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Contrasting Selection on GxE and Main Effect Loci for Soybean Grain Yield
Mary M Happ1, George L Graef1, Réka Howard2
1Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68503, USA.
Genetics
|June 19, 2026
Summary
Soybean breeding maintains adaptive potential by relaxing selection on genes with environmental interactions (GxE loci) while intensifying selection on a subset of conditionally neutral effects for yield.
Area of Science:
- Plant genetics
- Agricultural science
- Genomics
Background:
- Soybean breeding aims to maximize yield across diverse environments.
- Yield is a complex trait influenced by main effect loci and environment-interacting loci (GxE loci).
- Artificial selection can reduce genetic diversity around yield-enhancing loci.
Purpose of the Study:
- To investigate how artificial selection has shaped genomic regions related to main yield effects and GxE effects.
- To quantify diversity and divergence patterns across different types of genetic effects on yield.
Main Methods:
- Combined multi-environment yield trials with whole-genome resequencing in soybean.
- Integrated sliding window analyses of variance explained with population genetics statistics (Tajima's D, weighted Fst).
- Utilized permutation-based comparisons to assess selection signatures.
Main Results:
- Genomic regions with higher diversity and lower divergence were linked to greater GxE variance, suggesting relaxed selection.
- Conditionally neutral loci exhibited strong directional selection and contributed significantly to genetic variance.
- Both positive and negative selection were detected among GxE loci, with the strongest beneficial allele enrichment in conditionally neutral regions.
Conclusions:
- Elite soybean breeding preserves adaptive potential in many GxE loci while focusing selection on specific conditionally neutral effects.
- Different testing environments favor distinct types of GxE effects, impacting allele enrichment.
- Findings offer a framework for understanding environmental influences on genetic responses for yield and other traits.
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