Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA255921 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Genetic analysis of interspecific populations derived from crosses between the wild tomato species Solanum habrochaites f glabratum, which synthesizes and accumulates insecticidal methylketones (MKs) such as 2-undecanone and 2-tridecanone in glandular trichomes, and Solanum lycopersicum (cultivated tomato), which does not, demonstrated that MK metabolism in the wild species can be attributed to several loci. Comparative trascriptome analysis of the glandular trichomes of F2 segregants bulked into low- and high-MK plants identified several genes whose transcripts were either more or less abundant in the high-MK plants.
2009-06-05 | GSE16431 | GEO
Project description:Bulked segregants seqeuncing to map a mutation in Arabidopsis thaliana
| PRJNA136991 | ENA
Project description:The aim of this study was to conduct a genome-wide analysis for constituent tuber carotenoid QTL. Using a genetical genomics approach samples from clones with similar carotenoid traits were bulked and patterns of gene expression were measured for each bulk by microarray analysis. Variation of gene expression within these bulks may be due to either polymorphisms located near to or within the gene (cis-eQTL) or indirectly from a distant location on the genome (trans-eQTL). Differentially expressed clones from bulks with contrasting carotenoid traits were genetically mapped in order to re-enforce the QTL analysis, and provide a rapid means of developing gene markers closely associated with the target traits.
2011-12-26 | E-TABM-1200 | biostudies-arrayexpress
Project description:In this study, we describe the impact of genetic variation on transcript abundance in an F2 population of Arabidopsis thaliana. The RNA-seq resource generated by this study is suitable for expression quantitative trait locus (eQTL) mapping. From the aligned RNA-seq reads, and available genomic data for each of the parents of the cross, we imputed the genomes of each F2 individual (to allow genetic mapping of RNA abundance traits; briefly, genetic differences in aligned RNA-seq reads were used to impute each F2 genome). Our results show that heritable differences on gene expression can be detected using F2 populations (that is, single F2 plants), and shed light on the control of expression differences among strains of this reference plant.
2017-03-15 | GSE92568 | GEO
Project description:To identify biological processes as well as molecular markers for drip loss, the transcriptomes of logissimus dorsi from 6 sib pair of F2 animals Experiment Overall Design: 12 F2 animals of a resource population based on the breeds Duroc and Pietrain known to differ in meat quality and quantity traits were hybridized to Affymetrix Porcine Genome Arrays
2009-01-14 | E-GEOD-11193 | biostudies-arrayexpress
Project description:Association Genetics can quickly and efficiently delineate regions of the genome that control traits and provide markers to accelerate breeding by marker-assisted selection. The requirements for many markers and a genome sequence to order those markers have limited its exploitation in crops. To harness this approach for use in a broad range of crops, even those with complex genomes, we developed an approach based on transcriptome sequencing to exploit markers representing variation in both gene sequences and gene expression. We term this approach Associative Transcriptomics. Applying it successfully in Brassica napus, as an example, we identified that genomic deletions including orthologues of the transcription factor controlling aliphatic glucosinolate biosynthesis in Arabidopsis thaliana, HAG1 (At5g61420), underlie two QTL for glucosinolate content of seeds.
2012-07-04 | E-MTAB-4309 | biostudies-arrayexpress
Project description:Powdery mildew resistance gene Pm4b, originating from Triticum perscicum, is effective against the prevalent Blumeria graminis f. sp. tritici (Bgt) isolates from certain regions of wheat production in China. The lack of tightly linked molecular markers with the target gene prevents the precise identification of Pm4b during the application of molecular marker-assisted selection (MAS). The strategy that combines the RNA-seq technique and the bulked segregant analysis (BSR-seq) was applied in an F2:3 mapping population (237 families) derived from a pair of isogenic lines VPM1/7*Bainong 3217 F4 (carrying Pm4b) and Bainong 3217 to develop more closely linked molecular markers. RNA-seq analysis of the two phenotypically contrasting RNA bulks prepared from the representative F2:3 families generated 20,745,939 and 25,867,480 high-quality read pairs, and 82.8% and 80.2% of them were uniquely mapped to the wheat whole genome draft assembly for the resistant and susceptible RNA bulks, respectively. Variant calling identified 283,866 raw single nucleotide polymorphisms (SNPs) and InDels between the two bulks. The SNPs that were closely associated with the powdery mildew resistance were concentrated on chromosome 2AL. Among the 84 variants that were potentially associated with the disease resistance trait, forty-six variants were enriched in an about 25 Mb region at the distal end of chromosome arm 2AL. Four Pm4b-linked SNP markers were developed from these variants. Based on the sequences of Chinese Spring where these polymorphic SNPs were located, 98 SSR primer pairs were designed to develop distal markers flanking the Pm4b gene. Three markers, Xics13, Xics43 and Xics76, were incorporated in the new genetic linkage map, which located Pm4b in a 3.0 cM genetic interval spanning a 6.7 Mb physical genomic region. This region had a co-linear relationship with Brachypodium distachyum chromosome 5, rice chromosome 4, and sorghum chromosome 6. Seven genes associated with disease resistance were predicted in this collinear genomic region, which included protein kinases of PKc_like super family, C2 domain protein, peroxidase activity protein, Mlo family protein, and catalytic domain of the serine/threonine kinases (PKc_like super family). The markers developed in the present study facilitate identification of Pm4b during its MAS practice.
