Response of salt stress resistance in highland barley (Hordeum vulgare L. var. nudum) through phenylpropane metabolic pathway
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SUBMITTER: Xue Z
PROVIDER: S-EPMC10547159 | biostudies-literature | 2023 Jan
REPOSITORIES: biostudies-literature
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Project description:BackgroundThe harsh environment on the Qinghai-Tibetan Plateau gives Tibetan hulless barley (Hordeum vulgare var. nudum) great ability to resist adversities such as drought, salinity, and low temperature, and makes it a good subject for the analysis of drought tolerance mechanism. To elucidate the specific gene networks and pathways that contribute to its drought tolerance, and for identifying new candidate genes for breeding purposes, we performed a transcriptomic analysis using two accessions of Tibetan hulless barley, namely Z772 (drought-tolerant) and Z013 (drought-sensitive).ResultsThere were more up-regulated genes of Z772 than Z013 under both mild (5439-VS-2604) and severe (7203-VS-3359) dehydration treatments. Under mild dehydration stress, the pathways exclusively enriched in drought-tolerance genotype Z772 included Protein processing in endoplasmic reticulum, tricarboxylic acid (TCA) cycle, Wax biosynthesis, and Spliceosome. Under severe dehydration stress, the pathways that were mainly enriched in Z772 included Carbon fixation in photosynthetic organisms, Pyruvate metabolism, Porphyrin and chlorophyll metabolism. The main differentially expressed genes (DEGs) in response to dehydration stress and genes whose expression was different between tolerant and sensitive genotypes were presented in this study, respectively. The candidate genes for drought tolerance were selected based on their expression patterns.ConclusionsThe RNA-Seq data obtained in this study provided an initial overview on global gene expression patterns and networks that related to dehydration shock in Tibetan hulless barley. Furthermore, these data provided pathways and a targeted set of candidate genes that might be essential for deep analyzing the molecular mechanisms of plant tolerance to drought stress.
| S-EPMC5637072 | biostudies-literature
Project description:BackgroundHulless barley is attracting increasing attention due to its unique nutritional value and potential health benefits. However, the molecular biology of the barley grain development and nutrient storage are not well understood. Furthermore, the genetic potential of hulless barley has not been fully tapped for breeding.Methodology/principal findingsIn the present study, we investigated the transcriptome features during hulless barley grain development. Using Illumina paired-end RNA-Sequencing, we generated two data sets of the developing grain transcriptomes from two hulless barley landraces. A total of 13.1 and 12.9 million paired-end reads with lengths of 90 bp were generated from the two varieties and were assembled to 48,863 and 45,788 unigenes, respectively. A combined dataset of 46,485 All-Unigenes were generated from two transcriptomes with an average length of 542 bp, and 36,278 among were annotated with gene descriptions, conserved protein domains or gene ontology terms. Furthermore, sequences and expression levels of genes related to the biosynthesis of storage reserve compounds (starch, protein, and β-glucan) were analyzed, and their temporal and spatial patterns were deduced from the transcriptome data of cultivated barley Morex.Conclusions/significanceWe established a sequences and functional annotation integrated database and examined the expression profiles of the developing grains of Tibetan hulless barley. The characterization of genes encoding storage proteins and enzymes of starch synthesis and (1-3;1-4)-β-D-glucan synthesis provided an overview of changes in gene expression associated with grain nutrition and health properties. Furthermore, the characterization of these genes provides a gene reservoir, which helps in quality improvement of hulless barley.
| S-EPMC4037191 | biostudies-literature
Project description: Not available
| S-EPMC11241897 | biostudies-literature
Project description:BackgroundColored barley, which may have associated human health benefits, is more desirable than the standard white variety, but the metabolites and molecular mechanisms underlying seedcoat coloration remain unclear.ResultsHere, the development of Tibetan hulless barley was monitored, and 18 biological samples at 3 seedcoat color developmental stages were analyzed by transcriptomic and metabolic assays in Nierumuzha (purple) and Kunlun10 (white). A total of 41 anthocyanin compounds and 4186 DEGs were identified. Then we constructed the proanthocyanin-anthocyanin biosynthesis pathway of Tibetan hulless barley, including 19 genes encoding structural enzymes in 12 classes (PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, DFR, ANS, ANR, GT, and ACT). 11 DEGs other than ANR were significantly upregulated in Nierumuzha as compared to Kunlun10, leading to high levels of 15 anthocyanin compounds in this variety (more than 25 times greater than the contents in Kunlun10). ANR was significantly upregulated in Kunlun10 as compared to Nierumuzha, resulting in higher contents of three anthocyanins compounds (more than 5 times greater than the contents in Nierumuzha). In addition, 22 TFs, including MYBs, bHLHs, NACs, bZips, and WD40s, were significantly positively or negatively correlated with the expression patterns of the structural genes. Moreover, comparisons of homologous gene sequences between the two varieties identified 61 putative SNPs in 13 of 19 structural genes. A nonsense mutation was identified in the coding sequence of the ANS gene in Kunlun10. This mutation might encode a nonfunctional protein, further reducing anthocyanin accumulation in Kunlun10. Then we identified 3 modules were highly specific to the Nierumuzha (purple) using WGCNA. Moreover, 12 DEGs appeared both in the putative proanthocyanin-anthocyanin biosynthesis pathway and the protein co-expression network were obtained and verified.ConclusionOur study constructed the proanthocyanin-anthocyanin biosynthesis pathway of Tibetan hulless barley. A series of compounds, structural genes and TFs responsible for the differences between purple and white hulless barley were obtained in this pathway. Our study improves the understanding of the molecular mechanisms of anthocyanin accumulation and biosynthesis in barley seeds. It provides new targets for the genetic improvement of anthocyanin content and a framework for improving the nutritional quality of barley.
