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.
Project description:Nitrogen and Sulfur supply play an important role in modulating wheat grain development. We studied the short-term effect of shifting N and S supply levels at mid-way through grain filling on gene expression by microarray analysis. Please note: Factor Value[sampling time]: indicates when the samples were sampled, e.g. 3 hours after we shift the treatment as explained in the protocol TREATMENT and indicated in the protocol SAMPLING. Factor Value[growth condition] (a, b, c, d, e, f) corresponds to the treatments explained in the protocol TREATMENT: a) 3mM nitrogen and 0.02mM sulfur; b) 15mM nitrogen and 0.02mM sulfur; c) 3mM nitrogen and 2mM sulfur. At mid-way through grain filling, three additional N and S supply levels were introduced as follows: d) shifting treatment a) to 15mM nitrogen and 0.02mM sulfur; e) shifting treatment b)to 15mM nitrogen and 2mM sulfur; f) shifting treatment c) to 15mM nitrogen and 2mM sulphur.
Project description:Seed storage proteins (SSP) play a central role in providing carbon (C), nitrogen (N), and sulfur (S) resources during seed germination. Their content and composition are essential determinants shaping wheat end-use value. Molecular mechanisms underlying the developmental and nutritional regulation of SSP accumulation in wheat grain are as yet poorly understood. We were interested to elucidate the effects of N and S supplies on the gene expression of the entire system of wheat grain. For this purpose, we performed microarray analysis using a custom T.aestivum NimbleGen 40k microarray (ref. A-MEXP-1928) in wheat grains of 8 developmental stages and four N and S treatments.
Project description:Fusarium Head Blight (FHB) is a disease of wheat and other cereal crops, where Fusarium graminearum and related species infects the wheat inflorescence during and post-anthesis. The fungus produces trichothecene toxins that accumulate in the grain of infected head, and are required for disease spread. Microarrays were used to observe differential gene expression in the uninoculated spikelets of FHB-challenged wheat spikes in three wheat genotypes. A summary of our findings will be published in Plant Pathology. Three wheat genotypes were used: (1) 'Superb', an FHB-susceptible Canadian wheat cultivar; (2) GS-1-EM0040 (CIMMYT11x'Superb'*2), a double haploid line with good resistance to initial infection (Type 1 resistance), and moderate resistance to disease spread (Type 2 resistance); and (3) GS-1-EM0168 (CM82036x'Superb'*2), a double haploid line with moderate Type 1 resistance, and good Type 2 resistance. Five inocula were used: (A) water, (B) FgTri5+ (GZ3639, a trichothecene-producing F. graminearum strain); (C) FgTri5- (GZT40, a trichothecene-non-producing mutant of the F. graminearum strain GZ3639); (D) FgTri5 supplemented with deoxynivalenol (DON), which is the main trichothecene produced by FgTri5+; and (E) DON. The inocula were injected into two spikelets near the center of the spike during early stages of anthesis, and spikelets above and below the inoculation point were collected at 3, 8, and 24 h after inoculation. A zero-hour un-inoculated control was also collected from each line. Total RNA was extracted from collected spikelets, and microarray analysis was perfomed using the Affymetrix Wheat GeneChip.
Project description:Eight tissues of cultivar Morex (three biological replications each) earmarking stages of the barley life cycle from germinating grain to maturing caryopsis were selected for deep RNA sequencing (RNA-seq)
Project description:Near isogenic wheat lines(NILs), differing in the presence of both or none of the FHB-resistance QTL Fhb1 and Qfhs.ifa-5A, have been sequenced using Illumina HiSeq2000 under disease pressure (3, 6, 12, 24, 36, 48 hai) as well as with mock-inoculation, to discern transcriptional differences induced by Fusarium graminearum. The NILs are BC5F2 lines generated from the Mexican Spring wheat line CM-82036, the resistance QTL donor line, as recurrent background and the susceptible German Spring wheat line Remus as the donor of the susceptible QTL alleles.
Project description:Near isogenic wheat lines, differing in the presence of the FHB-resistance QTL Fhb1 and Qfhs.ifa-5A, have been sequenced using Illumina HiSeq2000 under disease pressure (30 and 50 hai) as well as with mock-inoculation, to discern transcriptional differences induced by Fusarium graminearum.
Project description:Sperm cells represent the male partner that fuses with the egg cell during fertilization in all multi-cellular eukaryotic organisms, and, in flowering plants, is a founder of both embryo and nutritive endosperm. We examined the transcriptome of Oryza sativa ssp. japonica using the Affymetrix 57K rice genome GeneChip to provide an overview of genes activated in the paternal gamete. We used microarrays to detail the global program of gene expression in mature pollen and sperm cells at anthesis, which constitutes the stage immediately preceding pollen germination and gamete deposition leading up to fertilization. This documents the condition of the male gametophytic cells prior to fertilization. Keywords: tissue expression profile, male gametophyte, sperm, pollen, seedling Male gametophytic cells consisting of isolated pollen and isolated sperm cells collected at anthesis were compared with seedlings containing leaf, stem, root and apical meristems as a vegetative sporophytic control; three separate biological replicates were used.