Ontology highlight
ABSTRACT:
PROVIDER: PRJNA915727 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Using genome-wide pattern analysis and quantitative-trait-locus (QTL) mapping, we identified that a natural allele of BrJMJ18, BrJMJ18Par, encoding a novel H3K36me3/2 Jumonji demethylase, confers thermotolerance by delayed flowering and stimulated vegetative growth on B. rapa.To assess the downstream genes of BrJMJ18, we conducted a chromatin immunoprecipitation (ChIP) seq experiment using a polyclonal antibody recognizing BrJMJ18 in Par plants under normal conditon (LD, 21℃) and high temperature condiation (LD, 28℃), respectively.
2024-01-31 | GSE223969 | GEO
Project description:Expression quantitative trait locus (QTL) mapping of 127 adult femoral bone samples from a Red Junglefowl x White Leghorn advanced intercross line. Bone trait QTL have been mapped in the same cross, allowing a genetical genomics approach to quantitative trait gene identification
2015-10-31 | E-MTAB-3141 | biostudies-arrayexpress
Project description:QTL-seq for flowering time variation in Brassica napus
| PRJEB33550 | ENA
Project description:Mutation generates the heritable variation that genetic drift and natural selection shape. In classical quantitative genetic models, drift is a function of the effective population size and acts uniformly across traits, while mutation and selection act trait-specifically. We identified thousands of quantitative trait loci (QTL) influencing transcript abundance traits in a cross of two C. elegans strains; although trait-specific mutation and selection explained some of the observed pattern of QTL distribution, the pattern was better explained by trait-independent variation in the intensity of selection on linked sites. Our results suggest that traits in C. elegans exhibit different levels of variation less because of their own attributes than because of differences in the effective population sizes of the genomic regions harboring their underlying loci.
2010-10-01 | GSE23857 | GEO
Project description:Fusarium graminearum causes Fusarium head blight (FHB), which represents one of the major wheat diseases worldwide, determining reduction in grain quality, yield and the accumulation of mycotoxins. To mine the molecular response associated to the wheat 2DL FHB resistance quantitative trait locus (QTL), derived from the cultivar Wuhan-1, and to identify candidate genes implicated in such resistance, a comprehensive transcriptomic analysis of the early response to F. graminearum infection at 3 days post inoculation of spikelet and rachis was performed with the RNA-Seq and miRNA-Seq techniques. The analyses were conducted on two Near Isogenic Lines (NILs) differing for the presence of the 2DL QTL (2-2618, resistant 2DL+ and 2-2890, susceptible null).
2018-02-28 | E-MTAB-6383 | biostudies-arrayexpress
Project description:Drought stress is one of the main environmental factors that affects growth and productivity of crop plants, including lentil. To gain insights into the genome-wide transcriptional regulation in lentil root and leaf under short- and long-term drought conditions, we performed RNA-seq on a drought-sensitive lentil cultivar (Lens culinaris Medik. cv. Sultan). After establishing drought conditions, lentil samples were subjected to de novo RNA-seq-based transcriptome analysis. The 207,076 gene transcripts were successfully constructed by de novo assembly from the sequences obtained from root, leaf, and stems. Differentially expressed gene (DEG) analysis on these transcripts indicated that period of drought stress had a greater impact on the transcriptional regulation in lentil root. The numbers of DEGs were 2915 under short-term drought stress while the numbers of DEGs were increased to 18,327 under long-term drought stress condition in the root. Further, Gene Ontology analysis revealed that the following biological processes were differentially regulated in response to long-term drought stress: protein phosphorylation, embryo development seed dormancy, DNA replication, and maintenance of root meristem identity. Additionally, DEGs, which play a role in circadian rhythm and photoreception, were downregulated suggesting that drought stress has a negative effect on the internal oscillators which may have detrimental consequences on plant growth and survival. Collectively, this study provides a detailed comparative transcriptome response of drought-sensitive lentil strain under short- and long-term drought conditions in root and leaf. Our finding suggests that not only the regulation of genes in leaves is important but also genes regulated in roots are important and need to be considered for improving drought tolerance in lentil.
2019-04-19 | GSE115199 | GEO
Project description:Boar taint is an offensive odour and/or taste from a proportion of non-castrated male pigs caused by skatole and androstenone accumulation during sexual maturity. Castration is widely used to avoid boar taint but is currently under debate because of animal welfare concerns. This study aimed to identify expression quantitative trait loci (eQTLs) with potential effects on boar taint compounds to improve breeding possibilities for reduced boar taint. Danish Landrace male boars with low, medium and high genetic merit for skatole and human nose score (HNS) were slaughtered at ~100 kg. Gene expression profiles were obtained by RNA-Seq, and genotype data were obtained by an Illumina 60K Porcine SNP chip. Following quality control and filtering, 10,545 and 12,731 genes from liver and testis were included in the eQTL analysis, together with 20,827 SNP variants. A total of 205 and 109 single-tissue eQTLs associated with 102 and 58 unique genes were identified in liver and testis, respectively. By employing a multivariate Bayesian hierarchical model, 26 eQTLs were identified as significant multi-tissue eQTLs. The highest densities of eQTLs were found on pig chromosomes SSC12, SSC1, SSC13, SSC9 and SSC14. Functional characterisation of eQTLs revealed functions within regulation of androgen and the intracellular steroid hormone receptor signalling pathway and of xenobiotic metabolism by cytochrome P450 system and cellular response to oestradiol. A QTL enrichment test revealed 89 QTL traits curated by the Animal Genome PigQTL database to be significantly overlapped by the genomic coordinates of cis-acting eQTLs. Finally, a subset of 35 cis-acting eQTLs overlapped with known boar taint QTL traits. These eQTLs could be useful in the development of a DNA test for boar taint but careful monitoring of other overlapping QTL traits should be performed to avoid any negative consequences of selection.
2018-04-18 | GSE113318 | GEO
Project description:A C57BL6/J (B6) x CAST/Ei (CAST) strain intercross has revealed a new quantitative trait locus (QTL) on Chromosome (Chr) 17 controlling total food volume (Tfv1; LOD=7.6). Compared with B6, the CAST mice consume 39% more food volume per body weight in a macronutrient diet selection paradigm. Linkage analyses of total food volume revealed the presence of suggestive QTL on Chrs 2, 6, and 15 and a significant locus on Chr 17. An interval-specific congenic strain, B6.CAST-17, was then developed which verified the QTL. Microarray analysis of stomach in congenic and wildtype B6 mice revealed Glp1r as an expression candidate with physiological relevance to food intake. Further functional analysis of this gene revealed this gene as potential candidate for total food volume trait in mice Keywords: Comparative gene expression analysis
2008-02-13 | GSE7756 | GEO