Ontology highlight
ABSTRACT:
PROVIDER: PRJNA624178 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR11514762_1.fastq.gz | Fastqsanger.gz | |||
| SRR11514762_2.fastq.gz | Fastqsanger.gz | |||
| SRR11514763_1.fastq.gz | Fastqsanger.gz | |||
| SRR11514763_2.fastq.gz | Fastqsanger.gz | |||
| SRR11514764_1.fastq.gz | Fastqsanger.gz |
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Project description:A 44K salmonid oligoarray was used to examine the influence of genotype and developmental stage on mRNA expression in wild-type (age matched and size matched to domesticated), domesticated and wild-domesticated hybrid populations. Significant differences were found in mRNA expression between genotypes. The largest proportion of differentially expressed mRNAs were found in comparisons of domesticated and wild-type groups. Significant differences were also noted in pairings of wild-domesticated hybrid progeny to both parental strains. Differences in gene expression were found in comparison of both wild-type age and size matched to each other and in combination with genotype analysis, showing a strong effect of fish developmental stage on differential gene expression. Domestication was found to modify biological pathways associated with transport, metabolism, cell tissue structure and development, stress and immune response and protein synthesis. Genotype analysis of hybrid progeny inheritance patterns showed similar levels of recessive, dominant and additive effects.
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Project description:Rice was domesticated independently in Asia and Africa, leading to two distinct but closely related crop species, Oryza sativa and Oryza glaberrima, respectively. The two domestications lead to morphological changes, in which a higher branching complexity of the panicles, influencing seed production and crop yield. Although much emphasis was placed on changes in transcriptional regulation during rice domestication and improvement, no large-scale study of small RNA regulation changes during domestication has been reported so far. To analyze whether rice domestication has altered the expression of small RNAs, we performed deep sequencing of small RNA transcriptomes from early developmental stages of panicles from 10 genotypes of the cultivated African species and 10 genotypes of its wild-relative O. barthii. Our study shows a drastic expression change of the 21-nucleotide smallRNA population. A total of 29% of these smallRNAs are overexpressed in panicles of O. barthii vs. O. glaberrima, corresponding mainly to 21-nucleotide phased siRNAs (or phasiRNAs). We also show that these changes are associated with a differential expression of a known regulator of phased siRNAs, miR2118 during early panicle development. Finally, these changes are associated to a heterochronic alteration of phasiRNAs and miR2118 expression pattern, during panicle development with a delayed expression in the domesticated species. Our study suggests a major reshaping of the regulation network from a specific class of small RNA during African rice domestication.
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Project description:There is growing evidence for the prevalence of DNA copy number variation (CNV) and its role in phenotypic variation in recent years. Comparative genomic hybridization (CGH) was used to explore the extent of this type of structural variation in the barley genome. In a panel of 14 genotypes including domesticated cultivars and wild barleys, we found that 14.9% of all the sequences on the array are affected by CNV. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. A substantial portion (37%) of the CNV events are present in both wild and domesticated barley. CNVs are enriched in telomeric regions for all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. CNV affected 9.5% of the coding sequences represented on the array. The genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases, suggesting the potential for CNV to influence variation for responses to biotic and abiotic stress. The analysis of CNV breakpoints indicated that DNA repair mechanisms of double-strand breaks (DSBs) via single-stranded annealing (SSA) and synthesis-dependent strand annealing (SDSA) play an important role in the origin of many structural changes in barley. Here we present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance.
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Project description:Growth rate can be genetically modified in many vertebrates by domestication and selection, and more recently by transgenesis overexpressing growth factor genes (e.g. growth hormone, GH). While the phenotypic end consequence is similar, it is currently not clear whether the same modifications to physiological pathways are occurring in both genetic processes, nor to what extent they may interact when combined. To examine these questions, we have used rainbow trout as a model species because non-domesticated wild strains are available as comparators to assess genetic and physiological changes that have arisen from domestication and from GH transgenesis. In addition to pure wild and pure domesticated strains, two different GH transgenes with markedly different growth effects were examined, both in a wild background and in hybrids which combined domesticated and wild genomes in addition to the transgene. We find that liver mRNAs show highly concordant changes in levels in both types of fast-growing fish, relative to wild type, for both up- and down-regulated genes. Further, among domesticated, transgenic, and their hybrid genotypes, a strong positive correlation was found between growth rate and the number of genes affected or their levels of mRNA. Functional analysis found that genes involved in immune function, carbohydrate metabolism, detoxification, transcription regulation, growth regulation, and lipid metabolism were affected in common by domestication and GH transgenesis. The common responses of domesticated and GH transgenic strains is consistent with the GH pathway or its downstream effects being upregulated in domesticated animals during their modification from wild-type growth rates.
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Project description:Growth rate can be genetically modified in many vertebrates by domestication and selection, and more recently by transgenesis overexpressing growth factor genes (e.g. growth hormone, GH). While the phenotypic end consequence is similar, it is currently not clear whether the same modifications to physiological pathways are occurring in both genetic processes, nor to what extent they may interact when combined. To examine these questions, we have used rainbow trout as a model species because non-domesticated wild strains are available as comparators to assess genetic and physiological changes that have arisen from domestication and from GH transgenesis. In addition to pure wild and pure domesticated strains, two different GH transgenes with markedly different growth effects were examined, both in a wild background and in hybrids which combined domesticated and wild genomes in addition to the transgene. We find that liver mRNAs show highly concordant changes in levels in both types of fast-growing fish, relative to wild type, for both up- and down-regulated genes. Further, among domesticated, transgenic, and their hybrid genotypes, a strong positive correlation was found between growth rate and the number of genes affected or their levels of mRNA. Functional analysis found that genes involved in immune function, carbohydrate metabolism, detoxification, transcription regulation, growth regulation, and lipid metabolism were affected in common by domestication and GH transgenesis. The common responses of domesticated and GH transgenic strains is consistent with the GH pathway or its downstream effects being upregulated in domesticated animals during their modification from wild-type growth rates. Microarray analyses were performed on five individual rainbow trout per group of pure wild, pure domesticated, GH transgenic strain 1 in wild, GH transgenic strain 2 in wild, GH transgenic strain 1 in wild-domestic hybrid, and GH transgenic strain 2 in wild-domestic hybrid hybridized (one slide per individual) against a common wild-type RNA pool.
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