Spliceosome buffers cryptic genetic variation to enforce phenotypic robustness in Arabidopsis

Cryptic genetic variations (CGVs), which are phenotypically silent under normal conditions, can compromise phenotypic robustness when unmasked. Canalization buffers CGV to stabilize phenotypes, yet the underlying molecular mechanisms remain largely unknown. Here, we show that alternative splicing acts as a canalization mechanism in Arabidopsis. A natural single-nucleotide polymorphism in the functionally unknown gene Hidden Killer 1 (HIKI1) behaves as CGV and disrupts embryonic robustness dependent on genetic background when SKIP is compromised among natural Arabidopsis populations. SKIP-containing spliceosome rescues CGV-perturbed HIKI1 pre-messenger RNA alternative splicing, thereby buffering the CGV and restoring normal embryogenesis. This buffering extends to postembryonic traits, demonstrating that alternative splicing is a general canalization mechanism. Our findings reveal how genetic decoding machinery maintains phenotypic robustness despite hidden variations and open previously unexplored routes for unlocking species-wide genetic potential and tuning trait penetrance.