Hordeum vulgare strain:landrace Transcriptome or Gene expression
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 2000
ORGANISM(S): Hordeum vulgare
SUBMITTER: Yu Maoqun
PROVIDER: E-MTAB-4307 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Transcriptome assembly and analysis of Tibetan Hulless Barley (Hordeum vulgare L. var. nudum) developing grains, with emphasis on quality properties.
Chen Xin X Long Hai H Gao Ping P Deng Guangbing G Pan Zhifen Z Liang Junjun J Tang Yawei Y Tashi Nyima N Yu Maoqun M
PloS one 20140528 5
<h4>Background</h4>Hulless 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.<h4>Methodology/principal findings</h4>In the present study, we investigated the transcriptome features during hulless barley grain development. Using Illumina pai ...[more]
Similar Datasets
Project description:We hypothesized that the genome segments of cultivated barley should show certain similarity with its ancestral wild barley. Instead of whole genome sequences, we employed RNA-Seq to investigated the genomic origin of modern cultivated barley using some representative wild barley genotypes from the Near East and Tibet, and representative world-wide selections of cultivated barley.
2014-10-06 | E-MTAB-4221 | biostudies-arrayexpress
Project description:In the current study, we characterized an miRNA, OsmiR397, which was found to be associated with increased grain size, more rice panicle branching and higher grain productivity. We also elucidated the molecular mechanisms by which OsmiR397 increased grain yield. This miRNA downregulated the expression of its target gene, OsLAC, which then affected the sensitivity of plants to brassinosteroids. These results should be useful for breeding high-yield crops through genetic engineering. We performed RNA-seq on the young panicles of the wild-type, OXmiR397b and OXLAC plants and found that lots of brassinosteroid-related genes were differentially expressed between the three samples
2013-07-17 | E-MTAB-4429 | biostudies-arrayexpress
Project description:The timing of reproductive development determines spike architecture and thus yield in temperate grasses such as barley (Hordeum vulgare L.). Reproductive development in barley is controlled by the photoperiod response gene Ppd-H1 which accelerates flowering time under long-day (LD) conditions. A natural mutation in Ppd-H1 prevalent in spring barley causes a reduced photoperiod response, and thus, late flowering under LD. However, it is not very well understood how LD and Ppd-H1 control pre-anthesis development, and thus spike architecture and yield in barley. We performed a detailed morphological analysis of the pre-anthesis development in the spring barley cultivar Scarlett and its wild barley derived introgression line S42-IL107, carrying the photoperiod responsive Ppd-H1 allele. Characterization of shoot apex development in these genotypes indicated that floral transition and initiation of floral primordia occurred under LD (16h light/ 8h dark) and short day (SD, 8h light/ 16h dark) conditions, while inflorescence and seed development strictly required LDs. Additionally, a fast photoperiod response in the presence of the dominant Ppd-H1 allele promoted floret fertility under LDs. To characterize the effects of the photoperiod and allelic variation at Ppd-H1 on gene expression during pre-anthesis development we performed RNA sequencing of leaves and developing main shoot apices during the vegetative phase and early stages of inflorescence development in Scarlett and S42-IL107 grown under SD and LD conditions. Main shoot apices of both genotypes were sampled at defined developmental stages, i.e. Waddington stage W0.5, W1.0, W2.0 and W3.5, respectively. Leaf samples were harvested from plants before (W1.0) and after floral transition (W2.0). We identified genes that were specifically regulated at floral transition independent of day-length and Ppd-H1 and thus may serve as markers for the staging of floral transition. Furthermore, we identified transcripts differentially expressed between photoperiods and between genotypes in leaves and in shoot apices. This set of transcripts might act as candidates downstream of Ppd-H1 and are correlated with the promotion of shoot apex development and higher floret fertility under LD and in the presence of the photoperiod responsive Ppd-H1 allele.
