ABSTRACT: 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).
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.
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.
Project description:Soybean nested association mapping (NAM) parent lines were compared by CGH to catalog structurally variant (e.g. deletion and duplication) regions among these genotypes. The CGH comparisons reveal reveal putative deletions and duplications among the 41 lines. NAM parent lines were compared through a common reference, Wm82-ISU-01 (this is a sub-line isolated from the cultivar Williams 82 stock). Each NAM parent line was represented by a single individual plant. The reported values show the log2 ratio of the normalized NAM parent line hybridization signals (Cy3) over the normalized Wm82-ISU-01 hybridization signal (Cy5).
Project description: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)
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.
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.
Project description:There is growing evidence for the prevalence of DNA copy number variation (CNV) and its role in phenotypic variation in recent years. Comparative genomic hybridization (CGH) was used to explore the extent of this type of structural variation in the barley genome. In a panel of 14 genotypes including domesticated cultivars and wild barleys, we found that 14.9% of all the sequences on the array are affected by CNV. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. A substantial portion (37%) of the CNV events are present in both wild and domesticated barley. CNVs are enriched in telomeric regions for all chromosomes except 4H, which is also the barley chromosome with the lowest proportion of CNVs. CNV affected 9.5% of the coding sequences represented on the array. The genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases, suggesting the potential for CNV to influence variation for responses to biotic and abiotic stress. The analysis of CNV breakpoints indicated that DNA repair mechanisms of double-strand breaks (DSBs) via single-stranded annealing (SSA) and synthesis-dependent strand annealing (SDSA) play an important role in the origin of many structural changes in barley. Here we present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. 1-2 replications of 8 barley cultivars and 6 wild barley accessions were hybridized to an array designed from 115,003 whole genome shotgun (WGS) contigs of the ‘reference’ genome of cv. Morex
Project description:Two soybean near-isogenic lines (NILs) differing in seed protein content were genotyped to determine differential genetic introgressions from the wild relative Glycine soja. The CGH comparison reveals loci that are differentially introgressed between the two lines. Comparison of HiPro (LD0-15154) and LoPro (LD0-15146) soybean NILs; the reported values show the log2 ratio of the normalized HiPro hybridization signal (Cy3) over the normalized LoPro hybridization signal (Cy5)
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.
Project description:Different individuals of the same species are generally thought to have very similar genomes. However, there is growing evidence that structural variation in the form of copy number variation (CNV) and presence-absence variation (PAV) can lead to variation in the genome content of individuals within a species. In order to investigate the potential contribution of CNV and PAV to genomic diversity in maize we used array comparative genomic hybridization (CGH) to compare gene content and copy number variation among 25 diverse maize inbreds 14 genotypes of the wild ancestor of maize, teosinte. The microarray included multiple probes for each of the ~32,500 stringently filtered genes identified in the B73 reference genome. We identified 479 genes exhibiting higher copy number in some genotypes (UpCNV) and 3,410 genes that have either fewer copies or are missing in the genome of at least one genotype relative to B73 (DownCNV/PAV). Many of these DownCNV/PAV are examples of genes that are present in B73 but missing from the genome of several other genotypes. Over 70% of the CNV/PAV examples are identified in multiple genotypes and the majority of events are observed in both maize and teosinte suggesting that these reflect relatively old variants that are not associated with domestication or maize improvement. Many of the genes affected by CNV/PAV are either maize-specific or members of genes families suggesting that the gene loss can be tolerated through buffering by redundant functions encoded elsewhere in the genome. Many plant genomes are relatively large and contain the remnant of whole genome duplications which may provide the ability to tolerate high levels of structural variation. While this structural variation may not result in major qualitative variation due to genetic buffering, it may significantly contribute to quantitative variation. 1-2 replications of 25 maize inbred and 14 teosinte genotypes were hybridized to an array designed from the ~32,400 genes in the maize B73 reference genome.