Identification and expression pattern analysis of the OsSnRK2 gene family in rice

Genome-Wide Identification, Evolutionary Analysis, and Functional Studies of APX Genes in Melon (Cucuis melo L.)

The antioxidative enzyme ascorbate peroxidase (APX) exerts a critically important function through scavenging reactive oxygen species (ROS), alleviating oxidative damage in plants, and enhancing their tolerance to salinity. Here, we identified 28 CmAPX genes that display an uneven distribution pattern throughout the 12 chromosomes of the melon genome by carrying out a bioinformatics analysis. Phylogenetic analyses revealed that the CmAPX gene family comprised seven different clades, with each clade of genes exhibiting comparable motifs and structures. We cloned 28 CmAPX genes to infer their encoded protein sequences; we then compared these sequences with proteins encoded by rice APX proteins (OsAPX2), Puccinellia tenuiflora APX proteins (PutAPX) and with pea APX proteins. We found that the CmAPX17, CmAPX24, and CmAPX27 genes in Clade I were closely related, and their structures were highly conserved. CmAPX27 (MELO3C020719.2.1) was found to promote resistance to 150 mM NaCl salt stress, according to quantitative real-time fluorescence PCR. Transcriptome data revealed that CmAPX27 was differentially expressed among tissues, and the observed differences in expression were significant. Virus-induced gene silencing of CmAPX27 significantly decreased salinity tolerance, and CmAPX27 exhibited differential expression in the leaf, stem, and root tissues of melon plants. This finding demonstrates that CmAPX27 exerts a key function in melon's tolerance to salt stress. Generally, CmAPX27 could be a target in molecular breeding efforts aimed at improving the salt tolerance of melon; further studies of CmAPX27 could unveil novel physiological mechanisms through which antioxidant enzymes mitigate the deleterious effects of ROS stress.

A transposon-derived gene family regulates heading date in rice

As a consequence of transposon domestication, transposon-derived proteins often acquire important biological functions. However, there have been limited studies on transposon-derived proteins in rice, and a systematic analysis of transposon-derived genes is lacking. Here, for the first time, we conducted a comprehensive analysis of the DDE_Tnp_4 (DDE) gene family, which originated from transposons but lost their transpositional ability and acquired new gene functions in Oryza species. A total of 58 DDE family genes, categorized into six groups, were identified in Oryza species, including 13 OsDDE genes in Oryza sativa ssp. japonica. Our analysis indicates that gene duplication events were not the primary mechanism behind the expansion of OsDDE genes in rice. Promoter cis-element analysis combined with haplotype analysis confirmed that OsDDEs regulate the heading date in rice. Specifically, OsDDE9 is a nuclear-localized protein expressed ubiquitously, which promotes heading date by regulating the expression of Ghd7 and Ehd1 under both short-day and long-day conditions. Single-nucleotide polymorphism (SNP) variations in the OsDDE9 promoter leads to changes in promoter activity, resulting in variations in heading dates. This study provides valuable insights into the molecular function and mechanism of the OsDDE genes.

Characterization and expression analysis of SnRK2, PYL, and ABF/ AREB/ ABI5 gene families in sweet potato

Abscisic acid (ABA) signaling in plants is essential to several aspects of plant development, such as tolerance to environmental stresses and growth. ABA signaling is also important for storage organ formation in crops, such as sweet potato. However, the repertoire of I. batatas ABA signaling gene families has not yet been fully characterized, so that it is unclear which members of these families are necessary for tuberization. Therefore, genome-wide identification of the sweet potato ABF/ AREB/ ABI5, SnRK2, and PYL gene families was performed, along with phylogenetic, motif, cis-regulatory element (CRE), and expression analyses. Nine ABF, eight SnRK2, and eleven PYL gene family members were identified, and there was high sequence conservation among these proteins that were revealed by phylogenetic and motif analyses. The promoter sequences of these genes had multiple CREs that were involved in hormone responses and stress responses. In silico and qRT-PCR expression analyses revealed that these genes were expressed in various tissues and that IbABF3, IbABF4, IbDPBF3, IbDPBF4, IbPYL4, IbSnRK2.1, and IbSnRK2.2 were significantly expressed during storage root development. These results are an important reference that can be used for functional validation studies to better understand how ABA signaling elicits storage root formation at the molecular level.

The rice SnRK family: biological roles and cell signaling modules

Stimulus-activated signaling pathways orchestrate cellular responses to control plant growth and development and mitigate the effects of adverse environmental conditions. During this process, signaling components are modulated by central regulators of various signal transduction pathways. Protein phosphorylation by kinases is one of the most important events transmitting signals downstream, via the posttranslational modification of signaling components. The plant serine and threonine kinase SNF1-related protein kinase (SnRK) family, which is classified into three subgroups, is highly conserved in plants. SnRKs participate in a wide range of signaling pathways and control cellular processes including plant growth and development and responses to abiotic and biotic stress. Recent notable discoveries have increased our understanding of how SnRKs control these various processes in rice (Oryza sativa). In this review, we summarize current knowledge of the roles of OsSnRK signaling pathways in plant growth, development, and stress responses and discuss recent insights. This review lays the foundation for further studies on SnRK signal transduction and for developing strategies to enhance stress tolerance in plants.

Identification of CmACL genes in melon and analysis of their potential functions in fruit sugar and acid accumulation

Citric acid is the most important organic acid in melon and has a great influence on fruit flavor quality. ATP-citrate (pro-S) lyase (ACL) is a key regulator in the acetyl-CoA pathway and plays an important role in citric acid metabolism. In this study we analyzed the structure and phylogenetics of CmACL genes and their functions in sugar and acid accumulation in melon. A total of four CmACL genes were identified in the melon genome, and phylogenetic analysis assigned these genes into the α subfamily (CmACLα1 and CmACLα2) and the β subfamily (CmACLβ1 and CmACLβ2). Conserved motif and gene structure analyses showed that members of the same subfamily shared identical conserved motifs and gene structures, and probably have similar biological functions. Analysis of cis-acting elements revealed that CmACL promoter sequences contained regulatory elements related to light, stress, phytohormones, and growth and development, indicating that CmACL genes may be involved in melon growth and stress responses. The prediction of protein interaction network showed that CmACL proteins were closely related to the proteins belonging to tricarboxylic acid cycle, glyoxylic acid cycle and glycolytic pathway, suggesting that CmACL proteins may play an important role in sugar and acid metabolism. The expression of CmACLβ1 was significantly and positively correlated with sucrose content, and CmACLβ2 expression was significantly positively correlated with citric acid content, suggesting that CmACLβ1 and CmACLβ2 have important roles in sugar and acid accumulation in melon. Our results offer novel insights and avenues for the regulation of sugar and acid levels in melon and provide a theoretical foundation for breeding high-quality melon cultivars.