Natural variation in the evolutionarily conserved F-box gene SDEF promotes seed dormancy in rice

Insufficient seed dormancy causes pre-harvest sprouting (PHS) and severe yield losses in rice; however, genetic resources with practical breeding value remain limited. Here, we isolated a major dormancy gene, SDEF, via map-based cloning using chromosomal single segment substitution lines (SSSLs), identifying a functional SNP (Arg-to-Trp) as the causal mutation. CRISPR/Cas9-mediated knockout of SDEF led to PHS susceptibility, while overexpression significantly enhanced dormancy. Importantly, SDEF enhanced seed dormancy without compromising grain yield in SSSLs, confirming it as a promising breeding target. Moreover, SDEF encodes an angiosperm-conserved, nuclear-localized F-box protein and is preferentially expressed in the embryo, with expression increasing during seed maturation and declining upon germination. Mechanistically, protein interaction assays confirmed that SDEF recruits OSK1, with the Trp-type SDEF^K exhibiting a more stable interaction than the Arg-type SDEF^H. SDEF is induced by abscisic acid (ABA) and appears to promote seed dormancy through the ABA pathway by activating ABA signaling genes and repressing α-amylase genes, as evidenced by the reduced ABA sensitivity of sdef mutants. Additionally, haplotype analysis revealed that natural variation in SDEF is associated with divergent dormancy levels, and reduced nucleotide diversity in cultivated rice indicates that SDEF was selected during domestication. Collectively, our results provide insights into the molecular basis of SDEF-mediated dormancy, providing an ideal target for breeding PHS-resistant rice.