2015-03-10 | E-MTAB-4114 | biostudies-arrayexpress
Project description:We analyzed the transcriptome profiles for rice grain from heat-tolerant and -sensitive lines in response to high night temperatures at the early milky stage using the Illumina Sequencing method. On the 8th day after the labeled florets flowered, plants with the same label were transferred to chambers and maintained at a temperature of 38.0â±â0.5°C (treatment) or 25.0â±â0.5°C (control) for the dark period (10 h), and 26.0â±â0.5°C (both treatment and control) for the light period (14 h). Three biological replicates of the temperature treatments were grown under the same conditions. After 48 h of treatment, samples containing 45 grains with labels from the same region (middle to bottom part) of labelled ears were harvested, packed in aluminum foil, and flash-frozen in liquid nitrogen until further use. A total of 12 rice grain samples were harvested, i.e., controls (TC1, TC2 and TC3) and treatments (TT1, TT2 and TT3) of the three biological replicates of the heat-tolerant line, and controls (SC1, SC2 and SC3) and treatments (ST1, ST2 and ST3) of the three biological replicates of the heat-sensitive line.
2014-12-01 | E-MTAB-4348 | biostudies-arrayexpress
Project description:To study the expression profiles of hexaploid wheat chromosome 3B genes during the life cycle of a wheat plant and establish a transcriptome atlas for this chromosome, deep transcriptome sequencing was conducted in duplicates in 15 wheat samples corresponding to five different organs (leaf, shoot, root, spike, and grain) at three developmental stages each. Strand-non-specific and strand-specific libraries were used to produce 2.52 billion paired-end reads (232 Gb) and 615.3 single-end reads (62 Gb), respectively.
2014-09-08 | E-MTAB-4484 | biostudies-arrayexpress
Project description:The concurrent epigenetic changes during this period of remarkable improvement in maize grain yield remain unknown. Here, we performed MethylC-seq and RNA-seq on 4 related inbred lines with known pedigree information. Analysis of epigenetic changes over the course of historical maize breeding is a valuable new avenue in the exploration for crop improvement. These data lead us to suggest that novel epihaplotypes, in addition to DNA variation, are a substrate of selection during breeding, and that epigenetic variation between parents may also contribute to heterosis in hybrids. Xie, S; et al. 2013. Maize Genetics Conference Abstracts. 54:P326
2015-06-01 | E-MTAB-4238 | biostudies-arrayexpress
Project description:A biological phenomenon in which hybrids exhibit superior phenotypes from its parental inbred lines known as heterosis, has been widely exploited in plant breeding and extensively used in crop improvement. Hybrid rice has immense potential to increase yield over other rice varieties and hence is crucial in meeting increasing demand of rice globally. Moreover, the molecular basis of heterosis is still not fully understood and hence it becomes imperative to unravel its genetic and molecular basis. In this context, RNA sequencing technology (RNA-Seq) was employed to sequence transcriptomes of two rice hybrids, Ajay and Rajalaxmi, their parental lines, CRMS31A (sterile line, based on WA-CMS) and CRMS32A (sterile line based on Kalinga-CMS) respectively along with the common restorer line of both hybrids, IR-42266-29-3R at two critical rice developmental stages viz., panicle initiation (PI) and grain filling (GF). Identification of differentially expressed genes (DEGs) at PI and GF stages will further pave the way for understanding heterosis. In addition, such kind of study would help in better understanding of heterosis mechanism and genes up-regulated and down-regulated during the critical stages of rice development for higher yield.
