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A Method for Identifying Environmental Stimuli and Genes Responsible for Genotype-by-Environment Interactions From a
Akio Onogi1, Daisuke Sekine2,3, Akito Kaga3
1Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Japan.
Frontiers in Genetics
|January 14, 2022
Summary
This study introduces a data-driven method (ECGC) to uncover environmental factors and genes driving genotype-by-environment interactions in crops. It reveals how weather impacts traits like soybean yield, aiding agricultural breeding.
Area of Science:
- Agricultural Science
- Genetics
- Environmental Science
Background:
- Genotype-by-environment (GxE) interactions are crucial for crop adaptation but poorly understood in field conditions.
- Large-scale, multi-environment datasets offer potential to dissect GxE interactions.
- Identifying specific environmental stimuli and responsive genes is key for targeted breeding strategies.
Purpose of the Study:
- To develop and apply a data-driven approach to identify environmental factors and genes associated with GxE interactions.
- To analyze GxE interactions in soybean using a large multi-environment dataset.
- To understand the influence of meteorological factors on crop traits and their genetic basis.
Main Methods:
- Developed Environmental Covariate Search Affecting Genetic Correlations (ECGC), a data-driven approach.
- Applied ECGC to a soybean dataset with 25,158 records across 52 environments.
- Utilized genome-wide association mapping to identify genes responsible for GxE interaction sensitivities.
Main Results:
- ECGC identified specific meteorological factors (e.g., precipitation, sunshine hours) influencing GxE interactions for traits like yield, flowering time, and protein content in soybean.
- The timing of environmental factors (e.g., around sowing, pre-maturity) critical for GxE interactions was determined.
- Candidate and known genes mediating GxE interactions were discovered through association mapping.
Conclusions:
- Data-driven approaches like ECGC can effectively reveal novel insights into field-level GxE interactions.
- Understanding specific environmental triggers and genetic responses enhances the potential for precision agriculture and crop improvement.
- The study highlights the importance of considering environmental context in genetic analyses for crop breeding.
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