Due to their immobility and possession of underground parts, plants have evolved various mechanisms to endure and adapt to abiotic stresses such as extreme temperatures, drought, and salinity. However, the contribution of long noncoding RNAs (lncRNAs) to different abiotic stresses and distinct rice seedling parts remains largely uncharacterized beyond the protein-coding gene (PCG) layer. Using transcriptomics and bioinformatics methods, we systematically identified lncRNAs and characterized their expression patterns in the roots and shoots of wild type (WT) and ososca1.1 (reduced hyperosmolality-induced [Ca²⁺]_i increase in rice) seedlings under hyperosmolarity and salt stresses. Here, 2937 candidate lncRNAs were identified in rice seedlings, with intergenic lncRNAs representing the largest category. Although the detectable sequence conservation of lncRNAs was low, we observed that lncRNAs had more orthologs within the Oryza. By comparing WT and ososca1.1, the transcription level of OsOSCA1.1-related lncRNAs in roots was greatly enhanced in the face of hyperosmolality stress. Regarding regulation mode, the co-expression network revealed connections between trans-regulated lncRNAs and their target PCGs related to OsOSCA1.1 and its mediation of hyperosmolality stress sensing. Interestingly, compared to PCGs, the expression of lncRNAs in roots was more sensitive to hyperosmolarity stress than to salt stress. Furthermore, OsOSCA1.1-related hyperosmolarity stress-responsive lncRNAs were enriched in roots, and their potential cis-regulated genes were associated with transcriptional regulation and signaling transduction. Not to be ignored, we identified a motif-conserved and hyperosmolarity stress-activated lncRNA gene (OSlncRNA), speculating on its origin and evolutionary history in Oryza. In summary, we provide a global perspective and a lncRNA resource to understand hyperosmolality stress sensing in rice roots, which helps to decode the complex molecular networks involved in plant sensing and adaptation to stressful environments.

Tibetan hulless barley (qingke) grains are becoming more popular because of their high nutritional benefits. Comparative metabolomics and proteomics analyses of qingke grains (at 16, 20, 36, and 42 days after flowering) were conducted to explore the metabolic dynamics during grain filling and compare the differences in quality among three different varieties, Dulihuang, Kunlun 14, and Heilaoya. A total of 728 metabolites and 4864 proteins were identified. We first found that both the metabolite and protein profiles were more closely associated with the grain developmental stage in each cultivar than across different stages in a single cultivar. Next, we focused on the energy metabolism and biosynthesis pathways of key quality components, such as flavonoids, starch, and β-glucans in qingke grains. Quantitative analysis revealed significant variation in the abundance of cellulose synthase-like enzyme (CslF) among the three cultivars. Notably, Heilaoya displayed substantially lower CslF6 levels at 36 and 42 DAF than Kunlun 14 and Dulihuang did. These observed differences in CslF6 abundance may represent a key regulatory mechanism underlying the distinct β-glucan biosynthesis patterns among the three cultivars. Collectively, our results enhance the understanding of metabolic networks involved in qingke grain development and serve as a foundation for advancing breeding studies.

LncRNAs, a type of RNAs exceeding 200 nucleotides (nt) and lacking representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth and development processes in plants. While substantial progress has been made in interpreting the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley remains incomplete. To elucidate the coordination of drought stress responses in Tibetan hulless barely by lncRNAs, we analyzed the previously published RNA-seq data from two cultivars of hulless barley, drought-tolerant (Z772) and drought-sensitive (Z013), subjected to varying durations of drought treatment (0, 1, and 5 h). Initially, we identified a total of 2877 lncRNAs through a strict pipeline, of which 2179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the trans-regulatory functions of lncRNAs, we utilized WGCNA and uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring PCGs were co-clustered in key control modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as TFs. Two of these pairs were validated by qRT-PCR in the Tibetan hulless barley cultivar Kunlun 14. These findings suggested that lncRNAs may participate in regulatory networks involved in drought adaptation in Tibetan hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties.

Long noncoding RNAs (lncRNAs), which are a type of RNA exceeding 200 nucleotides and lack representative open reading frames (ORFs), have emerged as crucial regulatory molecules that modulate numerous growth processes in plants. While substantial progress has been made in understanding the functions and regulatory mechanisms of coding RNAs, the study of lncRNAs in Tibetan hulless barley (Hordeum vulgare L. var. nudum) still remain incompletely understood. To elucidate the coordination of drought stress responses by long non-coding RNAs (lncRNAs), a study analyzed previously published RNA sequencing (RNA-seq) data from two cultivars of hulless barley, Z772 (drought-tolerant) and Z013 (drought-sensitive), subjected to varying durations of drought treatment (0, 1, and 5 h). The objective was to determine the expression profiles of long non-coding RNAs (lncRNAs) in hulless barley. Initially, we identified a total of 2,877 lncRNAs, of which 2,179 were co-expressed in both cultivars. Additionally, 331 and 367 lncRNAs showed cultivar-specific expression patterns in Z772 and Z013, respectively. Given the trans-regulatory functions of lncRNAs, we uncovered 11 modules that were enriched in drought-responsive pathways. Within these modules, lncRNAs and neighboring protein-coding genes (PCGs) were co-clustered in key regulatory modules. The GO enrichment analysis of potential lncRNA-PCG pairs primarily involved processes related to the response to water deprivation, regulation of abiotic stress, and RNA metabolic processes. Notably, 12 high-confidence lncRNA-PCG pairs displayed concordant expression profiles, with some annotated as acting as transcription factors (TFs). Two of these pairs were validated by qRT-PCR in the hulless barley cultivar Kunlun 14. These findings suggest that lncRNAs may participate in regulatory networks involved in drought adaptation in hulless barley, offering novel insights into the drought resistance mechanisms of Poaceae crops and potential targets for breeding drought-resistant varieties.