Chlorogenic acids (CGAs) are important secondary metabolites produced in sweet potato. However, the mechanisms of their biosynthesis and regulation remain unclear. To identify potential genes involved in CGA biosynthesis, analysis of the dynamic changes in CGA components and RNA sequencing were performed on young leaves (YL), mature leaves (ML), young stems (YS), mature stems (MS) and storage roots (SR). Accordingly, we found that the accumulation of six CGA components varied among the different tissues and developmental stages, with YS and YL recording the highest levels, while SR exhibited low levels. Moreover, the transcriptome analysis yielded 59,287 unigenes, 3,767 of which were related to secondary-metabolite pathways. The differentially expressed genes (DEGs) were identified based on CGA content levels by comparing the different samples, including ML vs. YL, MS vs. YS, SR vs. YL and SR vs. YS. A total of 501 common DEGs were identified, and these were mainly implicated in the secondary metabolites biosynthesis. Additionally, eight co-expressed gene modules were identified following weighted gene co-expression network analysis, while genes in darkgrey module were highly associated with CGA accumulation. Darkgrey module analysis revealed that 12 unigenes encoding crucial enzymes (PAL, 4CL, C4H, C3H and HCT/HQT) and 42 unigenes encoding transcription factors (MYB, bHLH, WD40, WRKY, ERF, MADS, GARS, bZIP and zinc finger protein) had similar expression patterns with change trends of CGAs, suggesting their potential roles in CGA metabolism. Our findings provide new insights into the biosynthesis and regulatory mechanisms of CGA pathway, and will inform future efforts to build a genetically improve sweet potato through the breeding of high CGA content varieties.

Although the functions of basic leucine zipper (bZIP) family transcription factors in the regulation of various abiotic stresses are beginning to be unveiled, the precise roles of bZIP proteins in plants coping with submergence stress remain unclear. Here we identified a bZIP gene GmbZIP71-4 from soybean, which localized in the nucleus. The GmbZIP71-4 over-expressed tabocco line showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the differences expressed genes between submergence treatment and control groups were specially enriched in plant hormone signal transduction items, especially those in response to ABA. Electrophoretic mobility shift assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2 gene, which is consistent with the ChIP-qPCR results. GmbZIP71-4 function as a negative regulator of soybean in responding to submergence stress through manipulating ABA signaling pathway. This findings will set a solid foundation for the understanding of submergence resistance in plants.

Exogenous melatonin has emerged as a pivotal multifunctional signaling molecule, recognized for its critical role in enhancing stress tolerance and improving crop productivity. N6‐methyladenosine (m6A) is the most prevalent internal modification found in eukaryotic mRNA and plays a crucial role in regulating plant growth, development, and stress responses. Despite its importance, the regulatory mechanisms of the m6A pathway in rice exposed to exogenous melatonin remain inadequately investigated. This study investigates systematic analysis of m6A‐regulatory gene families in rice. We identified a total of 124 genes, which include 7 writers, 22 readers, and 95 erasers. The distribution of these genes is uneven across the 11 chromosomes of the rice genome. Analysis of conserved domains revealed structural signatures that are specific to each gene family. Phylogenetic relationships with dicot and monocot species offered insights into evolutionary trajectories. Notably, gene structure and motif analyses revealed functional divergence within and between gene families. Cis‐element analysis identified abundance motifs associated with stress adaptation, hormonal signaling, and TFs, including ABRE, DRE, and MYB. Furthermore, synteny analysis unveiled both conserved regions and lineage‐specific expansions, particularly within the YTH and ALKBH families. The protein interaction network revealed robust connections among subgroups and identified 10 hub genes. GO and KEGG analyses indicated significant enrichment in stress‐related pathways, including secondary metabolite biosynthesis, flavonoid biosynthesis, and cysteine and methionine metabolism. RT‐qPCR validates that melatonin Osm6As significantly influences the expression of targeted genes, with melatonin upregulations exhibiting a time‐dependent pattern. Furthermore, GFP tagging of OsECT2 revealed that protoplasts are evenly distributed, suggesting robust nuclear enrichment of fluorescence. This study offers new insights into the epitranscriptomic regulatory responses of the m6A‐modifier.

Shanlan upland rice is a unique genetic resource from the mountainous regions of Hainan, China, yet its genetic diversity and agronomic potential remain poorly characterized. This study systematically evaluated 114 Shanlan upland rice landraces using phenotypic assessment and 38 genome-wide Insertion/Deletion (InDel) markers. Significant phenotypic variability was observed in key agronomic traits, including plant height, tiller number, and yield components. The molecular analysis revealed a moderate level of genetic diversity (average PIC = 0.43) and consistently grouped the landraces into three distinct genetic subpopulations. To facilitate efficient germplasm management, we developed a DNA fingerprinting system using a reduced set of 19 core InDel markers, which was integrated with a phenotypic QR code database. Furthermore, a network-based strategy identified a core collection of 54 accessions, streamlining the resource for future breeding and conservation efforts. These findings provide a robust molecular framework for the conservation and genetic improvement of Shanlan upland rice.

Background Although the role of the basic leucine zipper (bZIP) family of transcription factors in response to various abiotic stresses has been investigated, few studies have been conducted on their function in submergence stress. Results In this study, we localized a bZIP gene GmbZIP71-4 in the nucleus of soybean and constructed a GmbZIP71-4overexpressing tabocco line, which showed reduced submergence resistance due to the decreased abscisic acid (ABA) content. GO and KEGG pathway enrichment analysis based on chromatin immunoprecipitation assay sequencing (ChIP-seq) indicated that the most significant differences were the expression levels of the factors in plant hormone signal transduction, especially those in response to ABA. Electrophoretic Mobility Shift Assays (EMSA) demonstrated that GmbZIP71-4 bound to the promoter of GmABF2, which is consistent with the ChIP-qPCR result. Conclusions Our study showed that GmbZIP71-4 was a negative regulator of submergence stress tolerance. The findings in this work will set a solid foundation for the understanding of submergence resistance in plants.