Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Hordeum vulgare Transcriptome or Gene expression

ABSTRACT: 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.

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Hordeum vulgare subsp. spontaneum

SUBMITTER: Guoping Zhang

PROVIDER: E-MTAB-4221 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley.

Dai Fei F Chen Zhong-Hua ZH Wang Xiaolei X Li Zefeng Z Jin Gulei G Wu Dezhi D Cai Shengguan S Wang Ning N Wu Feibo F Nevo Eviatar E Zhang Guoping G

Proceedings of the National Academy of Sciences of the United States of America 20140902 37

The domestication of cultivated barley has been used as a model system for studying the origins and early spread of agrarian culture. Our previous results indicated that the Tibetan Plateau and its vicinity is one of the centers of domestication of cultivated barley. Here we reveal multiple origins of domesticated barley using transcriptome profiling of cultivated and wild-barley genotypes. Approximately 48-Gb of clean transcript sequences in 12 Hordeum spontaneum and 9 Hordeum vulgare accession ...[more]

PMID: 25197090

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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.

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.

Dataset Information

Hordeum vulgare Transcriptome or Gene expression

Publications

Transcriptome profiling reveals mosaic genomic origins of modern cultivated barley.

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