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Study of the transcriptional consequences of a growth qtl candidate (sg1)-Functional characterization of Shoot Growth 1 (Sg1)

ABSTRACT: ra11-04_qtl - study of the transcriptional consequences of a growth qtl candidate (sg1) - We want to compare the transcriptome of Sg1 insertion mutant to a WT background to understand if this candidate has a role in gene expression regulation at the genome-wide level. - We are analysing a QTL named Sg1 quantitatively affecting the shoot growth in Arabidopsis thaliana. Sg1 mutation exhibits a large set of phenotypic consequences (growth, fitness,…), and the penetrance of these defects increase over generations. The CATMA collaboration aims to perform a T-DNA mutant vs WT analysis, with the WT control being derived from the heterozygous T-DNA parent. A first homozygous generation hypotheticaly derived from the heterozygous T-DNA parent and a 4th homozygous generation showing more severe phenotypes are being compared to the WT (dye swap, biological repetitions). Whole plants were harvested 10 DAG at 11am for each genotype.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE39248 | GEO | 2012/07/23

SECONDARY ACCESSION(S): PRJNA171114

REPOSITORIES: GEO

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study of the transcriptional consequences of a growth qtl candidate (sg1)-Functional characterization of Shoot Growth 1 (Sg1)

Project description:ra11-04_qtl - study of the transcriptional consequences of a growth qtl candidate (sg1) - We want to compare the transcriptome of Sg1 insertion mutant to a WT background to understand if this candidate has a role in gene expression regulation at the genome-wide level. - We are analysing a QTL named Sg1 quantitatively affecting the shoot growth in Arabidopsis thaliana. Sg1 mutation exhibits a large set of phenotypic consequences (growth, fitness,M-bM-^@M-&), and the penetrance of these defects increase over generations. The CATMA collaboration aims to perform a T-DNA mutant vs WT analysis, with the WT control being derived from the heterozygous T-DNA parent. A first homozygous generation hypotheticaly derived from the heterozygous T-DNA parent and a 4th homozygous generation showing more severe phenotypes are being compared to the WT (dye swap, biological repetitions). Whole plants were harvested 10 DAG at 11am for each genotype. 4 dye-swap - gene knock out

2012-07-22 | E-GEOD-39248 | biostudies-arrayexpress

sg1-sg3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

Project description:ra09-01_qtlleafgrowth - sg1-sg3 - What are the transcriptional consequences of the allelic contrast at SG3, SG1 and EGO3 loci mapped for its effect on shoot growth and identified at the gene level - Plants were grown in the in vitro conditions where we have mapped and cloned the concerned QTL and which allows us to see the phenotype linked to the segregation of the natural alleles. We are comparing 2 genotypes descending from a RIL from the Bur x Col RIL set, homozygous and identical everywhere in the genome except for the 23.4 kb at SG1 loci where one genotype is Bur (97.4 and 175.4) and the other is Col (97.1 and 175.1). 4 dye-swap - genotype comparison

2012-03-27 | E-GEOD-36656 | biostudies-arrayexpress

sg1-sg3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

2012-03-28 | GSE36656 | GEO

ego3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

Project description:ra09-01_qtlleafgrowth - ego3 - What are the transcriptional consequences of the allelic contrast at SG3, SG1 and EGO3 loci mapped for its effect on shoot growth and identified at the gene level - Plants were grown in the in vitro conditions with 60 mM mannitol, where we have mapped and cloned the concerned QTL which allows us to see the phenotype linked to the segregation of the natural alleles. We are comparing 2 genotypes descending from a RIL from the Cvi x Col (H1 is Col allele containing HIF, and A2 is Cvi allele containing HIF). 2 dye-swap - genotype comparison

2012-04-06 | E-GEOD-36698 | biostudies-arrayexpress

ego3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

2012-04-07 | GSE36698 | GEO

Arabidopsis thaliana

Project description:study of the transcriptional consequences of a growth qtl candidate (sg1)-Functional characterization of Shoot Growth 1 (Sg1)

| PRJNA171114 | ENA

Arabidopsis thaliana

Project description:sg1-sg3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

| PRJNA156997 | ENA

Arabidopsis thaliana

Project description:ego3-Studying the transcriptional consequences of a QTL for shoot growth (SG3, SG1). Studying the transcriptional consequences of a QTL for shoot growth under mannitol condition (EGO3).

| PRJNA158121 | ENA

The chromatin remodeler protein DDM1 regulates early seedling growth hybrid vigor by modulating gene expression in Arabidopsis

Project description:Despite of the paramount importance of heterosis in agriculture, the molecular mechanisms underlying heterosis remain elusive. Recent studies in Arabidopsis suggested possible involvement of DNA methylation in heterosis. We tested this hypothesis genetically by crossing homozygous mutants in DNA methylation-related genes in the Columbia (Col) ecotype with homozygous mutants in the same DNA methylation-related genes in the C24 ecotype. When genes in the RNA-directed DNA methylation (RdDM) pathway were mutated, the resultant F1 hybrids did not show appreciable loss of best parent heterosis (BPH) performances in early seedling growth. In contrast, mutations in the putative chromatin remodeling protein DECREASE OF DNA METHYLATION 1 (DDM1) caused ddm1-Col like growth pattern of ddm1-F1 hybrids, a mid-parent heterosis (MPH) performance. To understand the underlying molecular mechanisms, we compared the transcriptomes of the parental plants and reciprocal F1 hybrids in the wild type and ddm1 mutant backgrounds, and identified 183 non-additively expressed (NAE) genes, which were functionally enriched in defense response, a group of genes negatively associated with plant size. Interestingly, for the expression levels of the NAE genes, WT-F1 hybrids were enriched in the Golden Ration between mid-parent values (MPVs) and Col parents in WT, but ddm1-F1 hybrids were comparable to ddm1-Col parent in ddm1 mutant, which explained the MPH performance of ddm1-F1 hybrids. DNA methylation analyses revealed only one third of the NAE genes with highly methylated promoters whose expression is negatively associated with DNA methylation of promoters, strongly suggesting that DDM1 regulates heterosis by multiple epigenetic modifications.

2016-11-07 | GSE74551 | GEO

Analysis of the 4AL QTL for grain dormancy in wheat

Project description:We generated multiple NILs segregating for the 4A-1 QTL following a method based on HIFs analysis. Five F7 RILs from the mapping population were chosen as founders of HIFs on the basis of being heterozygote for the 4A-1 QTL region, while maximizing homozygosity for the background genome (about 97 % homozygosis). From them, five F8 HIFs were obtained by self-pollination and were phenotyped and genotyped. In every HIF, homozygote individuals for the Yitpi allele showed low GI while homozygous for the other alleles showed high GI. Heterozygous individuals showed intermediate GI values in at least four out of the five HIFs. From each HIF, homozygous individuals with contrasting QTL effects were selected and self-pollinated to generate five F9 sets of NILs. Those NILs were finally grown together with the four parent varieties, and grain samples collected at 15, 25 and 35 days post-anthesis (DPA). RNA was isolated from those samples and pooled together in two groups, one containing all samples coming from NILs carrying the QTL (pool A) and the other containing all samples coming from NILs without the QTL (pool B). Samples collected from the four parents at the same DPA were also included in the corresponding RNA pool. This innovative pooling approach allowed us to distinguish a real signal coming from the targeted selected region (segregating equally in each set of NILs) while background noise coming from the rest of the genome is neutralized (different in every set of NILs).

2015-04-23 | E-MTAB-4254 | biostudies-arrayexpress

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