Identification of differentially expressed genes in salt-tolerant oilseed sunflower (Helianthus annuus L.) genotype by RNA sequencing

Genome-Wide-Association-Analysis-Based Identification of Genetic Loci and Candidate Genes Associated with Cold Germination in Sweet Corn

Sweet corn is highly susceptible to low temperatures, especially during seed germination, which severely affects plant growth and crop yield. This study used 100 sweet corn micro-core germplasms to evaluate two key germination traits under cold stress: seed storage material utilization efficiency (SRUE) and mobilization weight (WMSR). To investigate the genetic basis of cold germination in sweet corn, we selected the BLINK model for GWAS due to its ability to minimize false positives. A total of nine SNPs were found to be significantly associated with cold germination. These SNPs explained between 9.8% and 17.2% of the phenotypic variance (PVE). Within the confidence interval, 63 functionally annotated genes were identified. Fourteen candidate genes associated with cold germination were identified through GO functional analysis and the functional expression of homologous genes. A literature analysis indicated that these genes are primarily involved in seed germination, cold tolerance, and responses to other abiotic stresses. These findings enhance our understanding of the genetic and molecular mechanisms underlying cold germination, establishing a theoretical foundation for breeding cold-tolerant sweet corn varieties.

Identification of R2R3-MYB Gene Family and Functional Analysis of Responses of S22 Subfamily to Abiotic Stresses in Dandelion (Taraxacum mongolicum Hand.-Mazz.)

Dandelions possess a wide range of medicinal properties and demonstrate remarkable adaptability and tolerance to salinity and alkalinity. MYB genes in plants are implicated in growth, differentiation, metabolism, and responses to both biotic and abiotic stresses. The function of MYB genes in dandelions, particularly the R2R3-MYB gene family, requires further investigation. In this study, we identified a total of 130 members of the dandelion R2R3-MYB gene family at the genome-wide level, all of which were mapped to eight dandelion chromosomes. MEME analysis revealed that TmR2R3-MYB proteins contain three conserved motifs. Phylogenetic analysis categorized all TmR2R3-MYBs into 29 subfamilies. Transcriptomic studies in different tissues indicated that TmR2R3-MYBs exhibit distinct expression patterns in different tissues, indicating their diverse functions in dandelions. Notably, TmMYB44 from the S22 subfamily displayed the highest expression level in roots. Additionally, six representative TmR2R3-MYBs were selected from the S22 subfamily for expression profiling under salinity and alkalinity treatments. The results demonstrated that the TmR2R3-MYBs from the S22 subfamily are involved in the response to salinity and alkalinity stress. These findings provide a basis for further exploration of the functions of TmR2R3-MYBs in abiotic stress tolerance.

Integration of metabolomics and transcriptomics to reveal the mechanism of Gerberae piloselloidis herba in alleviating bronchial asthma

ETHNOPHARMACOLOGICAL RELEVANCE

Gerberae Piloselloides Herba (GPH) is derived from Gerbera piloselloides (Linn.) Cass. It is a commonly used traditional medicine in China, featured by its special bioactivities as antitussive, expectorant, anti-asthma, anti-bacterial and anti-tumor. It is often used as an effective treatment for cough and sore throat as well as bronchial asthma (BA) in China. It was demonstrated in our previous studies that GPH exerted significant effects on the treatment of BA, but its underlying mechanism remains unclear.

AIM OF THE STUDY

This study was aimed at revealing the mechanism through which GPH protects against BA.

MATERIALS AND METHODS

The protective effect of GPH against BA was evaluated in a mouse model of BA induced by ovalbumin. Through integrated metabolomics and transcriptomics analysis, the most critical pathways were discovered. The effects of GPH in regulating these pathways was verified through molecular biology experiments and molecular docking.

