Multi-omics profiling identifies potential biological nitrification inhibitor 1,9-decanediol biosynthesis and secretion mechanisms in diverse rice varieties.

1,9-Decanediol (1,9-D) was identified as the first fatty alcohol with biological nitrification inhibition (BNI) activity in rice root exudates. In a previous study, transcriptomic and untargeted metabolomic analyses contrasted two rice varieties, suggesting metabolic pathways and associated gene families involved in 1,9-D biosynthesis and secretion. However, due to the small number of varieties and technical constraints, the pool of candidate genes remained extensive, impeding precise identification and functional validation. Here, we employ ten rice varieties with diverging root-secretion properties for integrated transcriptomic and targeted metabolomic profiling. Our results demonstrate that ammonium treatment significantly enhances 1,9-D secretion across varieties, indicating a potentially conserved regulatory mechanism in rice. Integrated analysis revealed that α-linolenic acid (LN) and linoleic acid (LA) may serve as biosynthetic precursors of 1,9-D and identified key candidate genes in LN/LA metabolism, including Os04g37430, Os04g47120, Os08g39840, Os08g39850, and Os08g08220. Furthermore, our data show that root secretion of 1,9-D is actively regulated by specific transporters, including the major facilitator superfamily (MFS) member Os11g04104, the ATP-binding cassette (ABC) transporter Os01g07870, and the multidrug and toxic compound extrusion (MATE) transporter Os10g20390. This study reveals a novel multi-gene regulatory network underlying 1,9-D synthesis and secretion, providing candidate targets for improving nitrogen-use efficiency in rice.