Background: Waterlogging stress (WS) negatively impacts crop growth and productivity, making it important to understand crop resistance processes and discover useful WS resistance genes. In this study, rye cultivars and wild rye species were subjected to 12-day WS treatment, and the cultivar Secale cereale L. Imperil showed higher tolerance. Whole transcriptome sequencing was performed on this cultivar to identify differentially expressed (DE) messenger RNAs (DE-mRNAs) and long non-coding RNAs (DE-lncRNAs) involved in WS response. Results: Among the 6 species, Secale cereale L. Imperil showed higher tolerance than wild rye species against WS. The cultivar effectively mitigated oxidative stress, and regulated hydrogen peroxide and superoxide anion. A total of 728 DE-mRNAs and 60 DE-lncRNAs were discovered. Among these, 318 DE-mRNAs and 32 DE-lncRNAs were upregulated, and 410 DE-mRNAs and 28 DE-lncRNAs were downregulated. GO enrichment analysis discovered metabolic processes, cellular processes, and single-organism processes as enriched biological processes (BP). For cellular components (CC), the enriched terms were membrane, membrane part, cell, and cell part. Enriched molecular functions (MF) terms were catalytic activity, binding, and transporter activity. LncRNA and mRNA regulatory processes were mainly related to MAPK signaling pathway-plant, plant hormone signal transduction, phenylpropanoid biosynthesis, anthocyanin biosynthesis, glutathione metabolism, ubiquitin-mediated proteolysis, ABC transporter, Cytochrome b6/f complex, secondary metabolite biosynthesis, and carotenoid biosynthesis pathways. The signalling of ethylene-related pathways was not mainly dependent on AP2/ERF and WRKY transcription factors (TF), but on other factors. Photosynthetic activity was active, and carotenoid levels increased in rye under WS. Sphingolipids, the cytochrome b6/f complex, and glutamate are involved in rye WS response. Sucrose transportation was not significantly inhibited, and sucrose breakdown occurs in rye under WS. Conclusions: This study investigated the expression levels and regulatory functions of mRNAs and lncRNAs in 12-day waterlogged rye seedlings. The findings shed light on the genes that play a significant role in rye ability to withstand WS. The findings from this study will serve as a foundation for further investigations into the mRNA and lncRNA WS responses in rye.

Glutaredoxins (GRXs) are widely distributed oxidoreductase enzymes that play important roles in plant growth, development, and responses to various stresses. In this study, bioinformatics methods were used to identify and analyze the wheat GRX gene family and predict their properties and potential functions. RNA-seq and RT-qPCR expression analyses were used to investigate their regulatory functions under hormone treatment and fungal diseases. In this study, 86 GRX genes were identified in wheat and classified into CC-type, CGFS-type, and CPYC-type categories with no TaGRX located on chromosome 4B. The results show that TaGRXs regulate wheat transcriptional responses and have an integrative role in biotic and abiotic stress responses. TaGRXs are involved in wheat responses to Fusarium graminearum, Puccinia striiformis, and Erysiphe graminis diseases. TaGRX73-7D, TaGRX20-3A, and TaGRX29-3B play a negative regulatory role in E. graminis infection but a positive regulatory role in F. graminearum and P. striiformis infection. These TaGRXs play potential regulatory functions in wheat responses to the plant hormones and signaling molecules, including IAA, ABA, H₂O₂, and SA. The findings of this study lay the groundwork for further investigation of the functions of wheat GRX genes and their potential use as candidate genes for molecular breeding of stress-resistant wheat varieties.

Acetolactate synthase (ALS) is an important enzyme in plant branched-chain amino acid biosynthesis and the target of several major herbicide classes. Despite its agronomic importance, the role of ALS genes in stress adaptation in the invasive weed Amaranthus palmeri remains unstudied. In this study, four ApALS genes with high motif conservation were identified and analyzed in A. palmeri. Phylogenetic analysis classified ApALS and other plant ALS proteins into two distinct clades, and the ApALS proteins were predicted to localize to the chloroplast. Gene expression analysis demonstrated that ApALS genes are responsive to multiple stresses, including salt, heat, osmotic stress, glufosinate ammonium, and the ALS-inhibiting herbicide imazethapyr, suggesting roles in both early and late stress responses. Herbicide response analysis using an Arabidopsis thaliana ALS mutant (AT3G48560) revealed enhanced imazethapyr resistance, associated with higher chlorophyll retention. Furthermore, high sequence homology between AT3G48560 and ApALS1 suggests a conserved role in protecting photosynthetic function during herbicide stress. This study provides the first comprehensive analysis of the ALS gene family in A. palmeri and offers important insights into its contribution to stress resilience. These findings establish a vital foundation for developing novel strategies to control this pervasive agricultural weed and present potential genetic targets for engineering herbicide tolerance in crops.