2015-08-02 | E-MTAB-4291 | biostudies-arrayexpress
Project description:Phosphorus (P) is an essential macronutrient for plant growth and development, and a plant must balance P uptake, mobilisation, and partitioning to various organs to modulate P homeostasis. The underlying molecular mechanisms of wheat under phosphate (Pi) starvation conditions remain elusive despite wheat is an important cultivated food crop worldwide. We generated transcriptome profiles of wheat variety Chinese Spring (CS) in response to Pi starvation (-P) for 10 days using RNA-Seq methods.We used 73.8 million high-quality reads obtained from libraries for de novo assembly. Overall, a set containing 29,617 non-redundant wheat transcripts was constructed with 15,047 assemblies and 14,570 non-redundant, full-length cDNAs in TriFLDB. Of the transcripts, 10,656 of the 15,047 assemblies were unaligned against barley full-length cDNAs, suggesting that many of them might be distinct of barley transcripts. The distribution of average expression levels for the assembly was lower than that for cDNAs, suggesting that the assemblies contained rare transcripts limited availability using full-length cDNA library construction methods. Within the transcript set, we identified 892-2,833 up- or downregulated transcripts in root and shoot, including 18.9-40.5% assemblies, uncovered by cDNAs in TriFLDB under -P in each condition. In the results, the expression level of wheat IPS1 (induced by phosphate starvation 1) homolog, TaIPS1, was 358.6-fold higher in the root and 12.6-fold higher in the shoot, which was confirmed by qRT-PCR analysis. Comparative analysis between wheat (a rice orthologue) and rice responsive transcripts under -P conditions showed that 39 (root) and 21 (shoot) responsive transcripts were commonly upregulated, and most of them seemed to be involved in a general response to -P; IPS1-mediated signal transduction and its downstream function such as Pi remobilization, Pi uptake and change metabolism.Our transcriptome profiling demonstrates the impact of -P in wheat. This study shows that enhancing the Pi-mediated signalling pathway through IPS1 is conserved as a potent adaptation to Pi starvation in both wheat and rice, and also that our constructed strategy using short read next generation sequencing (NGS) data was successful for the transcriptome analysis in wheat without reference genome. Note: Samples in SRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2014-04-22 | E-MTAB-4245 | biostudies-arrayexpress
Project description:We generated multiple NILs segregating for the 4A-1 QTL following a method based on HIFs analysis. Five F7 RILs from the mapping population were chosen as founders of HIFs on the basis of being heterozygote for the 4A-1 QTL region, while maximizing homozygosity for the background genome (about 97 % homozygosis). From them, five F8 HIFs were obtained by self-pollination and were phenotyped and genotyped. In every HIF, homozygote individuals for the Yitpi allele showed low GI while homozygous for the other alleles showed high GI. Heterozygous individuals showed intermediate GI values in at least four out of the five HIFs. From each HIF, homozygous individuals with contrasting QTL effects were selected and self-pollinated to generate five F9 sets of NILs. Those NILs were finally grown together with the four parent varieties, and grain samples collected at 15, 25 and 35 days post-anthesis (DPA). RNA was isolated from those samples and pooled together in two groups, one containing all samples coming from NILs carrying the QTL (pool A) and the other containing all samples coming from NILs without the QTL (pool B). Samples collected from the four parents at the same DPA were also included in the corresponding RNA pool. This innovative pooling approach allowed us to distinguish a real signal coming from the targeted selected region (segregating equally in each set of NILs) while background noise coming from the rest of the genome is neutralized (different in every set of NILs).
2015-04-23 | E-MTAB-4254 | biostudies-arrayexpress
Project description:The hemibiotrophic fungus Zymoseptoria tritici causes Septoria tritici blotch disease of wheat (Triticum aestivum). Pathogen reproduction on wheat occurs without cell penetration, suggesting that dynamic and intimate intercellular communication occurs between fungus and plant throughout the disease cycle. We used deep RNA sequencing and metabolomics to investigate the physiology of plant and pathogen throughout an asexual reproductive cycle of Z. tritici on wheat leaves. Over 3,000 pathogen genes, more than 7,000 wheat genes, and more than 300 metabolites were differentially regulated. Intriguingly, individual fungal chromosomes contributed unequally to the overall gene expression changes. Early transcriptional down-regulation of putative host defense genes was detected in inoculated leaves. There was little evidence for fungal nutrient acquisition from the plant throughout symptomless colonization by Z. tritici, which may instead be utilizing lipid and fatty acid stores for growth. However, the fungus then subsequently manipulated specific plant carbohydrates, including fructan metabolites, during the switch to necrotrophic growth and reproduction. This switch coincided with increased expression of jasmonic acid biosynthesis genes and large-scale activation of other plant defense responses. Fungal genes encoding putative secondary metabolite clusters and secreted effector proteins were identified with distinct infection phase-specific expression patterns, although functional analysis suggested that many have overlapping/redundant functions in virulence. The pathogenic lifestyle of Z. tritici on wheat revealed through this study, involving initial defense suppression by a slow-growing extracellular and nutritionally limited pathogen followed by defense (hyper) activation during reproduction, reveals a subtle modification of the conceptual definition of hemibiotrophic plant infection.
2015-03-12 | E-MTAB-4116 | biostudies-arrayexpress