Identification of Rf genes in hexaploid wheat (Triticum aestivum L.) by RNA-seq.
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina HiSeq 4000
ORGANISM(S): Triticum aestivum
SUBMITTER: Magdalena Szeliga
PROVIDER: E-MTAB-10131 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Plants of two non-restorer varieties of hexaploid winter wheat (Astoria, Grana) and two restorers ones (Patres and Primépi) were used to Representational Difference Analysis (cDNA-RDA) to identify effective Rf (fertility restorer) genes. Anthers at the microspore stage were used as testers while anthers excised at the stage of pollen tetrads were selected as driver. The tester:driver ratio in three subsequent rounds of subtractive hybridization increased from 1:50, and 1:400 to 1:200000. Differential products obtained in the third subtraction of the size range from 200 to 800 bp were sequenced.
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Project description:RNA from wheat lodicules in two highly-chasmogamous (HCH) (Piko and Poezja) and two low-chasmogamy (LCH) (Euforia and KWS Dacanto) varieties at two developmental stages - pre-flowering and early flowering were used to Representational Difference Analysis (cDNA-RDA). Lodicules at the pre-flowering were used as testers while the lodicules early flowering were selected as driver probes. This procedure results in accumulation of unique sequences upregulated in pre-flowering. The analysis was taken in three replicates for each variety (Piko, Poezja, Euforia, KWS Dacanto). The tester:driver ratio in three subsequent rounds of subtractive hybridization increased from 1:50, and 1:400 to 1:200000. Difference products obtained from the third subtraction in the size range from 200 to 800 bp were sequenced.
2022-09-18 | E-MTAB-12139 | biostudies-arrayexpress
Project description:In this study, we performed a large-scale leaf phosphoproteomic analysis of two wheat genotypes HX10 and NC47 to explore the complex protein phosphorylation network of signaling and regulatory events affecting rapid vegetative growth in wheat. We used TiO2 affinity chromatography combined with LC-MS/MS and Maxquant software to identify phosphopeptides and phosphorylated sites. Finally, 2,336 phosphopeptides containing 2,734 phosphorylation sites were identified from the two wheat genotypes HX10 and NC47 in our study.
2014-04-01 | PXD000540 | Pride
Project description:Comparative transcriptome profiling in winter wheat grown under different agricultural practices
2012-11-30 | E-MTAB-903 | biostudies-arrayexpress
Project description:To improve our understanding of the organization and regulation of the wheat gene space, we established the first transcription map of a wheat chromosome (3B) by hybridizing the newly developed INRA GDEC Triticum aestivum NimbleGen 12x40k unigenes microarray with BAC pools from a new version of the 3B physical map as well as with cDNA probes from five tissues at three developmental stages each. By hybridizing the BAC pools with the wheat NimbleGen 40K unigenes chip we managed to map almost 3000 unigenes on the wheat chromosome 3B BACs and to study the organization of the wheat gene space along chromosome 3B. The sequences of the unigenes helped to perform functional and evolutionary analyses of these unigenes. By hybridizing the 15 cDNA samples from five organs at three developmental stages each we established the expression profiles of more than 32000 wheat unigenes. Particularly we focused on the expression of the unigenes mapped on wheat chromosome 3B to perform coexpression analyses.
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Project description:The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. To identify smRNA targets in the wheat TGMS line, we applied the degradome sequencing method, which globally and directly identifies the remnants of smRNA-directed target cleavage. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress. Examination of 2 mRNA degradome libraries in spike tissues during cold and control condition
2012-04-11 | E-GEOD-37134 | biostudies-arrayexpress
Project description:The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress. Examination of 7 small RNA libraries in spike tissues during cold and control condition
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Project description:Background: The use of cytoplasmic male sterility (CMS) in F1 hybrid seed production of chili pepper is increasingly popular. However, the molecular mechanisms of cytoplasmic male sterility and fertility restoration remain poorly understood due to limited transcriptomic and genomic data. Therefore, we analyzed the difference between a CMS line 121A and its near-isogenic restorer line 121C in transcriptome level using next generation sequencing technology (NGS), aiming to find out critical genes and pathways associated with the male sterility. Results: We generated approximately 53 million sequencing reads and assembled de novo, yielding 85,144 high quality unigenes with an average length of 643 bp. Among these unigenes, 27,191 were identified as putative homologs of annotated sequences in the public protein databases, 4,326 and 7,061 unigenes were found to be highly abundant in lines 121A and 121C, respectively. Many of the differentially expressed unigenes represent a set of potential candidate genes associated with the formation or abortion of pollen. Conclusions: Our study profiled anther transcriptomes of a chili pepper CMS line and its restorer line. The results shed the lights on the occurrence and recovery of the disturbances in nuclear-mitochondrial interaction and provide clues for further investigations. Anther transcriptomes of a chili pepper CMS line 121A and its nearisogenic restorer line 121C were generated by deep sequencing, using Illumina HiSeq 2000.
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Project description:Wheat leaf rust caused by the pathogenic fungus Puccinia triticina, is a serious threat to bread wheat and durum production in many areas of the world. This plant-pathogen interaction has been studied extensively at the molecular genetics level, however proteomics data are still relatively scarce. The present study investigated temporal changes in the abundance of the apoplastic fluid proteome of wheat leaves infected with either virulent or avirulent races of P. triticina, using a label-free LC-MS-based approach. In general, there was very little difference between inoculated and control apoplastic proteomes as a result of either race of pathogen, until haustoria had become well established in the incompatible interaction, although the resistant host responds to pathogen challenge sooner than the susceptible. In the earlier samplings (up to 72 h after inoculation), there were 46 host proteins with significantly changing abundance, however pathogen proteins were detected only rarely and not reproducibly. This is consistent with the hemi-biotrophic life-style of P. triticina; the pathogen infection is characterized by an early phase of a symbiosis-like relationship, followed by a later stage of pathogenesis, with tissue damage and parasitism. The majority of the host proteins with altered abundance up to 72 h post-inoculation were pathogen-response-related, including peroxidases, chitinases, β-1-3-endo-glucanases and PR-proteins. Five days after inoculation with the incompatible race it was possible to detect 150 PT proteins and 117 host proteins which had significantly increased in abundance as well as 33 host proteins which had significantly decreased in abundance and which represent potential targets of pathogen effectors. The pathogen-expressed proteins – seen most abundantly in the incompatible interaction – were mostly uncharacterized proteins, however many of their functions could be inferred through homology-matching with pBLAST. Pathogen proteins also included several candidate effector proteins, some novel and some which have been reported previously from the purified haustoria proteome.
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