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Single feature polymorphism discovery in rice.

Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT - PLoS ONE (2007)

Bottom Line: The efficacy of such method was tested in rice, and the results presented in the paper indicate high sensitivity in predicting SFP.The sensitivity of polymorphism detection was further demonstrated by the fact that no biasness was observed in detecting SFP with either single or multiple nucleotide polymorphisms.The high density SFP data that can be generated quite effectively by the current method has promise for high resolution genetic mapping studies, as physical location of features are well-defined on rice genome.

View Article: PubMed Central - PubMed

Affiliation: Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America. kumarr@missouri.edu

ABSTRACT
The discovery of nucleotide diversity captured as single feature polymorphism (SFP) by using the expression array is a high-throughput and effective method in detecting genome-wide polymorphism. The efficacy of such method was tested in rice, and the results presented in the paper indicate high sensitivity in predicting SFP. The sensitivity of polymorphism detection was further demonstrated by the fact that no biasness was observed in detecting SFP with either single or multiple nucleotide polymorphisms. The high density SFP data that can be generated quite effectively by the current method has promise for high resolution genetic mapping studies, as physical location of features are well-defined on rice genome.

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SAM plot of normalized data for CP&LG (a) and CP&RT (b) and LG&RT(c) pairs.Observed d-statistics (y-axis) is plotted against the expected d-statistics (x-axis) as determined by permutations and SFPs exceeding the threshold are shown in green. The sign (+/−) with SFPs indicates direction of polymorphism. In (a) the (-) sign (i.e. CP-SFP) indicates polymorphism in LG (i.e. CP>LG) and (+) sign (i.e. LG-SFP) polymorphism in CP (i.e. LG>CP); in (b) the (-) sign (i.e. CP-SFP) signifies polymorphism in RT(i.e. CP>RT) and the (+) sign (i.e. RT-SFP) polymorphism in CP(i.e. RT>CP) and in (c) the (-) sign (i.e. LG-SFP) indicates polymorphism in RT (i.e. LG>RT) and (+) sign (i.e. RT-SFP) polymorphism in LG (i.e. RT>LG). CP = Cypress, LG = LaGrue and RT = RT0034.
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pone-0000284-g003: SAM plot of normalized data for CP&LG (a) and CP&RT (b) and LG&RT(c) pairs.Observed d-statistics (y-axis) is plotted against the expected d-statistics (x-axis) as determined by permutations and SFPs exceeding the threshold are shown in green. The sign (+/−) with SFPs indicates direction of polymorphism. In (a) the (-) sign (i.e. CP-SFP) indicates polymorphism in LG (i.e. CP>LG) and (+) sign (i.e. LG-SFP) polymorphism in CP (i.e. LG>CP); in (b) the (-) sign (i.e. CP-SFP) signifies polymorphism in RT(i.e. CP>RT) and the (+) sign (i.e. RT-SFP) polymorphism in CP(i.e. RT>CP) and in (c) the (-) sign (i.e. LG-SFP) indicates polymorphism in RT (i.e. LG>RT) and (+) sign (i.e. RT-SFP) polymorphism in LG (i.e. RT>LG). CP = Cypress, LG = LaGrue and RT = RT0034.

Mentions: The distribution of gene-chip predicted SFPs (at ≥10% estimated FDR) among polymorphic probesets in the three datasets is shown in Table 2. The observation of ∼6-7xs polymorphism in CP&RT or LG&RT datasets compared to CP&LG in the present study is therefore in agreement with significantly higher genetic divergence between japonica and indica variety of rice [3]–[4], [15] than those observed between varieties of similar genetic background [16]. The SAM plot of normalized data of all the PM probes on array for all the three datasets is shown in Figure 3. The probes exceeding the threshold, shown in green color, signify SFPs, sign (+/−) associated with SFP indicates direction of polymorphism and the values as its SAM d-stat value.


Single feature polymorphism discovery in rice.

