Leaf senescence, a pivotal process in plants, directly influences both crop yield and nutritional quality. Foxtail millet (Setaria italica) is a C₄ model crop renowned for its exceptional nutritional value and stress tolerance characteristics. However, there is a lack of research on the identification of senescence-associated genes (SAGs) and the underlying molecular regulatory mechanisms governing this process. In this study, a dark-induced senescence (DIS) experimental system was applied to investigate the extensive physiological and transcriptomic changes in two foxtail millet varieties with different degrees of leaf senescence. The physiological and biochemical indices revealed that the light senescence (LS) variety exhibited a delayed senescence phenotype, whereas the severe senescence (SS) variety exhibited an accelerated senescence phenotype. The most evident differences in gene expression profiles between these two varieties during DIS included photosynthesis, chlorophyll, and lipid metabolism. Comparative transcriptome analysis further revealed a significant up-regulation of genes related to polysaccharide and calcium ion binding, nitrogen utilization, defense response, and malate metabolism in LS. In contrast, the expression of genes associated with redox homeostasis, carbohydrate metabolism, lipid homeostasis, and hormone signaling was significantly altered in SS. Through WGCNA and RT-qPCR analyses, we identified three SAGs that exhibit potential negative regulation towards dark-induced leaf senescence in foxtail millet. This study establishes the foundation for a further comprehensive examination of the regulatory network governing leaf senescence and provides potential genetic resources for manipulating senescence in foxtail millet.

Carotenoids are important compounds of quality and coloration within sweet potato storage roots, but the mechanisms that govern the accumulation of these carotenoids remain poorly understood. In this study, metabolomic and transcriptomic analyses of carotenoids were performed using young storage roots (S2) and old storage roots (S4) from white-fleshed (variety S19) and yellow-fleshed (variety BS) sweet potato types. S19 storage roots exhibited significantly lower total carotenoid levels relative to BS storage roots, and different numbers of carotenoid types were detected in the BS-S2, BS-S4, S19-S2, and S19-S4 samples. β-cryptoxanthin was identified as a potential key driver of differences in root coloration between the S19 and BS types. Combined transcriptomic and metabolomic analyses revealed significant co-annotation of the carotenoid and abscisic acid (ABA) metabolic pathways, PSY (phytoene synthase), CHYB (β-carotene 3-hydroxylase), ZEP (zeaxanthin epoxidase), NCED3 (9-cis-epoxycarotenoid dioxygenase 3), ABA2 (xanthoxin dehydrogenase), and CYP707A (abscisic acid 8’-hydroxylase) genes were found to be closely associated with carotenoid and ABA content in these sweet potato storage roots. The expression patterns of the transcription factors OFP and FAR1 were associated with the ABA content in these two sweet potato types. Together, these results provide a valuable foundation for understanding the mechanisms governing carotenoid biosynthesis in storage roots, and offer a theoretical basis for sweet potato breeding and management.

Millet color is an important index for consumers to assess foxtail millet quality. The yellow color of millet is mainly because of the accumulation of carotenoids, which are essential for human nutrition. However, the discoloration of millet during storage due to carotenoid degradation seriously reduces the nutritional and commercial value of millet products. The essential quality traits of millet discoloration during storage were analyzed using two foxtail millet varieties, namely 9806-1 and Baomihunzi. We observed that the millet discoloration was caused by carotenoid degradation during storage, and different genotypes exhibited different discoloration rates. The carotenoid reduction rate in 9806-1 (32.2%) was higher than that in Baomihunzi (10.5%). The positive correlation between carotenoid reduction and the expression of SiLOX protein indicated that SiLOX from foxtail millet played a major role in carotenoid reduction during storage. The expression profiles of the SiLOX gene family were analyzed at different grain maturing stages, from S1 to S3, in these two varieties to determine the key SiLOX genes responsive to millet discoloration in foxtail millet. The consecutively low expression of SiLOX2, SiLOX3, and SiLOX4 contributed to the low level of SiLOX protein in Baomihunzi. Furthermore, the undetectable expression of SiLOX4 in the later stage of maturation in Baomihunzi was associated with low discoloration, indicating that SiLOX4 might be a key gene in regulating the discoloration of millet. This study provided critical information on the mechanism of carotenoid degradation during millet storage and laid the foundation for further understanding of carotenoid metabolism in foxtail millet.

Sweet potatoes (Ipomoea batatas (L.) Lam.) are a widely cultivated member of the Convolvulaceae family. Despite intensive agricultural interest, the metabolic determinants of sweet potato quality remain poorly understood owing to a lack of reliable or systematic sweet potato metabolite analyses. This study aimed to reveal the mechanism of flavonoid biosynthesis using widely targeted metabolomics and qRT-PCR analysis of white (S19) and yellow (BS) sweet potatoes. We found that the PAL, C4H, 4CL, CHS, CHI, IFS, F3H, F3’H, DFR, ANS, and ANR genes were differentially expressed in BS. Upregulation of PAL, C4H, 4CL, and CHS led to the accumulation of large amounts of chalcone, which is highly expressed in yellow flesh, resulting in the yellow color of BS. In S19, the high expression of FLS and the low expression of DFR inhibited pigment accumulation, while the low expression of CHS also inhibited flavonoid synthesis, ultimately leading to the white color. In conclusion, this study identified the main differentially expressed genes and their metabolites in the flavonoid biosynthesis pathway, and preliminarily elucidated the mechanism underlying the different flesh colors in sweet potato, thus providing new insights into the composition and abundance of metabolites in sweet potatoes with different-colored flesh.

Plant uridine diphosphate glycosyltransferases (UGTs) catalyze glycosylation, a pivotal biochemical modification essential for diverse metabolic and physiological processes. Foxtail millet ( Setaria italica ), a drought-tolerant C4 cereal crop, serves as an emerging model for studying abiotic stress adaptation. Here, we identified 173 UGT genes ( SiUGT s) in the foxtail millet genome, unevenly distributed across nine chromosomes and classified into 17 phylogenetically distinct subfamilies. Collinearity analysis revealed nine segmental duplicated duplication pairs under purifying selection, highlighting evolutionary conservation. Promoter analysis identified cis-acting elements associated with growth and development, biotic/abiotic stress responses, and hormonal regulation, suggesting functional versatility of SiUGT s. Transcriptome profiling under dark-induced leaf senescence (DIS) revealed 5 up-regulated and 27 down-regulated SiUGT s, implicating their roles in senescence regulation. Subsequently, RT-qPCR validated SiUGT26 as a senescence-responsive gene. Heterologous overexpression of SiUGT26 in Arabidopsis was associated with delayed leaf senescence and enlarged rosettes compared with wild-type plants. Co-expression analysis suggested that SiWRKY71 may be associated with the regulation of SiUGT26 . Collectively, this study provides a genomic resource for the UGT gene family in foxtail millet and identifies SiUGT26 as a senescence-responsive candidate gene. These findings provide a basis for further investigation of UGT-mediated regulation of leaf senescence in foxtail millet.