Structural variation among soybean cultivars
Ontology highlight
ABSTRACT:
ORGANISM(S): Glycine max
PROVIDER: GSE28905 | GEO | 2011/05/03
SECONDARY ACCESSION(S): PRJNA140667
REPOSITORIES: GEO
Similar Datasets
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:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used.
2015-07-02 | GSE65553 | GEO
Project description:To understand the responses of plants to environmental stresses will help mitigate the problems via creating stress-tolerant crop cultivars. We have carried out comparative expression analysis of roots of two soybean varieties Williams 82 and DT2008 that have constrasting drought-responsive phenotype under dehydration and well-watered (control) conditions. Affymetrix’s whole Soybean Gene Expression Microarray (66K) was used. The Williams 82 and DT2008 soybean plants were grown for 14 days in the vermiculite soil under greenhouse conditions. The whole plants of 14-d-old plants were detached and exposed to dehydration on KimTowel papers for 0 (well-watered, control), 2 and 10 h. All roots of independent 14-d-old plants were collected. Total RNA was prepared and used for the microarray hybridization. Three independent biological replicates were used for each plant sample.
2015-07-02 | E-GEOD-65553 | biostudies-arrayexpress
Project description:CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220. 114 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.
2011-08-01 | E-GEOD-31038 | biostudies-arrayexpress
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 compare induced structural variation among soybean fast neutron lines, developed in background M92-220.
2011-08-02 | GSE31038 | GEO
Project description:CGH was used to compare induced structural variation among soybean fast neutron lines, developed in background M92-220.
2011-08-03 | GSE31111 | GEO
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: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.
2010-12-14 | GSE25294 | GEO
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