Project description:Bovine mammary gland provide the largest amount of milk for dairy industry to date. Insight in functional adaptation of this organ is critical in order to improve efficiency of milk synthesis and milk quality. In the present experiment microarray analysis in combination with bioinformatics tools was performed in mammary tissue from 8 Holstein cows during the entire lactation cycle.
Project description:Bovine mammary gland provide the largest amount of milk for dairy industry to date. Insight in functional adaptation of this organ is critical in order to improve efficiency of milk synthesis and milk quality. In the present experiment microarray analysis in combination with bioinformatics tools was performed in mammary tissue from 8 Holstein cows during the entire lactation cycle. The mammary biopsy was performed at -30, -15, 1, 15, 30, 60, 120, 240, and 300 days (d) relative to parturition. A dye-swap reference design (reference = mixture of RNA from several bovine tissues) was used.
Project description:Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.
Project description:Understanding the mechanism of low temperature (LT) adaptation is crucial to the development of cold-tolerant crops. To identify the genes involved in the development of LT tolerance in the crown of hexaploid wheat we examined the global changes in genes expression during cold-treatment using the Affymetrix Wheat Genome Chip.
Project description:Take-all is a devastating soil-borne disease that affects wheat production. The continuous generation of disease-resistance germplasm is an important aspect of the management of this pathogen. In this study, we characterized the wheat-Psathyrostachys huashania Keng-derived progeny H139 that exhibits significantly improved resistance to wheat take-all disease compared with its susceptible parent 7182. GISH) and mc-FISH analyses revealed that H139 is a stable wheat-P. huashania disomic substitution line lacking wheat chromosome 2D.EST-STS marker and Wheat Axiom 660K Genotyping Array analysis further revealed that H139 was a novel wheat-P. huashania 2Ns/2D substitution line, and that the P. huashania 2Ns chromosome shares high sequence similarity to wheat chromosome 2D. These results indicate that H139, with its enhanced wheat take-all disease resistance and desirable agronomic traits, provides valuable genetic resources for wheat chromosome engineering breeding.
Project description:The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation.
Project description:The yield of wheat is highly impacted by environmental stresses. The combinatorial regulation of sequence-specific transcription factors(TFs) defines a regulatory network that underlies plant stress responses. Here we created a comprehensive catalog of genomic binding sites of 115 TFs underlying abiotic stress responses by leveraging DAP-seq in Triticum Urartu, along with epigenomic profiles. The majority of gene distant TF binding sites(TFBS) are embedded in transposable elements(TEs), whose functional relevance was supported by a signature of purifying selection and active epigenomic features. Furthermore, ~30% non-TE TFBS share high sequence similarity with TE-embeded TFBS, potentially derived from Triticeae-specific TEs and have almost no sequence homology in non-Triticeae species. The expansion of TE-derived TFBS in wheat linked to wheat-specific stress responsive genes, suggesting that TEs are an important driving force for regulatory innovation. Altogether, TEs have significantly and continuously shaped regulatory network in wheat adaptation.
Project description:Most DNA variants associated with common complex diseases fall outside the protein-coding regions of the genome, making them hard to detect and relate to a function. Although many computational tools are available for prioritizing functional disease risk variants outside the protein-coding regions of the genome, the precision of prediction of these tools is mostly unreliable and hence not close to cancer risk prediction. This study brings to light a novel way to improve prediction accuracy of publicly available tools by integrating the impact of cis-overlapping binding sites of opposing cancer proteins, such as P53 and cMYC, in their analysis to filter out deleterious DNA variants outside the protein-coding regions of the human genome. Using a biology-based statistical approach, DNA variants within cis-overlapping motifs impacting the binding affinity of opposing transcription factors can significantly alter the expression of target genes and regulatory networks. This study brings us closer to developing a generally applicable approach capable of filtering etiological non-coding variations in co-occupied genomic regions of P53 and cMYC family members to improve disease risk assessment.
Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA
Project description:Roots adaptation to drought stress was analyzed using transcriptome and metabolomics profiles in two wild emmer wheat (Triticum turgidum ssp. dicoccoides) genotypes: Y12-3 (drought resistance) and A24-39 (drought susceptible).