In this study, the LBD (Lateral Organ Boundaries Domain) gene family, a group of plant-specific transcription factors critical for plant growth and development as well as metabolic regulation, was comprehensively characterized in rice. We identified 36 LBD genes using multi-source genomic data and systematically classified them into Class I (31 genes) and Class II (5 genes). Analysis of their physicochemical properties revealed significant variations in amino acid length, molecular weight, isoelectric points, and hydropathicity. Motif analysis identified conserved LOB domains and other motifs potentially linked to functional diversity. Cis-acting element analysis indicated the involvement of these genes in various biological processes, including light response, hormone signaling, and stress response. Expression profiling demonstrated tissue-specific expression patterns, with several genes, such as XM_015770711.2, XM_015776632.2, and XM_015792766.2, showing relatively high expression in rice roots, implying their important role in root development. Transcriptome data further supported the involvement of specific genes in responses to phytohormones such as jasmonic acid (JA) and abscisic acid (ABA), as well as environmental stresses like cold and drought. Notably, XM_015770711.2, XM_015776632.2, and XM_015772758.2 may contribute to the regulation of rice environmental adaptability by mediating ABA and JA signaling pathways, respectively. In conclusion, this study identified members of the LBD gene family through the screening of two rice gene databases, and performed a comprehensive analysis of their physicochemical properties, evolutionary relationships, and expression profiles under various conditions. These findings provided valuable insights for further functional studies of LBD genes. Moreover, this study provides a foundation for targeting LBD genes to enhance stress resilience (e.g., drought/cold tolerance) and root architecture optimization. The LBD gene family possesses dual values in both stress resistance regulation and developmental optimization. The construction of its multidimensional functional map lays the theoretical and resource foundation for the precise design of high-yield and stress-resistant varieties.

Axillary bud outgrowth, a key factor in ratoon rice yield formation, is regulated by several phytohormone signals. The regulatory mechanism of key genes underlying ratoon buds in response to phytohormones in ratoon rice has been less reported. In this study, GR24 (a strigolactone analogue) was used to analyze the ratooning characteristics in rice cultivar Huanghuazhan (HHZ). Results show that the elongation of the axillary buds in the first seasonal rice was significantly inhibited and the ratoon rate was reduced at most by up to 40% with GR24 treatment. Compared with the control, a significant reduction in the content of auxin and cytokinin in the second bud from the upper spike could be detected after GR24 treatment, especially 3 days after treatment. Transcriptome analysis suggested that there were at least 742 and 2877 differentially expressed genes (DEGs) within 6 h of GR24 treatment and 12 h of GR24 treatment, respectively. Further bioinformatics analysis revealed that GR24 treatment had a significant effect on the homeostasis and signal transduction of cytokinin and auxin. It is noteworthy that the gene expression levels of OsCKX1, OsCKX2, OsGH3.6, and OsGH3.8, which are involved in cytokinin or auxin metabolism, were enhanced by the 12 h GR24 treatment. Taken overall, this study showed the gene regulatory network of auxin and cytokinin homeostasis to be regulated by strigolactone in the axillary bud outgrowth of ratoon rice, which highlights the importance of these biological pathways in the regulation of axillary bud outgrowth in ratoon rice and would provide theoretical support for the molecular breeding of ratoon rice.

Although recent research progress on the abundant C-to-U RNA editing events in plant chloroplasts and mitochondria has uncovered many recognition factors and their molecular mechanisms, the intrinsic regulation of RNA editing within plants remains largely unknown. This study aimed to establish a regulatory relationship in Arabidopsis between the plant hormone auxin and chloroplast RNA editing. We first analyzed auxin response elements (AuxREs) present within promoters of chloroplast editing factors reported to date. We found that each has more than one AuxRE, suggesting a potential regulatory role of auxin in their expression. Further investigation unveiled that the depletion of auxin synthesis gene YUC2 reduces the expression of several editing factors. However, in yuc2 mutants, only the expression of CRR4, DYW1, ISE2, and ECD1 editing factors and the editing efficiency of their corresponding editing sites, ndhD-2 and rps14-149, were simultaneously suppressed. In addition, exogenous IAA and the overexpression of YUC2 enhanced the expression of these editing factors and the editing efficiency at the ndhD-2 and rps14-149 sites. These results suggested a direct effect of auxin upon the editing of the ndhD-2 and rps14-149 sites through the modulation of the expression of the editing factors. We further demonstrated that ARF1, a downstream transcription factor in the auxin-signaling pathway, could directly bind to and inactivate the promoters of CRR4, DYW1, and ISE2 in a dual-luciferase reporter system, thereby inhibiting their expression. Moreover, the overexpression of ARF1 in Arabidopsis significantly reduced the expression of the three editing factors and the editing efficiency at the ndhD-2 and rps14-149 sites. These data suggest that YUC2-mediated auxin biosynthesis governs the RNA-editing process through the ARF1-dependent signal transduction pathway.

Plant senescence is a highly coordinated process that is intricately regulated by numerous endogenous and environmental signals. The involvement of phytic acid in various cell signaling and plant processes has been recognized, but the specific roles of phytic acid metabolism in Arabidopsis leaf senescence remain unclear. Here, we demonstrate that in Arabidopsis thaliana the multiple inositol phosphate phosphatase (AtMINPP) gene, encoding an enzyme with phytase activity, plays a crucial role in regulating leaf senescence by coordinating the ethylene signal transduction pathway. Through overexpressing AtMINPP (AtMINPP–OE), we observed early leaf senescence and reduced chlorophyll contents. Conversely, a loss-of-function heterozygous mutant (atminpp/+) exhibited the opposite phenotype. Correspondingly, the expression of senescence-associated genes (SAGs) was significantly upregulated in AtMINPP–OE but markedly decreased in atminpp/+. Yeast one-hybrid and chromatin immunoprecipitation assays indicated that the EIN3 transcription factor directly binds to the promoter of AtMINPP. Genetic analysis further revealed that AtMINPP–OE could accelerate the senescence of ein3–1eil1–3 mutants. These findings elucidate the mechanism by which AtMINPP regulates ethylene-induced leaf senescence in Arabidopsis, providing insights into the genetic manipulation of leaf senescence and plant growth.