2018-05-01 | GSE108697 | GEO
Project description:Maternal stress, anxiety, and depression increase the risk of psychiatric disorders in the progeny. These maternal effects can extend beyond the first generation and affect the grandchildren. In contrast to paternal, maternal effects can impact the offspring not only during gametogenesis, but also through fetal and early-postnatal life, increasing phenotypic complexity and the overall impact. To better understand its non-genetic structure, we dissected a complex maternally-transmitted phenotype to elementary behaviors and their corresponding transmission mechanisms. Chronic stress and depression are associated with reduced serotonin1A receptor (5-HT1AR) levels, and we reported that 5-HT1AR+/- dams transmit anxiety/stress-reactivity traits to their wild-type offspring. Here we show that the maternal effect is propagated to multiple generations, and that the behavioral traits are not transmitted in unison, but rather via parallel and segregated mechanisms, each with generation-dependent penetrance and gender specificity. The ârisk-avoidanceâ and âhypoactivityâ traits of anxiety were transmitted, via a neuro-immune pathway, consecutively from mother to the wild-type F1, F2, and occasionally F3 generation by iterative non-gametic-programming, while the âincreased stress-reactivityâ trait was transmitted to the F2 generation by gametic-programming. Iterative non-gametic-programming of anxiety was linked, via gene expression changes and clustered DNA hypo/hypermethylation at intragenic enhancers, to sphingolipid metabolism and GPCRs in the F1/F2 hippocampus, suggesting dysregulated lipid raft functioning/transmembrane signaling. Conversely, gametic-programming of behavior was predominantly associated with hypomethylation at different promoter-enhancing sequences within a set of genes with diverse neuronal functions. Since differential methylation appeared only postnatally in F2 neurons and was absent in F3 neurons, it is secondary to earlier F2 gametic changes that survive reprogramming in the early embryo, but are erased in F3 germ-cells. Our data introduce parallel and segregated non-genetic transmission of traits as a mechanism that may explain the propagation and pleiotropy of complex behavioral and psychiatric disease phenotypes across generations. Compared three generations of male offspring from wild-type and 5HT1A-R-/+ Swiss Webster mothers with two replicates per sample. Included as well is F2 embryo transfer from wild-type and het parents in wild-type surogates
2016-04-04 | E-GEOD-68713 | biostudies-arrayexpress
Project description:Despite the significance of nucleus genes in plant growth and development, little is known of the molecular bases of regulation of photosynthesis in woody plants.Hence discovering the genetic basis for photosynthesis related phenotypic variation and identifying the major genes controlling these complex traits in trees is essential. Combining the microarray technique and bulked segregant analysis strategy, we used poplar as a model to detect the nucleus genes differentially expressed in segregation population of photosynthesis traits. We measured the F1 interspecific population and segregated the stable extrem samples into two groups including three pools containing five incividuals.Use the Affymetrix poplar gene chip to decrypt the gene functions and mechanisms in different photosynthetic rate.
2014-05-31 | GSE47105 | GEO
Project description:Mapping the genetic architecture of RNA transcript abundances has potential for revealing molecular mechanisms underlying complex traits like disease. Gene expression microarrays allow monitoring genetic control on a whole transcriptome level, but validity and reproducibility of microarray data is a subject of ongoing scientific debate. Here we demonstrate how combining genetic and gene expression data provide a basis for biologically relevant assessment of the current state of microarray technology. We profile liver samples from a murine F2 intercross population using Agilent microarrays. Tissue profiling in a mouse F2 cross. We analyzed 298 Liver samples.
2011-02-02 | E-GEOD-20901 | biostudies-arrayexpress