RESULTS

GPH have anti-BA effects. In plasma and lung tissue, 5 and 17 differentially expressed metabolites (DEMs), respectively, showed a reversed tendency in the GPH group compared with the model group; apart from gamma-aminobutyric acid and butyrylcarnitine, these DEMs might aid in BA diagnosis. The DEMs were involved primarily in the regulation of lipid metabolism, followed by glucose metabolism and amino acid metabolism. Transcriptomic analysis indicated that GPH modulated 268 differentially expressed genes (DEGs). Integration analysis of metabolomics and transcriptomics revealed that GPH might regulate the PPAR signaling pathway, thus affecting the expression of key gene targets such as Cyp4a12a, Cyp4a12b, Adh7, Acaa1b and Gpat2; controlling fatty acid degradation, unsaturated fatty acid biosynthesis, glycerophospholipid metabolism and other lipid metabolic pathways; and ameliorating BA. This possibility was confirmed through reverse-transcription quantitative polymerase chain reaction, western blotting, immunofluorescence and molecular docking.

CONCLUSION

GPH was found to activate the PPAR signaling pathway, decrease the levels of Cyp4a12a and Cyp4a12b, and increase the levels of Adh7, Acaa1b and Gpat2, thereby regulating lipid metabolism disorder, decreasing the generation of inflammatory mediators and limiting lung injury.

Physiology and transcriptomics highlight the underlying mechanism of sunflower responses to drought stress and rehydration

Drought can adversely influence the crop growth and production. Accordingly, sunflowers have strong adaptability to drought; hence, we conducted analyses for sunflower seedlings with drought stress and rehydration drought acclimation through physiological measurements and transcriptomics. It showed that drought can cause the accumulation of ROS and enhance the activity of antioxidant enzymes and the content of osmolytes. After rehydration, the contents of ROS and MDA were significantly reduced concomitant with increased antioxidant activity and osmotic adjustment. Totally, 2,589 DEGs were identified among treatments. Functional enrichment analysis showed that DEGs were mainly involved in plant hormone signal transduction, MAPK signaling, and biosynthesis of secondary metabolites. Comparison between differentially spliced genes and DEGs indicated that bHLH025, NAC53, and SINAT3 may be pivotal genes involved in sunflower drought resistance. Our results not only highlight the underlying mechanism of drought stress and rehydration in sunflower but also provide a theoretical basis for crop genetic breeding.

Structural and functional analysis of stress-inducible genes and their promoters selected from young oil palm (Elaeis guineensis) under salt stress

Background

Soil salinity is a problem in more than 100 countries across all continents. It is one of the abiotic stress that threatens agriculture the most, negatively affecting crops and reducing productivity. Transcriptomics is a technology applied to characterize the transcriptome in a cell, tissue, or organism at a given time via RNA-Seq, also known as full-transcriptome shotgun sequencing. This technology allows the identification of most genes expressed at a particular stage, and different isoforms are separated and transcript expression levels measured. Once determined by this technology, the expression profile of a gene must undergo validation by another, such as quantitative real-time PCR (qRT-PCR). This study aimed to select, annotate, and validate stress-inducible genes—and their promoters—differentially expressed in the leaves of oil palm (Elaeis guineensis) plants under saline stress.

Results

The transcriptome analysis led to the selection of 14 genes that underwent structural and functional annotation, besides having their expression validated using the qRT-PCR technique. When compared, the RNA-Seq and qRT-PCR profiles of those genes resulted in some inconsistencies. The structural and functional annotation analysis of proteins coded by the selected genes showed that some of them are orthologs of genes reported as conferring resistance to salinity in other species. There were those coding for proteins related to the transport of salt into and out of cells, transcriptional regulatory activity, and opening and closing of stomata. The annotation analysis performed on the promoter sequence revealed 22 distinct types of cis-acting elements, and 14 of them are known to be involved in abiotic stress.

Conclusion

This study has helped validate the process of an accurate selection of genes responsive to salt stress with a specific and predefined expression profile and their promoter sequence. Its results also can be used in molecular-genetics-assisted breeding programs. In addition, using the identified genes is a window of opportunity for strategies trying to relieve the damages arising from the salt stress in many glycophyte crops with economic importance.