Soybean fast neutron genotyping: 700k Forward genetics
Ontology highlight
ABSTRACT:
ORGANISM(S): Glycine max
SUBMITTER: Robert Stupar
PROVIDER: E-GEOD-31038 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220. 11 different soybean fast neutron lines were hybridized against the parental reference genotype M92-220. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.
2011-08-02 | E-GEOD-31111 | biostudies-arrayexpress
Project description:CGH was used to map structural variation (introgressed regions) among soybean iron-inefficient NIL IsoClark with its iron-efficient recurrent parent Clark and donor parent T203. Another NIL series HiPro, LoPro was also used in the study. CGH Comparisions were made among a NIL IsoClark with its parents Clark and T203; also comparisions were made among HiPro and LoPro NIL series. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.
2011-08-01 | E-GEOD-31072 | biostudies-arrayexpress
Project description:Soybean is a self-pollinating crop species that has relatively low nucleotide polymorphism rates compared to other crop plant species. Despite the appearance of a low intervarietal nucleotide polymorphism rate, a wide range of heritable phenotypic variation exists. There is even evidence for heritable phenotypic variation among individuals within some varieties. ‘Williams 82,’ the soybean variety used to produce the reference genome sequence, was derived from backcrossing a phytophthora root rot resistance locus from the donor parent ‘Kingwa’ into the recurrent parent ‘Williams.’ To explore the genetic basis of intravarietal variation, we investigated the nucleotide, structural and gene content variation of different Williams 82 individuals. Williams 82 individuals exhibited variation in the number and size of introgressed Kingwa loci. In these regions of genomic heterogeneity, the reference Williams 82 genome sequence consists of a mosaic of Williams and Kingwa haplotypes. Genomic structural variation between Williams and Kingwa was maintained between the Williams 82 individuals within the regions of heterogeneity. Additionally, the regions of heterogeneity exhibited gene content differences between Williams 82 individuals. Collectively, these findings show that genetic heterogeneity in Williams 82 primarily originated from the differential segregation of polymorphic chromosomal regions following the backcross and single-seed descent generations of the breeding process. We conclude that soybean haplotypes can possess a high rate of structural and gene content variation, and the impact of intravarietal genetic heterogeneity may be much greater than previously assumed. This detailed characterization will be useful for interpreting soybean genomic data sets and highlights important considerations for research communities that are utilizing or working towards developing a reference genome sequence. Soybean variety Williams 82 (Wm82) was derived from a Williams x Kingwa BC6F3 population. CGH was performed to detect regions of Kingwa genomic introgression in Wm82; Williams was hybridized as a common reference against Kingwa and four different Wm82 individuals. Two different Wm82 individuals (SGC and ISU) were also hybridized with one another. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.
2010-12-14 | E-GEOD-25294 | biostudies-arrayexpress
Project description:CGH was used to compare structural variation among four soybean cultivars (Archer, Minsoy, Noir1 and Williams 82). Three different soybean cultivars (Archer, Minsoy and Noir1) were hybridized against the common reference genotype Williams 82. The soybean tiling array consists of 700k probes, spaced at approximately 1.1 kb intervals.
2011-05-03 | E-GEOD-28905 | biostudies-arrayexpress
Project description:Soybean fast neutron (FN) mutant lines were compared by CGH to catalog structurally variant (e.g. deletion and duplication) regions compared to the parent line (M92-220). The CGH comparisons reveal reveal putative deletions and duplications among the mutant lines. FN lines were compared through a common reference, M92-220 (this is a sub-line individual isolated from the M92-220 seed stock). Each FN line was represented by a single individual plant. The reported values show the log2 ratio of the normalized FN line hybridization signals (Cy3) over the normalized M92-220 hybridization signal (Cy5).
