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

Allopolyploid crops carry homoeologous gene copies from divergent subgenomes, an evolutionarily defined set of candidate interactions that association studies do not test directly. HomoeoGWAS uses these copies to define the unit of interaction testing, the homoeolog group, and analyses all eligible groups as one family with experiment-wide error calibration, combining three complementary genotype encodings per edge with a structure-aware parametric bootstrap. Family-wise error was controlled in 80-group tests in wheat, cotton and rapeseed under several null models and in full-family tests of all four crops under a structure-aligned global null (379-17,404 groups). The omnibus outperformed a SNP-by-SNP scan when interaction spanned several genotype dimensions. HomoeoGWAS detected homoeolog-group interactions for heading date in wheat, flowering time in rapeseed and fibre length in cotton; five groups at four loci retained support after regional conditioning. Rapeseed homoeolog coupling showed a weak but reproducible association with homoeologous-exchange frequency. Genome-wide interaction analyses took minutes.