Increasing the decision-making ability in plant breeding

Plant phenotyping, the study of observable characteristics based on how the plant’s genotype interacts with its environment, is integral to plant breeding and modern production agriculture. Field-based high-throughput phenotyping is a relatively new technology in this field and the primary focus of Texas A&M AgriLife researcher Alper Adak.

Adak, Ph.D., has been studying plant breeding since he first began his doctoral program in the Department of Soil and Crop Sciences in the Texas A&M College of Agriculture and Life Sciences. Now a postdoctoral research associate, he has expanded his research efforts and is making advances in high-throughput phenotyping through unmanned aerial vehicles.

Adak said this technology can increase the precision of decision-making for plant breeders and geneticists through novel optimizations, applications and statistical analysis. He aims to address these requirements as much as possible by dissecting data to better understand how these phenomic and genomic traits interact with diverse environments.

Adak grew up in Antalya, Turkey, and completed his undergraduate and master’s level coursework at Akdeniz University. He was awarded a scholarship by the Ministry of National Education of the Republic of Turkey to complete his doctoral education abroad. His search for a quantitative genetic lab focusing on corn with a progressive plant breeding program that contained both genomic and phenomic research led him to Texas A&M.

Having found his home in the Department of Soil and Crop Sciences, Adak plans to continue his impactful research and eventually run his own progressive plant breeding program.

After completing your doctorate, why did you choose to stay in the department for your postdoc work?

Over the years, a wealth of data has been collected by our research team, mostly drone images, as well as genomic data from various corn populations grown at Texas A&M. However, graduate students, including myself, were often only able to use a small portion of this data for the limited time that we were working in our degree programs. That can, at times, make it challenging to see the big picture in research. For these reasons, I wanted to pursue my career as a postdoc to focus, process and ultimately publish this big data.

What are you looking at when utilizing high-throughput phenotyping?

We can look at two corn plants and observe that they are both 6 feet tall. The question we ask when studying phenotype and genotype is, “As these two plants grew to 6 feet, were their height changes the same during their development, or were they different?” One plant may have followed the growth of 3 feet, 4.5 feet and 6 feet, while the other followed the growth of 3 feet, 5 feet and 6 feet. This means that although they are 6 feet when you measure them, their height growth during development is different. What we need to understand from this result is that one-time measurement will cause us to think erroneously and incompletely. With a single measurement, we cannot observe the changes in plant heights over time, which is very critical data for understanding plant biology and genetics.

With high-throughput phenotyping, we fly drones equipped with different sensors, like cameras, over thousands of plants multiple times and record pictures during each flight. Thus, we can calculate the height of thousands of plants at different developmental stages. This technology was not common before, but now, thanks to its advancement, we can study the development of plants more precisely.

What do you wish people knew about high-throughput phenomics and genomics?

Many agriculturally important characteristics such as grain yield in corn are related to many factors such as genetic architecture of plants or environmental parameters. These relationships are dynamic and should be observed throughout the developmental stages of plants. A better understanding of these relationships requires more precise observations.

Genomic prediction was the technology that has been used for more than two decades in plant breeding. The yield of newly developed plants with no yield records was being predicted using their thousands of genomic markers at seedling stages. We have made the same prediction but using phenomic features obtained by drone images and observed that using phenomic features can outperform the genomic markers in predicting the yield of newly developed plants.

From this, we can deduce that conventional phenotyping is insufficient and even misleading when making decisions in plant breeding programs, and that high-throughput technologies in phenotyping has lagged those in genomics. However, recent advances in phenotyping are paving the way for new discoveries in plant biology, thanks to the collection of many novel phenotypic data that were previously impossible to record. High-throughput technologies in plant phenotyping will be used more frequently in the near future and facilitate the selection of desired plants for target environments through integration with genomic data or alone.

What is a change you anticipate in the industry?

Thanks to big data including genomic, phenomic and environmental data, experts in the industry analyze this big data as an increasing trend. What we likely will see is this big data will be analyzed by machine learning, artificial intelligence and computer vision algorithms. Thus, we will enter a new era in agriculture in which there are more profitable, innovative, productive, result-oriented and environmentally friendly ideas and practices in agriculture.

What influenced your decision to study plant phenomics and genomics?

I have been positively influenced by different people at various times in my life, and what they all have in common is that they are all closely related to agriculture and plant breeding and genetics. Therefore, these people had a great influence on my choice of this field.

My father, Selahattin Adak, is a horticultural expert and devoted his life to vegetable breeding and growing. He instilled in me the love of nature and agriculture.

I started my graduate education at Akdeniz University in Antalya, Turkey. My advisor at the time, Dr. Cengiz Toker, was very influential in my choice of a career in plant breeding and genetics.

When I came to Texas A&M, I joined Dr. Seth Murray’s lab to start my doctoral work in corn breeding and genetics. Dr. Murray’s vision impressed me deeply, and he is the person who made me a critical thinker. I can easily say that he is the real person behind my scientific success. As one of his mentees, he consistently and patiently helped me to be successful. He has always generously and sincerely cared about my achievements and elevated me. I feel very lucky to have had the opportunity to work with him.

What advice would you give to current students interested in pursuing an educational or career path like yours?

I will share a habit that has worked for me in my professional life and is one I believe can be helpful for students. I’ve heard the scientists I admire say that innovative ideas are often timid, that they do not always visit our imaginations. Throughout my career, I have had many examples that confirm this phenomenon. Therefore, I have always tried to keep my own world of thought as ready and attractive as possible so that when any innovative ideas come up, I can welcome them and combine them with my world of thought. In this way, I was able to construct some new ideas in my imagination that created a fruitful diversity in my world of thought. In short, current students may design their mindset to think sustainably, and this can help them learn that new ideas require long-term thinking throughout their lives.

What do you like most about what you do?

I think my favorite part of my job is to exchange ideas with scientists from the same or different disciplines. Sometimes developing an idea on your own can be difficult. However, working and brainstorming with experts in different fields has always elevated me and helped me develop my ideas more strongly. 

What is a fond memory you have of your time here at Texas A&M?

I received the 2022 Vice Chancellor’s Award for Excellence in the Graduate Student Research Award category. This is one of my most important and beautiful memories during my time here at Texas A&M.

What would you be doing if you weren’t a postdoctoral research associate?

From a realistic perspective, I would be doing vegetable growing and breeding to help our small family business. From an imaginary point of view, I would love to be a composer in the baroque era or be an electric solo guitar virtuoso in the 1980s.