2014-06-04 | E-GEOD-58172 | biostudies-arrayexpress
Project description:We used aCGH data for detailed analysis of the natural killer gene complex (NKC) of multiple inbred strains, providing insight both into aCGH analysis of polymorphic gene clusters as well as structural information on the NKC itself. By unsupervised clustering analysis, the aCGH data can be precisely correlated with overall genome structural variation of the NKC as detected by RFLP variants in retrospective and prospective analyses. On a high resolution level, aCGH could be used to detect a small deletion within an NKC gene that is confined to only one mouse strain examined out of 22. The NKC region on mouse chromosome 6 is known to be an area with structural variation based on studies which reveal restriction fragment length polymorphic (RFLP) variants among inbred mouse strains. To verify predictive power of the unsupervised clustering algorithms, we prospectively collected aCGH data from two strains of mice (CBA/J, and NZW/LacJ) that were not among the original 20 strains (GEO accession # GSE10656) analyzed but represented strains whose Ly49 and Nkrp1 RFLP had been determined previously. We performed comparative genomic hybridization using a long-oligonucleotide array containing 2,149,887 probes evenly spaced across the reference genome with a median inter-probe spacing of 1,015 bases. Labeling, hybridization, washing, and array imaging were performed as previously described (PMID:18334530). To capture the variability along chromosome 6, the log2 signal ratios were organized into bins (a defined chromosome length in terms of bp). The entire chromosome was divided into consecutive bins, beginning with the position of the first probe. We used the variance of each bin to represent the variability along the chromosome. We performed two types of unsupervised clustering analysis of the log2 ratios of signal intensities of each probe (normalized). One is the non-hierarchical clustering using the partitioning among medoids (PAM) function as implemented in R's 'cluster' package. The other is the agglomerative hierarchical clustering based on the Euclidean distance. The average linkage method was used in clustering the strains as implemented in the hclust function in R's 'cluster' package.
2010-06-26 | E-GEOD-20090 | biostudies-arrayexpress
Project description:Pulmonary arterial hypertension (PAH) is a severe and incurable pulmonary vascular disease. One of the primary origins of PAH is pulmonary endothelial dysfunction leading to vasoconstriction, aberrant angiogenesis and smooth muscle cell proliferation, endothelial-to-mesenchymal transition, thrombosis and inflammation. Our objective was to study the epigenetic variations in pulmonary endothelial cells (PEC) through a specific pattern of DNA methylation. DNA was extracted from cultured PEC from patients with idiopathic PAH (n=11), heritable PAH (n=10) and controls (n=18). ). DNA methylation was assessed using the Illumina HumanMethylation450 Assay. After normalization, samples and probes were clustered according to their methylation profile. Differential clusters were functionally analysed using bioinformatics tools.
2016-07-15 | E-GEOD-84395 | biostudies-arrayexpress
Project description:Transcriptional profling of a Listeria monocytogenes under pressure comparing ctsR mutant and wild type one condition (pressure 450 Moa, 3min) experiment, mutant vs. wild type, 2 biological replicates, two technical replicates
2011-06-10 | E-GEOD-22819 | biostudies-arrayexpress
Project description:The G. hirsutum mutant li1 is caused by a dominant mutation which has pleiotropic effects on plant development. To get information for molecular effects by li1 mutation on cotton fiber development, we examined expression patterns of over 5000 genes by cDNA array from 6 to 18 DPA in a 3-day interval between li1 mutant and normal fibers. RNAs from li1 mutant fibers at 6-, 9-, 12-, 15-, and 18-DPA were compared to normal fiber RNA at each corresponding time points. Four biological repeats were carried out including two dye-swap ones.
2010-07-01 | E-GEOD-4643 | biostudies-arrayexpress
Project description:Specialized chromatin exists at centromeres and must be precisely transmitted during DNA replication. The mechanisms involved in the propagation of these structures remain elusive. Fission yeast centromeres are composed of two chromatin domains: the central CENP-ACnp1 kinetochore domain and flanking heterochromatin domains. Here we show that fission yeast Mcl1, a DNA polymerase ? (Pol?) accessory protein, is critical for maintenance of centromeric chromatin. In a screen for mutants that alleviate both central domain and outer repeat silencing, we isolated several cos mutants, of which cos1 is allelic to mcl1. The mcl1-101 mutation causes reduced CENP-ACnp1 in the central domain and an aberrant increase in histone acetylation in both domains. These phenotypes are also observed in a mutant of swi7+, which encodes a catalytic subunit of Pol?. Mcl1 forms S-phase-specific nuclear foci, which colocalize with those of PCNA and Pol?. These results suggest that Mcl1 and Pol? are required for propagation of centromere chromatin structures during DNA replication. Keywords: ChIP-chip analysis, S. pombe Antibodies used were ?-acetyl-histone H4 antiserum (Upstate) and ?-histone H4 pan antibody (Upstate). ChIP-on-chip was carried out using IVT amplification method. ChIP-chip data were comfirmed by real-time PCR.
2008-07-22 | E-GEOD-11102 | biostudies-arrayexpress