The Genetic Diversity of crops provides immense potential to understand how certain plant species adapt and survive in challenging as well as changing environments.
Sujan Mamidi, our next pathbreaker, Computational Biologist, analyzes genomic data to identify economically important plant species that can improve crop breeding and other agricultural practices that will eventually help farmers and food producers.
Sujan talks to Shyam Krishnamurthy from The Interview Portal about the amount of data generated that is vast and working on ways to develop new methods for understanding biology through data that can help solve real world problems.
For students, if you want to take the challenge of applying statistical models to next generation DNA sequencing data to uncover a genetic basis for specific traits (Phenotypes) in different species of plants, this is the career for you.
Sujan, tell us about your background?
I am from a middle-class family in Andhra Pradesh. My Dad was a college principal and knew the importance of education. My mother did her BA and MA in open university after her marriage. My parents helped me realize the importance of education at an early age.
What did you do for graduation/post-graduation?
I wanted to be a Doctor, but couldn’t make it, given the limited seats in medicine. I opted for B.Sc (agriculture) as an alternative. During the early stages of graduation, I was determined to achieve something big. I always wanted to make myself stand out from the rest of class by acquiring extra skills. So, I prepared for other competitive exams. My entire 2nd and 3rd years of undergrad were focused on Math, English, General Studies since these subjects form the core of all competitive exams. My goal then was to get selected in civil services. I needed a second optional subject other than agriculture and so I did a single sitting BA and MA in economics. I prepared and succeeded in a few exams (Civil Service Prelims, CAT, CBI officer, SBI officers, GRE, TOEFL and a few others).
On the other hand, I also prepared for Masters in Agricultural Statistics specialization. With limited knowledge in Math and Statistics, I prepared for all math and stat levels equivalent to that of a degree student. This helped me secure a top rank (3rd) at all India level. At the end of undergrad, I had a few options in hand – MS in USA, Bank PO, Civil Services prelims, MSc (Agricultural statistics) admission in a premier institute in India.
Preparing for all these exams needed extra time and money. My family then couldn’t afford for the extra books and exam fees. I worked part time in the evenings (STD booths, Internet café) for about 2 years to make extra money and spent all of it on books.
What made you choose such an offbeat, unconventional and unique career?
With many options in hand, it was a very difficult situation to make a choice for masters. I was selected in civil service prelims, but there was a long road ahead with little success (clearing mains and interview). The other jobs had a joining date of more than 6 months or needed a huge fee. Coming from a lower middle-income family, making money was a major criterion for selecting MS in USA. The thought then was that I could complete my masters in 2 years, get a job and save a lot of money, which by the way never happened. After ruling out things that need money and that would take time to start, I had two options – Masters in Agricultural Statistics in India, Masters in Plant breeding in USA. Visa was then the deciding factor among the two and I opted for MS in USA. After landing here, it was quite difficult to adjust to culture, the education system and the horrible winters (-30C).
My advisor in the Master’s program was the one who noticed the potential in me and guided me in the right way. He made me realize that my knowledge in statistics and computers makes me a better computational biologist. After my third semester, it was clear that I needed a PhD to get a decent job. For that I wrote the GRE and achieved a 99.9 percentile. I got accepted into 3 universities for PhD, but my boss who liked my work gave me an option to do an integrated PhD (no masters) with him. This would save me a couple of years and i readily accepted this. The only intention then was to settle better and faster. He gave me time and resources to grow. He never taught me but made me self-learn most of things and we ended up discussing things to make sure what I learnt was right. During this time, impressed by my work and knowledge, he offered me a position of Research Scientist too after my PhD. To distinguish myself from my fellow classmates, I did all the coursework in Statistics (PhD Level) too.
Tell us about your career path
My present path was never planned. But, in every step, I always wanted to stay ahead of others and worked hard for that. I always looked for other options and took the one that worked for me, since we can miss our goal due to various other factors beyond our control. My target was to be a plant breeder which has many job prospects, but I had to change to Genomics and Bioinformatics to get financial assistance at the university. This was a big turning point in making me what I am today. I can never forget the financial and moral help of my friends Ajay Jha, and Shipra Mittal without whom I would have quit my MS after the first semester, given that my stipend got cancelled. I should also mention a dear senior Nethala Suvarna Raju who guided me throughout my graduation and PhD, helping me make the right decisions in my career.
My current career is mostly influenced by the people around me in the US. I learnt a lot from many people that helped me become what I am today. My PhD/Research advisor Dr.Phillip Mcclean provided me the best guidance that helped shape my career. He not only taught me science but things in life at a larger scale. My roommate Gatta Srinivas helped me understand the scientific field, how to look at a bigger picture of the problem and provided suggestions to keep myself updated with scientific knowledge, which I follow even today by reading at least two papers a day. My senior mentor Suresh Bhamidimarri helped me understand the basics of plant biotechnology and the importance of thinking big rather than just doing the assigned work.
I ended up with my present job as Sr. Scientist at HudsonAlpha Institute for Biotechnology which is a pioneer in Plant Genomics. I was fortunate to work with Jeremy Schmutz on many projects and get my work published in very high impact journals like Nature Biotechnology and Nature. This was possible only because of the support I got from my supervisor and my continuous hard work in learning new things and of course, reading a lot.
Each of these stages in my career have not been easy, but my constant hard work and determination to distinguish myself made me what I am today. Other than my regular study/job, I always read a lot, especially subjects which might be useful one day. For example, my knowledge in statistics helps me propose novel methods, my knowledge in economics helps me in budgeting.
