Decoupling the chemical and physical origins of the seed spectral manifold in sorghum.

Biological structures interact with light as complex manifolds, yet genomic studies often reduce these phenotypes to scalar traits. Here we resolve the sorghum seed spectral manifold into separable axes corresponding primarily to pigment-associated and structure-associated optical variation. Path analysis indicates that near-infrared (NIR) reflectance is associated primarily with an indirect path through seed mass, supporting partial decoupling from pigmentation-related variation. We identify a chromosome 6 region associated with NIR reflectance and spectral entropy, consistent with a contribution to the physical-structural axis of the seed optical phenotype. Furthermore, in silico perturbation analyses suggest that major axes of seed optics are structured and can be predictably shifted within the observed phenotypic manifold. By linking spectral variation to morphology and genetic association, this work provides a framework for interpreting seed optical phenotypes beyond simple color categories and for studying how light-matter interactions are shaped by plant structure and chemistry.