| S-EPMC9351122 | biostudies-literature
Project description:Highland barley Transcriptome
| PRJNA527673 | ENA
Project description:highland barley microRNA-seq
| PRJNA553630 | ENA
Project description:huless barley Raw sequence reads
| PRJNA675977 | ENA
Project description:Plants show varied cellular responses to salinity that are partly associated with maintaining low cytosolic Na(+) levels and a high K(+)/Na(+) ratio. Plant metabolites change with elevated Na(+), some changes are likely to help restore osmotic balance while others protect Na(+)-sensitive proteins. Metabolic responses to salt stress are described for two barley (Hordeum vulgare L.) cultivars, Sahara and Clipper, which differed in salinity tolerance under the experimental conditions used. After 3 weeks of salt treatment, Clipper ceased growing whereas Sahara resumed growth similar to the control plants. Compared with Clipper, Sahara had significantly higher leaf Na(+) levels and less leaf necrosis, suggesting they are more tolerant to accumulated Na(+). Metabolite changes in response to the salt treatment also differed between the two cultivars. Clipper plants had elevated levels of amino acids, including proline and GABA, and the polyamine putrescine, consistent with earlier suggestions that such accumulation may be correlated with slower growth and/or leaf necrosis rather than being an adaptive response to salinity. It is suggested that these metabolites may be an indicator of general cellular damage in plants. By contrast, in the more tolerant Sahara plants, the levels of the hexose phosphates, TCA cycle intermediates, and metabolites involved in cellular protection increased in response to salt. These solutes remain unchanged in the more sensitive Clipper plants. It is proposed that these responses in the more tolerant Sahara are involved in cellular protection in the leaves and are involved in the tolerance of Sahara leaves to high Na(+).
| S-EPMC2755029 | biostudies-literature
Project description:The phenolic profiles, hypoglycemic activity, and molecular mechanism of the effect on type 2 diabetes mellitus (T2DM) of four highland barley varieties were investigated in the present study. The fundamental phenolics in highland barley were ferulic acid, naringin, and catechin, which mainly existed in bound form. These varieties showed favorable hypoglycemic activity via inhibition of α-glucosidase and α-amylase activities, enhancement of glucose consumption, glycogen accumulation and glycogen synthase 2 (GYS2) activity, and down-regulation of glucose-6-phosphatase (G6Pase) and phosphoenolpyruvate carboxykinase (PEPCK) activities. Specifically, ZQ320 variety exhibited the strongest hypoglycemic activity compared to the other varieties. Highland barley phenolics could inhibit gluconeogenesis and motivate glycogen synthesis via down-regulating the gene expression of G6Pase, PEPCK, and glycogen synthase kinase 3β (GSK3β), while activating the expression of insulin receptor substrate-1 (IRS-1), phosphatidylinositol 3 kinase (PI3K), serine/threonine kinase (Akt), GYS2, and glucose transporter type 4 (GLUT4). Therefore, phenolics from highland barley could be served as suitable candidates for therapeutic agent in T2DM to improve human health.
| S-EPMC7072826 | biostudies-literature
Project description:Gene expression in plastids of higher plants is dependent on two different transcription machineries, a plastid-encoded bacterial-type RNA polymerase (PEP) and a nuclear-encoded phage-type RNA polymerase (NEP), which recognize distinct types of promoters. The division of labor between PEP and NEP during plastid development and in mature chloroplasts is unclear due to a lack of comprehensive information on promoter usage. Here we present a thorough investigation into the distribution of PEP and NEP promoters within the plastid genome of barley (Hordeum vulgare L). Using a novel differential RNA sequencing approach, which discriminates between primary and processed transcripts, we obtained a genome-wide map of transcription start sites in plastids of mature first leaves. PEP-lacking plastids of the albostrians mutant allowed for the unambiguous identifications of NEP promoters. We observed that the chloroplast genome contains many more promoters than genes. According to our data, most genes (including genes coding for photosynthesis proteins) have both PEP and NEP promoters. We also detected numerous transcription start sites within operons indicating transcriptional uncoupling of genes in polycistronic gene clusters. Moreover, we mapped many transcription start sites in intergenic regions, as well as opposite to annotated genes demonstrating the existence of numerous non-coding RNA candidates.
2011-11-23 | GSE33773 | GEO