What did you do as a Research Scientist at the university?
As a Research Scientist, I had the opportunity to work in the same lab as PhD, and on multiple projects, publish articles in high impact journals like Nature Genetics. In addition, I supervised/guided other students in the department that helped me gain immense knowledge in various crops and various aspects of genomics. These all helped me publish about 20 papers in international journals. I was able to propose new alternatives, statistical methods to understand genetics better. After this step, I was actively looking for positions in academia and unfortunately none of them worked out.
All the 12 years at NDSU, I was working with crops like Bean, Soybean, Wheat, Canola, Barley among a few others. The yield of crops is limited by diseases, pests and abiotic factors like drought, heat etc. My work was to identify diagnostic markers for these crops. This would help farmers and breeders in USA and world to use the right varieties and also develop new hybrids. As an example, based on weather data, lets suppose we may have a drought in a coming season and we have about 10 varieties suitable to that region. Among the 10, three are resistant (based on markers) to drought (perform well in drought) and the others are not. Farmers make a choice on using only those three for the coming season.
In terms of hybrid development, let’s assume we have a good variety “A” that is good in quality and quantity of grain, but is susceptible to a disease. We have other variety “B”, that is resistant to the disease, but does not perform good. We make a cross between A and B, with the intention that resistant gene from B gets into A. But this process takes about 10-14 years. For example, the 2nd generation of plants are about 500, of which we need to select a few and advance further. Growing all 500 in 3-4 places, in 3 replicates collecting all data takes ~6 months to 1 year based on crop and lot of resources. If we use diagnostic markers, we can select few just in a week or two, or we can reduce 500 to 50 that saves lot of resources.
How did you get your first break?
Getting a Research Scientist position in the same lab, immediately after my PhD (with a large grant) was my first break. But getting to work at HudsonAlpha is the best part in my life, given the scope and reach of my work.
What were some of the challenges you faced in your career? How did you address them?
I did face some financial hardships until I completed my PhD. Luckily, I had the support of family and friends. Also, I worked part time during my graduation and first years of Phd to make additional income to support my needs.
Finding a job in biotechnology is not easy, given the limited number of vacancies. Though disappointed, I did not lose hope and kept on trying.
Moral support from my wife is the single most important contributor that helped me through the many challenges I faced throughout.
Where do you work now? Tell us about your research
I am a Sr. Scientist (Computational Biology) working with large quantities of next generation DNA sequencing data. I analyze and interpret genomic data of economically important plant species to improve crop breeding and other agricultural practices. Major part of my work is on quantitative, population and evolutionary aspects of genomics. I also work on other aspects like epigenomics, transcriptomics and statistical genomics. A bit of programming knowledge is also required to automate the various steps involved in the analysis.
Quantitative genomics is basically linking DNA sequence variation in genes or DNA elements to analyze the phenotype of interest like yield, biotic (disease resistance) and abiotic factors (drought etc.). This helps identify and develop varieties that are better to grow and achieve global food security. In terms of plant breeding this approach reduces the duration of releasing a variety by a few years while utilizing only few resources that are necessary for testing and advancing generations. Population genetics is understanding the structure of populations, their association to a phenotype (traits) as well as climatic adaptations. Given the climatic change with raising temperatures, this helps understand plant biology which then can be applied for crop improvement. Evolutionary genomics is understanding the domestication and adaptation process of a species (when and how). This helps us understand the genetics of domestication, and the genes that can be selected to be used in breeding programs. All these help us understand what happened in the past, be it evolution or adaptation to a region that has applications for development and testing of a new variety. This will accelerate breeding and selection for improved crop varieties. I publish my work in high impact journals as open source, and make all data and results available.
The present-day research work needs knowledge of genetics, evolution, ecology and many related biological fields in addition to software and statistics. Most days, my work includes analyzing big data, presenting results and discussing with collaborators, reading and writing a bit and mostly thinking on the lines of what else can be done with the data and how that can be applied to real world problems. The best part of my job is providing a genetic basis for crops, which one day has huge applications for cultivar development.
How does your work benefit society?
My work provides a base for plant breeders to develop new plant varieties that are resistant to pests, diseases, drought and other anomalies in climate and can also provide better yield that can solve food crises.
Tell us an example of a specific memorable work you did that is very close to you!
During my work as Research Scientist I had the opportunity to work with the whole genome assembly and demographics of common bean varieties. I spent a couple of years learning and working on it and my work ultimately got published in a high impact journal. More recently I worked on various aspects of genomics of a wild grass, Setaria viridis, that helped us identify a shattering gene. This work is published in one of the highly rated journals, Nature Biotechnology.
Your advice to students based on your experience?
If you want to succeed, work towards your goal. Always have an alternative because things sometimes don’t work in our favor. Even if the first option fails, don’t give up and work towards your alternative. Always think “what makes me different from my fellow students”, because they compete for the same position that you are looking for.
If you want to be a researcher, come with an open mind, ready to learn, willing to consider alternate hypotheses too, willing to spend a lot of time learning and keeping abreast of the scientific advancements. Always lend a helping hand in research, share your knowledge to solve the research problems of others. Similarly have others help you.
I currently work in a place that is a pioneer in genomics research, whether it is assembly of whole genomes or analyzing various aspects of genomics and molecular biology. The amount of data generated is vast and we always develop new methods for understanding biology. I see a large gap with the research in India in this particular field. Limited resources could be one, but limited knowledge is a big one. My plan is to bridge the gap by being a mentor to interested candidates, do workshops and training on various aspects of Genetics, Genomics and Bioinformatics.