Waterlogging stress significantly impacts the growth and productivity of crops. As a traditional oil crop, sesame (Sesamum indicum L.) suffers substantial damage due to waterlogging stress. However, the mechanism underlying waterlogging stress in sesame is still unclear. In this study, we investigated the physiological indicators of two sesame genotypes under waterlogging stress. The results revealed that the activity of antioxidant enzymes in sesame was affected, with the contents of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) significantly increased. Additionally, transcriptional analysis identified a total of 15,143 differentially expressed genes (DEGs). Among them, 759 DEGs exhibited consistent differential expression across all time points, representing the core waterlogging-responsive genes. Gene Ontology (GO) enrichment analysis indicated that the DEGs were primarily associated with hypoxia, stimulus response, and oxidoreductase enzyme activities. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that these DEGs were mainly enriched in the metabolic and biosynthesis of secondary metabolites, glycolysis/gluconeogenesis, phenylpropanoid biosynthesis, MAPK signaling pathway-plant, carbon fixation by Calvin cycle, plant hormone signal transduction, and plant-pathogen interaction pathways. Furthermore, transcription factors (TFs) such as AP2/ERF, bHLH, bZIP, and WRKY may play key roles in the transcriptional changes induced by waterlogging stress. Combined with weighted gene co-expression network analysis (WGCNA) analysis and K-means clustering, a total of 5 hub genes and 56 genes were identified, including F-box protein (Sin09950 and Sin12912), bZIP (Sin04465, Sin00091), WRKY (Sin01376, Sin06113), and so on. In brief, this study explored the regulatory network involved in waterlogging stress in sesame at the transcriptome level, providing valuable insights into unraveling the molecular mechanisms of waterlogging stress and facilitating the breeding of improved waterlogging-tolerant sesame varieties.

Acacia melanoxylon (blackwood) is a valuable wood with excellent-quality heartwood extensively utilized worldwide. The main aim of this study was to confirm the horizontal and vertical variation and provide estimated values of genetic gains and clonal repeatabilities for improving the breeding program of A. melanoxylon. Six blackwood clones at 10 years old were analyzed in Heyuan and Baise cities in China. Stem trunk analysis was conducted for sample trees to explore the differences between heartwood and sapwood. The heartwood radius (HR), heartwood area (HA), and heartwood volume (HV) in heartwood properties decreased as the tree height (H) in growth traits increased, and the HV = 1.2502 DBH (diameter at breast height)^1.7009 model can accurately estimate the heartwood volume. Furthermore, G × E analysis showed that the heritabilities of the eleven indices, including DBH, DGH (diameter at ground height), H, HR, SW (sapwood width), BT (bark thickness), HA, SA (sapwood area), HV, HRP (heartwood radius percentage), HAP (heartwood area percentage), and HVP (heartwood volume percentage) were between 0.94 and 0.99, and repeatabilities of the eleven indices were between 0.74 and 0.90. Clonal repeatability of DBH (0.88), DGH (0.88), and H (0.90) in growth traits and HR (0.90), HVP (0.90), and HV (0.88) in heartwood properties were slightly higher than for SA (0.74), SW (0.75), HAP (0.75), HRP (0.75), and HVP (0.75). These data also implied that the growth characteristics of heartwood and sapwood of blackwood clones were less affected by the environment and had substantial heritability.

Acacia mangium is well known as a valuable commercial tree species in the Acacia genus. A. mangium was recently found to be self-incompatible (SI), but its SI mechanism is not clear, which has hindered the progress of genetic improvement of A. mangium with strong resistance. To confirm the SI type of A. mangium, pollen germination was observed via fluorescence microscopy at 0 h, 3 h, 6 h, 9 h, 12 h, and 24 h after self-pollination. We found over ninety percent of the pollen grains produced no pollen tube growth on the stigma/style. To further explore the SI molecular mechanism of A. mangium, tests of the transcriptome and metabolome were carried out after self-pollination. Observations of pollen germination after self-pollination using fluorescence microscopy suggested that the SI type of A. mangium is gametophytic self-incompatibility (GSI). A combined transcriptomic and metabolomic analysis showed that DEGs (differentially expressed genes) related to SI (6 S-glycoproteins, 93 F-box proteins, 69 26S proteasomes, 38 calcium-dependent protein kinases/calmodulin and 41 thioredoxin genes) were significantly enriched in six KEGG (sulfur metabolism, tyrosine metabolism, phenylalanine metabolism, butanoate metabolism, and valine, leucine, and isoleucine degradation). Further analysis of these six pathways revealed the enrichment of SI-related DEGs corresponding to succinate, methylmalonate, and 3-hydroxypropane. These three metabolites were significantly downregulated. The analysis of transcripts and metabolites suggested that transcripts of SI-related gene families (thioredoxin and F-box protein) were significantly upregulated under the regulation of transcription factors (TFs) after self-pollination, leading to a decrease in metabolites (such as succinate, methylmalonate, and 3-hydroxypropionate). We also further speculated that TFs (MYB, HB-HD-ZIP, AP2/ERF-ERF, and bZIP) and gene families (thioredoxin and F-box protein) were important factors related to the SI of A. mangium.