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goldengate genotyping assay  (GoldenGate Software Inc)

 
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    GoldenGate Software Inc goldengate genotyping assay
    Goldengate Genotyping Assay, supplied by GoldenGate Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/goldengate+genotyping/goldengate+genotyping+assay/10__1007_slash_s42161___024___01815___9-82-0-0
    Average 90 stars, based on 1 article reviews
    goldengate genotyping assay - by Bioz Stars, 2026-11
    90/100 stars

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    Related Articles

    Sequencing:

    Article Title: Resolving drug selection and migration in an inbred South American Plasmodium falciparum population with identity-by-descent analysis.
    Article Snippet: GoldenGate calls were decoded using genotyping results from a 3D7 lab strain that were then compared to the PlasmoDB 3D7 reference sequence, as well as Dd2, Santa Lucı́a, HB3 and 7G8 [86,87]. .. Sixteen samples from Colombia had undergone both GoldenGate genotyping and whole genome sequencing, and we confirmed that the two platforms made identical calls in all cases with the exception of one site that was then masked from analysis. ..

    Genotyping:

    Article Title: SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping
    Article Snippet: Among the 360 genotype × SNP data, 357 (99.2%) were in agreement with the GoldenGate genotyping and Sanger sequences. .. In two cases (PSY-C-246 for 'Eureka' lemon and LCY2-P-75 for 'Sunki' mandarin), the GoldenGate genotyping concluded heterozygosity, while the Sanger sequencing inferred homozygosity. ..

    Article Title: Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea
    Article Snippet: .. Our study shows that the GoldenGate genotyping is very reliable, as also demonstrated in wheat [ ]. ..

    Article Title: SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species
    Article Snippet: .. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. ..

    Article Title: SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping
    Article Snippet: To validate the genotyping data, 24 of the 54 Citrus accessions that were genotyped with the GoldenGate array were sequenced (Sanger) for 15 SNPs from five genes. .. Among the 360 genotype × SNP data, 357 (99.2%) were in agreement with the GoldenGate genotyping and Sanger sequences. .. In two cases (PSY-C-246 for 'Eureka' lemon and LCY2-P-75 for 'Sunki' mandarin), the GoldenGate genotyping concluded heterozygosity, while the Sanger sequencing inferred homozygosity.

    DNA Sequencing:

    Article Title: SNP mining in C. clementina BAC end sequences; transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic mapping
    Article Snippet: Among the 360 genotype × SNP data, 357 (99.2%) were in agreement with the GoldenGate genotyping and Sanger sequences. .. In two cases (PSY-C-246 for 'Eureka' lemon and LCY2-P-75 for 'Sunki' mandarin), the GoldenGate genotyping concluded heterozygosity, while the Sanger sequencing inferred homozygosity. ..

    Recombinant:

    Article Title: SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species
    Article Snippet: .. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. ..

    Article Title: A transcriptome map of perennial ryegrass ( Lolium perenne L.)
    Article Snippet: In more complex genomes such as soybean, GoldenGate genotyping has been used for linkage mapping in recombinant inbred line mapping populations [ ]. .. In more complex genomes such as soybean, GoldenGate genotyping has been used for linkage mapping in recombinant inbred line mapping populations [ ]. .. However, the rate of 89% successfully scored SNPs indicated that the genome complexity of soybean had limited impact on GoldenGate performance in a carefully selected SNP panel [ ].



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    Examples of SNP graphs observed in Lolium oligo pool assay (LOPA1) GoldenGate <t>genotyping.</t> SNP graphs are illustrated using the Software Illumina® GenomeStudio, version 2009.2. The normalized R (y-axis) is the normalized sum of intensities of the two dyes (Cy3 and Cy5), the normalized Theta (x-axis) is the deviation of Cy3 and Cy5 fluorescence from pure Cy3 and pure Cy5 signal (0 and 1). A normalized Theta value close to 0 and 1 is homozygous for SNP variant 1 and 2, respectively, a heterozygous sample is in between. The red, blue and purple ovals have the diameter of two standard deviations computed from the dispersal of the red, blue and purple dots, respectively. The numbers of plants in each cluster are indicated below the x-axis. ( A ) The 192 samples genotyped for SNP marker PTA.1021.C1 revealed fluorescence signal intensities close to 0, indicating assay failure. ( B ) Although the clustering algorithm at SNP PTA.1.C3 distinguished the three clusters at a GenTrain score of 0.40, such a genotyping pattern was considered inaccurate and this SNP was discarded from further analysis. ( C ) This illustration shows the SNP graph of monomorphic P9G02. ( D ) and ( E ) illustrate dominant SNPs being homozygous in one and heterozygous in the other mapping parent. For genetic linkage mapping, the markers PTA.109.C1 and PTA.291.C1 followed the segregation type nnxnp and lmxll, respectively . Dots corresponding to the parents of the VrnA mapping population (which are represented in duplicates) are highlighted in yellow. Graph ( F ) shows a classical example of a SNP marker being heterozygous in both parents following the segregation pattern hkxhk.
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    Image Search Results