Amaranthus palmeri is an aggressive, highly invasive weed that thrives across a wide range of adverse environments worldwide; nevertheless, the mechanisms underlying its rapid expansion remain largely unstudied. Glutathione peroxidase (GPX) is a crucial enzyme within the antioxidant defense system, belonging to the phylogenetic conserved family of oxidoreductases present in all living organisms. Despite its significance, the role of GPX in A. palmeri has not been reported. This study identified eight GPX genes (ApGPXs) in A. palmeri through comprehensive bioinformatics and gene expression analyses. The research examined the characteristics, evolutionary relationships, chromosomal mapping, gene structure, subcellular localization, conserved motifs, and cis-acting elements of these genes, as well as their evolutionary conserved functions in relation to Arabidopsis thaliana GPXs and RT-qPCR analysis under various stress conditions. The ApGPXs were distributed across scaffolds (2, 4, and 12) of the A. palmeri genome. Phylogenetic analysis grouped GPX genes into four subgroups, and conserved motifs were found within certain phylogenetic subgroups. We identified Actin8 as the most stable internal reference gene for A. palmeri under diverse stress conditions. Gene expression analysis revealed that ApGPXs participate in both early and late regulatory responses to oxidative stress induced by NaCl, high temperature, osmotic pressure, and glufosinate ammonium. The Arabidopsis GPX mutant (AT4G31870) exhibited a stronger flg22-induced oxidative burst than the wild type, and qPCR confirmed that AtGPXs contribute significantly to glufosinate ammonium stress responses. Evolutionary analysis found high sequence similarity between ApGPX4 and AT1G63460, as well as ApGPX3 and AT4G11600. Also, ApGPX3 and AT4G11600 shared similar expression patterns under glufosinate ammonium stress. This research presents the first gene family study in A. palmeri and provides foundational insights for future studies in this economically critical species. Our findings establish a framework for mitigating A. palmeri’s impact on crop production and exploring ApGPXs in developing herbicide- and stress-tolerant cultivars.

High temperature attributed to climate change is a major obstacle to rice production. This study examined how alternate wetting and drying (AWD) irrigation can mitigate the effects of high temperatures on rice production. Three indica rice cultivars-Ye Xiang You You Si (YXYYS), Jing Zhan 1 (JZ1), and Qing Xiang You Yi 19 (QXYY19)-with varying heat susceptibility levels were used to analyse the impact of AWD on spikelet fertility, grain traits, and the biosynthesis of 2-acetyl-1-pyrroline (2-AP) from heading to harvest in rice grown under high temperature. The findings revealed that AWD significantly reduced spikelet fertility in all cultivars, but its effect on spikelet fertility depends on the heat susceptibility level of each cultivar. AWD alleviated the negative effect of high temperature on the biosynthesis of 2-AP and increased 2-AP content in leaves and grains of rice. This study also provided new insights on the effect of starch granules and brown rice grain width on chalkiness and demonstrated that starch granule arrangement and airspaces-not starch granule size-as well as brown rice grain width influenced chalkiness in rice. It also revealed that rice husk affected grain shape. Cooked rice elongation and rice whiteness were significantly increased by AWD, but it reduced the seed germination rate. This study presents a roadmap for the improvement of spikelet fertility in rice grown under high temperature. It also presents a simplified and cost-effective means to further increase the biosynthesis of 2-AP, proffered solutions for the reduction of chalkiness, and proposed methods for the improvement of grain shape by targeting genes, quantitative trait loci (QTLs), and signalling pathways associated with those traits in rice.