Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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CGH: IsoClark vs. Clark

ABSTRACT: Soybean near-isogenic lines (NILs) differing in iron deficiency chlorosis (IDC) tolerance were genotyped to determine differential genetic introgressions from the donor line T203 into the Clark background. The CGH comparison reveals T203 loci that are differentially introgressed between the IsoClark sub-lines. Comparison of IsoClark soybean NILs to the recurrent parent Clark; the reported values show the log2 ratio of the normalized IsoClark hybridization signals (Cy3) over the normalized Clark hybridization signal (Cy5)

ORGANISM(S): Glycine max

SUBMITTER: Robert Stupar

PROVIDER: E-GEOD-44789 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

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CGH: IsoClark vs. Clark

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