SiLRL1, a bHLH transcription factor from foxtail millet, promotes carotenoid accumulation and improves drought tolerance

Abstract Foxtail millet, an ancient cereal crop domesticated in China, is valued for its nutritional richness, particularly its carotenoid content. Carotenoids play critical roles in plant development and stress responses, and their metabolic pathways are regulated by various transcription factors (TFs). However, the transcriptional regulatory mechanisms controlling carotenoid accumulation in cereal crops remain poorly understood. In this study, we characterized SiLRL1, a basic helix-loop-helix (bHLH) TF in foxtail millet, and investigated its role in carotenoid metabolism and abiotic stress tolerance. Phylogenetic analysis classified SiLRL1 into subfamily XI of the bHLH family, which lacks a DNA-binding basic region but retains the HLH dimerization domain. Heterologous expression of SiLRL1 in Arabidopsis thaliana significantly enhanced carotenoid accumulation, particularly violaxanthin, and increased abscisic acid (ABA) levels. RNA-seq analysis revealed that SiLRL1 overexpression downregulated key carotenoid degradation genes (e.g., AtNCED4/CCD4) and upregulated genes involved in the mevalonate (MVA) and methylerythritol phosphate (MEP) pathways, as well as carotenogenic genes (e.g., AtPSY, AtLCYB, AtLCYE). Additionally, SiLRL1 overexpression improved drought tolerance and ABA sensitivity in transgenic Arabidopsis, accompanied by altered expression of ABA-responsive and drought-responsive genes. These findings establish SiLRL1 as a positive regulator of carotenoid biosynthesis and drought tolerance, providing insights into the genetic control of carotenoid metabolism and stress adaptation in foxtail millet.