Kumar R, Qiu J, Joshi T, Valliyodan B, Xu D, Nguyen HT - PLoS ONE (2007)

SAM plot of normalized data for CP&LG (a) and CP&RT (b) and LG&RT(c) pairs.Observed d-statistics (y-axis) is plotted against the expected d-statistics (x-axis) as determined by permutations and SFPs exceeding the threshold are shown in green. The sign (+/−) with SFPs indicates direction of polymorphism. In (a) the (-) sign (i.e. CP-SFP) indicates polymorphism in LG (i.e. CP>LG) and (+) sign (i.e. LG-SFP) polymorphism in CP (i.e. LG>CP); in (b) the (-) sign (i.e. CP-SFP) signifies polymorphism in RT(i.e. CP>RT) and the (+) sign (i.e. RT-SFP) polymorphism in CP(i.e. RT>CP) and in (c) the (-) sign (i.e. LG-SFP) indicates polymorphism in RT (i.e. LG>RT) and (+) sign (i.e. RT-SFP) polymorphism in LG (i.e. RT>LG). CP = Cypress, LG = LaGrue and RT = RT0034.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC1808426&req=5

pone-0000284-g003: SAM plot of normalized data for CP&LG (a) and CP&RT (b) and LG&RT(c) pairs.Observed d-statistics (y-axis) is plotted against the expected d-statistics (x-axis) as determined by permutations and SFPs exceeding the threshold are shown in green. The sign (+/−) with SFPs indicates direction of polymorphism. In (a) the (-) sign (i.e. CP-SFP) indicates polymorphism in LG (i.e. CP>LG) and (+) sign (i.e. LG-SFP) polymorphism in CP (i.e. LG>CP); in (b) the (-) sign (i.e. CP-SFP) signifies polymorphism in RT(i.e. CP>RT) and the (+) sign (i.e. RT-SFP) polymorphism in CP(i.e. RT>CP) and in (c) the (-) sign (i.e. LG-SFP) indicates polymorphism in RT (i.e. LG>RT) and (+) sign (i.e. RT-SFP) polymorphism in LG (i.e. RT>LG). CP = Cypress, LG = LaGrue and RT = RT0034.
Mentions: The distribution of gene-chip predicted SFPs (at ≥10% estimated FDR) among polymorphic probesets in the three datasets is shown in Table 2. The observation of ∼6-7xs polymorphism in CP&RT or LG&RT datasets compared to CP&LG in the present study is therefore in agreement with significantly higher genetic divergence between japonica and indica variety of rice [3]–[4], [15] than those observed between varieties of similar genetic background [16]. The SAM plot of normalized data of all the PM probes on array for all the three datasets is shown in Figure 3. The probes exceeding the threshold, shown in green color, signify SFPs, sign (+/−) associated with SFP indicates direction of polymorphism and the values as its SAM d-stat value.

Bottom Line: The efficacy of such method was tested in rice, and the results presented in the paper indicate high sensitivity in predicting SFP.The sensitivity of polymorphism detection was further demonstrated by the fact that no biasness was observed in detecting SFP with either single or multiple nucleotide polymorphisms.The high density SFP data that can be generated quite effectively by the current method has promise for high resolution genetic mapping studies, as physical location of features are well-defined on rice genome.

View Article: PubMed Central - PubMed

Affiliation: Division of Plant Sciences, University of Missouri-Columbia, Columbia, Missouri, United States of America. kumarr@missouri.edu

ABSTRACT
The discovery of nucleotide diversity captured as single feature polymorphism (SFP) by using the expression array is a high-throughput and effective method in detecting genome-wide polymorphism. The efficacy of such method was tested in rice, and the results presented in the paper indicate high sensitivity in predicting SFP. The sensitivity of polymorphism detection was further demonstrated by the fact that no biasness was observed in detecting SFP with either single or multiple nucleotide polymorphisms. The high density SFP data that can be generated quite effectively by the current method has promise for high resolution genetic mapping studies, as physical location of features are well-defined on rice genome.

Show MeSH