The relationship between a crop’s genetic traits and the environment it grows in is quite complex. A research group is working to assist breeders in understanding these interactions to enhance crop resilience and yields.
To create crop varieties that are sturdier and more productive, it is crucial to comprehend how both genetic traits and environmental factors influence them.
However, the detailed relationship between genetics and environmental conditions can be challenging to decipher. One reason is that plants sharing the same genetic background may react differently to changes in their surroundings. This phenomenon is known as phenotypic plasticity, which is the primary research focus of Jianming Yu, an agronomy professor at Iowa State University.
Crop breeders have typically viewed phenotypic plasticity as too complicated to effectively utilize in enhancing crop performance, according to Yu. A new study by his research group and collaborators seeks to emphasize plasticity by presenting a systematic method for gaining insights from the data that connects crop characteristics, genetics, and environmental conditions.
“We developed a quantitative framework for breeders and geneticists, allowing them to understand plasticity and examine all relevant factors simultaneously,” Yu explained. He holds the position of Pioneer Distinguished Chair in Maize Breeding and directs the Raymond F. Baker Center for Plant Breeding.
Yu’s team’s findings, shared in a recent issue of Genome Research, builds upon earlier research involving an extensive collection of corn plants studied over the last twenty years. The maize nested association mapping population comprises 5,000 corn lines cultivated at 11 different locations, and data on both genetic and physical traits of these plants is widely utilized by researchers. A study published in 2021 by a team led by Iowa State’s Matthew Hufford, an ecology, evolution, and organismal biology professor, sequenced the genomes of the 26 ancestors used to breed this 5,000-line population.
The new research led by Yu combines genomic data from these founders with observed traits and historical weather information, analyzing over 20 million genetic markers to understand 19 different traits in corn under varied environmental conditions throughout its growth stages.
“It’s incredible to pinpoint the key environmental elements influencing the plastic response of the maize population during critical growth phases, and to link these findings to genome-wide genetic variations,” he remarked.
The overarching objective is to enhance breeding initiatives, making it simpler to anticipate how to cultivate corn with significantly higher yields or improved ability to endure harsh conditions. For example, a statistical analysis described in their study could predict the flowering time of untested genotypes in unfamiliar environments over 90% of the time. However, the predictive accuracy for traits related to plant structure and yield components was lower for untested genotypes and environments, though some individual traits in these categories exceeded 50% accuracy.
As climate change continues to influence agriculture, extracting further enhancements from corn and other crops will become increasingly vital. Advances in breeding that utilize comprehensive approaches—large datasets within real-world contexts—are particularly promising, Yu noted.
“We believe that when people conduct detailed studies using advanced technology, they often analyze only a small fraction of the available material,” he stated. “To address significant challenges, we must consider the complexities of natural field circumstances. That is where we can drive production forward.”
Yu’s team made their compiled research available on MaizeGDB, a public database for corn genomics, allowing other researchers to build upon their work. Yu is optimistic that their methodologies for compiling and analyzing data about phenotypic plasticity will be adopted by scientists working with various plant species. Leading breeding companies have also shown interest in this approach, he added.
“It’s more about the methodology than the specific results. This provides a captivating and valuable lens through which to examine the data,” he summarized.