    Examples of SNP graphs observed in Lolium oligo pool assay (LOPA1) GoldenGate genotyping. SNP graphs are illustrated using the Software Illumina® GenomeStudio, version 2009.2. The normalized R (y-axis) is the normalized sum of intensities of the two dyes (Cy3 and Cy5), the normalized Theta (x-axis) is the deviation of Cy3 and Cy5 fluorescence from pure Cy3 and pure Cy5 signal (0 and 1). A normalized Theta value close to 0 and 1 is homozygous for SNP variant 1 and 2, respectively, a heterozygous sample is in between. The red, blue and purple ovals have the diameter of two standard deviations computed from the dispersal of the red, blue and purple dots, respectively. The numbers of plants in each cluster are indicated below the x-axis. ( A ) The 192 samples genotyped for SNP marker PTA.1021.C1 revealed fluorescence signal intensities close to 0, indicating assay failure. ( B ) Although the clustering algorithm at SNP PTA.1.C3 distinguished the three clusters at a GenTrain score of 0.40, such a genotyping pattern was considered inaccurate and this SNP was discarded from further analysis. ( C ) This illustration shows the SNP graph of monomorphic P9G02. ( D ) and ( E ) illustrate dominant SNPs being homozygous in one and heterozygous in the other mapping parent. For genetic linkage mapping, the markers PTA.109.C1 and PTA.291.C1 followed the segregation type nnxnp and lmxll, respectively . Dots corresponding to the parents of the VrnA mapping population (which are represented in duplicates) are highlighted in yellow. Graph ( F ) shows a classical example of a SNP marker being heterozygous in both parents following the segregation pattern hkxhk.

    Journal: BMC Genomics

    Article Title: A transcriptome map of perennial ryegrass ( Lolium perenne L.)

    doi: 10.1186/1471-2164-13-140

    Figure Lengend Snippet: Examples of SNP graphs observed in Lolium oligo pool assay (LOPA1) GoldenGate genotyping. SNP graphs are illustrated using the Software Illumina® GenomeStudio, version 2009.2. The normalized R (y-axis) is the normalized sum of intensities of the two dyes (Cy3 and Cy5), the normalized Theta (x-axis) is the deviation of Cy3 and Cy5 fluorescence from pure Cy3 and pure Cy5 signal (0 and 1). A normalized Theta value close to 0 and 1 is homozygous for SNP variant 1 and 2, respectively, a heterozygous sample is in between. The red, blue and purple ovals have the diameter of two standard deviations computed from the dispersal of the red, blue and purple dots, respectively. The numbers of plants in each cluster are indicated below the x-axis. ( A ) The 192 samples genotyped for SNP marker PTA.1021.C1 revealed fluorescence signal intensities close to 0, indicating assay failure. ( B ) Although the clustering algorithm at SNP PTA.1.C3 distinguished the three clusters at a GenTrain score of 0.40, such a genotyping pattern was considered inaccurate and this SNP was discarded from further analysis. ( C ) This illustration shows the SNP graph of monomorphic P9G02. ( D ) and ( E ) illustrate dominant SNPs being homozygous in one and heterozygous in the other mapping parent. For genetic linkage mapping, the markers PTA.109.C1 and PTA.291.C1 followed the segregation type nnxnp and lmxll, respectively . Dots corresponding to the parents of the VrnA mapping population (which are represented in duplicates) are highlighted in yellow. Graph ( F ) shows a classical example of a SNP marker being heterozygous in both parents following the segregation pattern hkxhk.

    Article Snippet: Here, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome.

    Techniques: Pool Assay, Software, Fluorescence, Variant Assay, Marker