“Novel insights into genetic and environmental regulation of reproductive stages in soybean”

Swapan Chakrabarty, PhD, Postdoc Research Associate

Wednesday, January 28^th, 2026

Agronomy 3140, 3:00-4:00pm—extended discussion open until 5pm

Seminar Description: The reproductive stage of soybean is influenced by the effect of genotype, environment, and their interactions. While days to flowering and days to full maturity have been studied, a systematic and comprehensive study that investigates the variation in days to each stage and the role of maturity-related genes and environmental variables is lacking. Therefore, we studied 508 unique accessions from the USDA germplasm collection from maturity group 0-IV, and a set of 67 near-isogenic lines differing for maturity-related genes. Field experiments and evaluations were conducted in central Iowa, USA. The days to each of the reproductive stages, R1-R8, were recorded. We report considerable variation in the duration of reproductive growth stages between flowering and maturity, which is largely explainable by known flowering and maturity genes as well as environmental variables, day length, and growing degree days. Besides the known maturity-related genes E1, E2, and Dt1, we identified a couple of novel SNPs as potential targets for genetic and environmental regulation of reproductive stages. Furthermore, we developed a random forest-based genetic maturity model that can predict genetic and environmental effects across a wide range of genotypes. This study broadens the understanding of the factors that contribute to reproductive development, which will help to develop cultivars that combine the optimal combinations of stage durations for a higher seed yield and enhanced resilience.

Dr. Swapan Chakrabarty has been working as a Postdoctoral research Associate at the Department of Agronomy, Iowa State University, since October 2024. He obtained his recent Ph.D. in Forest Molecular Genetics and Biotechnology, and M.S. in Data Science from Michigan Tech. Before joining Michigan Tech, he earned his first Ph.D. in Agricultural Entomology and Pest Control from the Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, China. He completed his first M.S. in Genetics and Plant Breeding and B.S. in Agriculture from Bangladesh. He is a plant geneticist and computational biologist with interdisciplinary research experience spanning plant breeding, molecular biology, quantitative genetics, genomics and bioinformatics, data science, statistical and predictive modeling, machine learning, and artificial intelligence. His research interest focused on integrating experimental biology with advanced computational and AI-based approaches to dissect complex traits, stress resilience, and genotype-environment interactions in agricultural crops and forest species, translating data-driven insights into practical breeding and agricultural solutions. Experienced in leading and collaborating on international, multi-institutional research projects, with a strong record of peer-reviewed publications, grant writing, and mentoring.   

“Phenotypic Plasticity of Flowering Time is Associated with Cis-Regulatory Element Variation in Maize”

Dongdong Li, PhD, Postdoc Research Associate

Wednesday, January 28^th, 2026

Agronomy 3140, 3:00-4:00pm—extended discussion open until 5pm

Seminar Description: Phenotypic plasticity is the property of a given individual to produce different phenotypes in response to distinct environmental conditions. Flowering time is a representative trait for studying phenotypic plasticity, as it exhibits a diverse outcome of the gene–environment interplay. Cis-regulatory elements, such as promoters, enhancers, and silencers, are non-coding sequences that regulate gene expression. In a multi-parent population, we identified ZmCCT10 as a key gene driving phenotypic plasticity. Our findings reveal that a ~5 kb transposable element insertion upstream of ZmCCT10 alters DNA methylation and likely disrupts cis-regulatory elements, leading to differential gene expression. This study clarifies the link between cis-regulatory variation and phenotypic plasticity, offering new targets for breeding climate-resilient crops.

Dr. Dongdong Li is a Postdoctoral Research Associate in the Department of Agronomy at Iowa State University, working under the supervision of Dr. Jianming Yu. His research addresses fundamental questions in plant breeding by integrating quantitative genetics, statistical genomics, and cutting-edge technologies to dissect the complexity of quantitative traits, with a focus on phenotypic plasticity and heterosis in maize. He also served as a member of the MaizeGDB Editorial Board in 2025.