Natural variation in <i>SL6</i> determines fatty acid components and seed longevity in rice.

Abstract

Seed longevity (SL) is vital for ensuring food security worldwide. However, the genetic basis of SL has been scarcely documented. Here, we report the cloning of a major SL locus, <i>qSL6</i>, encoding a fatty acyl-ACP thioesterase type B. SL6 is functionally conserved in regulating palmitic acid synthesis in seeds, conferring higher oxidation durability and SL in various species. Through the VP1-<i>SL6</i> module, a seed desiccation-derived ABA signal is transmitted via VP1, which directly activates <i>SL6</i> transcription to alter the fatty acid composition and elevate SL in seeds. The ancestral elite allele <i>SL6^HHZ</i> harbors a virus-derived CT-rich motif <i>cis</i>-element in the 5'UTR, which serves as a universal, bidirectional mRNA stabilizer, contributing to the divergence between <i>indica</i> and <i>japonica</i> in terms of SL. Moreover, manipulating <i>SL6</i> expression via marker-assisted selection or transgenic approaches notably improved SL in rice cultivars and F₁ hybrids without affecting major agronomic traits. Our findings provided a promising genetic locus for improving SL in rice.