Combined “omics” and physiological approaches highlight the roles of the GABA shunt and mitochondria-related functions in rice seed longevity

In the context of global warming, the ability of seeds to withstand higher temperatures and humidity during dry storage is critical to maintain food production. Seed longevity, also referred to as storability, is therefore an essential trait. As a major staple crop, rice ( Oryza sativa L. ) has been widely studied to identify the genetic determinants of seed longevity, primarily through QTL mapping and molecular analyses. However, integrated multi-omics data remain limited, especially compared to advances made for other seed physiological features (e.g., dry quiescence, germination). This study investigates the molecular determinants of rice seed longevity under varying storage conditions using controlled deterioration treatments (CDTs) at 25°C (no deterioration), 40°C (reduction of germination speed and uniformity) and 45°C (loss of germinative capacity) under high relative humidity. Through physiological characterizationand multi-omics analyses, we identified key metabolic pathways and genetic factors associated with seed aging. By integrating transcriptomic, proteomic, and metabolomic data, we pinpointed specific pathways critical to seed viability loss. CDTs revealed that only a small number of genes and proteins are significantly affected. In particular, our results highlight a major impact of CDTs on the GABA shunt and mitochondrial factors as the DEAD-box ATP-dependent RNA helicase 9. Altogether, this work opens the way for in-depth functional studies on a small number of mitochondria-related genes involved in rice seed longevity. • In contrast to germination or dormancy release, a relatively small number of genes and proteins have their expression and abundance altered during loss of rice seed longevity. • Mitochondria-related factor including the DEAD-box ATP-dependent RNA helicase 9 (OsRH9) and other regulators such as the MOTHER of FT and TFL1 homolog 2 (OsMFT2) appear likely involved in rice seed longevity. • As in Arabidopsis, methionine metabolism appears positively related to rice seed longevity. • The mitochondrial GABA shunt appears as a central component of rice seed longevity.