the time, it is trial and error. Many times, experiments fail without any reason. You must be patient, and if you are lucky, you’ll get interpretable results! I find joy in all aspects of research. Forget getting positive or negative outcomes, I get ecstatic when I design a perfect experiment. Observing plants every day and trying to understand biology a bit more each day is what I love about this job.
How does your work benefit society?
Soybean and maize are among the world’s most widely grown crops, and improving their productivity is critical for feeding the growing population. My PhD work provided insights into the potential use of induced epigenetic variation in plant breeding for yield and stability related traits in soybean. Changing weather patterns makes it important to develop crop varieties that show yield stability when grown in different environments.
The USA is one of the largest producers of maize. However, due to its tropical origins, maize cannot withstand low temperatures during its growth cycle. My current project aims to translate low-temperature tolerance from Tripsacum into maize. Tripsacum is a close relative of maize, native to the major corn-growing areas in the USA. Improving low-temperature tolerance in maize will significantly contribute to global food security.
In science, discoveries that are minor shifts from traditional knowledge usually lead to larger ripples, which in turn allows for making giant strides. When you consider the growing population and the strain on natural resources like water and land to produce food, it’s critical to make progress in multiple avenues to reach the target of global food security. Every bit helps!!
Tell us an example of a specific memorable work you did that is very close to you!
Publishing my first first-author paper was an extraordinary moment for me. I began the work in 2012, and within the first six months, I got excellent results building off of work done by previous members of the lab. However, the final paper came out in 2018, and the time in between was filled with highs and lows. More importantly, I realized that the journey teaches you more than the end product. It is a great satisfying feeling to get a task to its completion.
Your advice to students based on your experience?
There is not a blueprint for an excellent career or even life. Some are driven by passion, some by hard work, and others do things just for the heck of it. I do not think any one of these is better than the other. Contrary to what many think, passion is not the only factor. There are numerous other factors, all of which play an equally significant role in determining how your career shapes up.
If you realize today that you are passionate about something and want to pursue it as a career, make sure that most of your actions from this point must lead you towards that goal. Seek guidance, know as much about it as possible, and be ready to put in work and give your best to reach the goal. If you are not sure what you are passionate about, talk to your teachers, professors, parents, friends, and mentors. They may help you discover your strengths and passion. As you can see from my story, networking is critical in our careers. If you see someone who has the position you aspire for, go talk to them, build a relationship. Often, they would like to help you reach your dreams. Once you are on the path towards your dream, make it uniquely yours and own it!!
In my opinion, it’s essential to love or learn to love the path towards your goal. If you want to become a great scientist and make amazing discoveries and win awards, you have to love the whole path that’ll lead to it, from washing glassware in the lab and removing weeds in the research field to performing experiments and collecting data, analyzing, and discovering new things. If you love the process, then every day does not feel like work, it feels like fun.
I plan to get a faculty position and start my independent research group working on utilizing epigenomic variation in wild relatives for stress adaptation in crop improvement. I would like to build a diverse team of researchers exploring a broad range of research spanning basic biology to plant breeding applications.