Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and plays an important role in crop heterosis utilization. Circular RNAs (circRNAs) are a vital type of non-coding RNAs, which play crucial roles in microRNAs (miRNAs) function and post-transcription control. To explore the expression profile and possible functions of circRNAs in the soybean CMS line NJCMS1A and its maintainer NJCMS1B, high-throughput deep sequencing coupled with RNase R enrichment strategy was conducted. CircRNA libraries were constructed from flower buds of NJCMS1A and its maintainer NJCMS1B with three biological replicates. A total of 2867 circRNAs were identified, with 1009 circRNAs differentially expressed between NJCMS1A and NJCMS1B based on analysis of high-throughput sequencing. Of the 12 randomly selected circRNAs with different expression levels, 10 showed consistent expression patterns based on high-throughput sequencing and quantitative real-time PCR analyses. Tissue specific expression patterns were also verified with two circRNAs by quantitative real-time PCR. Most parental genes of differentially expressed circRNAs were mainly involved in biological processes such as metabolic process, biological regulation, and reproductive process. Moreover, 83 miRNAs were predicted from the differentially expressed circRNAs, some of which were strongly related to pollen development and male fertility; The functions of miRNA targets were analyzed using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG), and the target mRNAs were significantly enriched in signal transduction and programmed cell death. Furthermore, a total of 165 soybean circRNAs were predicted to contain at least one internal ribosome entry site (IRES) element and an open reading frame, indicating their potential to encode polypeptides or proteins. Our study indicated that the circRNAs might participate in the regulation of flower and pollen development, which could provide a new insight into the molecular mechanisms of CMS in soybean.

DNA methylation is an important epigenetic modification. It can regulate the expression of many key genes without changing the primary structure of the genomic DNA, and plays a vital role in the growth and development of the organism. The genome-wide DNA methylation profile of the cytoplasmic male sterile (CMS) line in soybean has not been reported so far. In this study, genome-wide comparative analysis of DNA methylation between soybean CMS line NJCMS5A and its maintainer NJCMS5B was conducted by whole-genome bisulfite sequencing. The results showed 3527 differentially methylated regions (DMRs) and 485 differentially methylated genes (DMGs), including 353 high-credible methylated genes, 56 methylated genes coding unknown protein and 76 novel methylated genes with no known function were identified. Among them, 25 DMRs were further validated that the genome-wide DNA methylation data were reliable through bisulfite treatment, and 9 DMRs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. Finally, 8 key DMGs possibly associated with soybean CMS were identified. Genome-wide DNA methylation profile of the soybean CMS line NJCMS5A and its maintainer NJCMS5B was obtained for the first time. Several specific DMGs which participated in pollen and flower development were further identified to be probably associated with soybean CMS. This study will contribute to further understanding of the molecular mechanism behind soybean CMS.

Sesbania cannabina (Retz.) Pers., as a legume, has strong waterlogging tolerance, but the lack of genomic information limits the exploration of key genes and molecular mechanisms. In this study, single-molecule real-time technology was used to sequence stems RNA of two Sesbania varieties at five time points under waterlogging stress through the PacBio Iso-Seq platform. The full-length transcriptome information contained 42 Gb raw data, 32,503 transcripts with an average length of 1912.28 nt, N50 length of 2059 nt and GC content of 42.69%. A total of 32,143 coding sequences (CDSs), 1745 transcription factors (TFs), 282 long non-coding RNAs (LncRNAs), 7497 simple sequence repeats (SSRs) and 202 alternative splicing (AS) events were identified through sequence alignment and software analysis. The analysis showed that 10,075 transcripts were enriched in 137 KEGG pathways, and 519 transcripts were included in plant hormone signal transduction, of which 103 and 123 transcripts were, respectively, involved in the ethylene and auxin pathways. The assembly and annotation of full-length transcriptome data of Sesbania provided reliable and accurate genomic information for the exploration of key genes and the study of molecular mechanisms in stem response to waterlogging stress.

Mitogen-Activated Protein Kinases (MAPKs) play crucial roles in plant stress signaling, but the mechanisms of MAPK genes in Portulaca oleracea remain functionally uncharacterized. In this study, transcriptomic screening of P. oleracea under salt stress identified PoMPK3 as a candidate gene, showing significant root-specific upregulation. Phylogenetic analysis classified it as a Group A MAPK protein, and subcellular localization confirmed its membrane association. Heterologous expression of PoMPK3 in Arabidopsis thaliana significantly enhanced salt tolerance, as evidenced by improved seed germination rates, longer primary roots, increased biomass, and reduced stress symptoms. Mechanistically, PoMPK3 expression activated ABA signaling, leading to increased ABA levels and upregulation of AtNCED3, AtPYR1, and AtABF3. Furthermore, it strengthened the antioxidant defense, as evidenced by elevated antioxidant enzyme activity, leading to a reduction in oxidative stress. The transgenic lines also demonstrated enhanced osmotic adjustment through osmolytes accumulation and ionic homeostasis, evidenced by tissue-specific Na⁺/K⁺ ratios (low in shoots, high in roots) resulting from the concerted upregulation of AtSOS1, AtNHX1, and AtHKT1. In addition, gene co-expression network analysis and molecular docking predicted phosphorylation of WRKY transcription factors, suggesting a novel mechanism for transcriptome reprogramming. Collectively, our findings not only advance the understanding of salt tolerance mechanisms in purslane but also identify PoMPK3 as a key genetic determinant, thereby laying the foundation for its use in breeding programs aimed at enhancing salt stress resilience in crops.

Saline–alkali land is a critical factor limiting agricultural production and ecological restoration. Utilizing salt-tolerant plants for bioremediation represents an environmentally friendly and sustainable approach to soil management. This study employed the highly salt-tolerant crop Portulaca oleracea L. cv. “Su Ma Chi Xian 3” as the test material. A plot experiment was established in coastal saline soils with planting P. a- oleracea (P) and no planting (CK) under three blocks with the different salt levels (S1: 2.16 g/kg; S2: 4.08 g/kg; S3: 5.43 g/kg) to systematically evaluate its salt accumulation capacity and effects on soil physicochemical properties. The results demonstrated that P. oleracea exhibited adaptability across all three salinity levels, with aboveground biomass following the trend PS2 > PS3 > PS1. The ash salt contents removed through harvesting were 1.29, 2.03, and 1.74 t/ha, respectively, in PS1, PS2, and PS3. Compared to no planting, a significant reduction in bulk density was observed in the 0–10 and 10–20 cm soil layers (p < 0.05). A significant increase in porosity by 9.72%, 16.29%, and 12.61% was found under PS1, PS2, and PS3, respectively, in the 0–10 cm soil layer. Soil salinity decreased by 34.20%, 50.23%, and 48.26%, in the 0–10 cm soil layer and by 14.43%, 32.30%, and 26.42% in the 10–20 cm soil layer under PS1, PS2, and PS3, respectively. The pH exhibited a significant reduction under the planting treatment in the 0–10 cm layer. A significant increase in organic matter content by 13.70%, 12.44%, and 13.55%, under PS1, PS2, and PS3, respectively, was observed in the 0–10 cm soil layer. The activities of invertase and urease were significantly enhanced in the 0–10 and 10–20 cm soil layers, and the activity of alkaline phosphatase also exhibited a significant increase in the 0–10 cm layer under the planting treatment. This study indicated that cultivating P. oleracea could effectively facilitate the improvement of coastal saline soils by optimizing soil structure, reducing salinity, increasing organic matter, and activating the soil enzyme system, thereby providing theoretical and technical foundations for ecological restoration and sustainable agricultural utilization of saline–alkali lands.