HomoeoGWAS enables experiment-wide homoeolog-group interaction mapping in allopolyploid crops

HomoeoGWAS controlled family-wise error across 80-group interaction tests in wheat, cotton, and rapeseed and detected homoeolog-group interactions for key traits.

• Why it matters: Allopolyploid crops have divergent homoeolog copies, but association studies rarely test interactions at the homoeolog-group level, leaving a gap in experiment-wide interaction mapping.
• What they did: The method defines the interaction unit as a homoeolog group, analyzes eligible groups as one family, and calibrates error using experiment-wide bootstrap with three genotype encodings per edge under structure-aware null models.
• The result: It found trait-linked homoeolog-group interactions—heading date in wheat, flowering time in rapeseed, and fibre length in cotton—and retained support for five groups at four loci after regional conditioning; rapeseed coupling weakly but reproducibly tracked homoeologous-exchange frequency.

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