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…
Allopolyploid crops possess homoeologous gene copies from distinct subgenomes, a group of genetically related interactions that traditional association studies do not examine. HomoeoGWAS leverages these copies to establish the interaction testing unit called the homoeolog group and conducts analysis across all eligible groups collectively, while maintaining experimental-wide error calibration.
This is achieved by incorporating three different genotype encodings for each edge, utilizing a structure-aware parametric bootstrap.
The technique was successfully tested in wheat, cotton, and rapeseed, employing 80-group tests under multiple null models, and full-family tests for all four crops under a structure-aligned global null hypothesis involving 379 to 404 groups. The omnibus test outperformed SNP-by-SNP scans when interactions extended over multiple genotype dimensions.
HomoeoGWAS successfully identified homoeolog-group interactions responsible for heading date in wheat, flowering time in rapeseed, and fibre length in cotton. Five groups across four loci maintained statistical significance upon regional conditioning. Interestingly, rapeseed homoeolog coupling demonstrated a weak yet reproducible association with homoeologous-exchange frequency. Overall, genome-wide interaction analyses were completed in a matter of minutes.
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