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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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Density plots for the raw PM probes intensity data.The data are in log2 scale and the biological replicate arrays for rice varieties CP, LG and RT are shown in black, red and green color respectively. CP = Cypress, LG = LaGrue, RT = RT0034 and PM = perfect match.
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pone-0000284-g001: Density plots for the raw PM probes intensity data.The data are in log2 scale and the biological replicate arrays for rice varieties CP, LG and RT are shown in black, red and green color respectively. CP = Cypress, LG = LaGrue, RT = RT0034 and PM = perfect match.

Mentions: The biotin labeled probes generated from labeling of g-DNA was hybridized to Affymetrix rice expression array (see experimental procedure). Following hybridization the preliminary data quality was assessed from GCOS1.3 software (Affymetrix) generated expression report according to guidelines (see Affymetrix manual) set for such experiments. The average background, noise (RawQ) and the call rate was comparable among all the three rice varieties viz. Cypress (CP), LaGrue (LG) and RT0034 (RT) and also among their biological replicates (data not shown). However to get better assessment of data quality the raw intensity data of only perfect match (PM) probes/features of rice varieties viz. CP, LG and RT were log2 transformed and studied by density plots (Figure 1) and pair-wise scatter plots (Figure 2) respectively. The results obtained from density plot indicated no major deviations as replicates of rice varieties were correlated to each other. For scatter plot study 12000 randomly chosen features were plotted against each other for all pair-wise combinations (Figure 2) as suggested in Borevitz's methods paper [12]. No major variation was observed among biological replicates of each variety as most of the features were falling along the diagonal. The features falling above or below diagonal lines indicate their differential hybridization intensity and thus qualify for SFPs. The number of such features showing differential hybridization in CP&LG (blue box) was much less than those in CP&RT (red box) or LG&RT (green box) pairs respectively as one would expect between varieties of same than to different genetic background.


Single feature polymorphism discovery in rice.

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

Density plots for the raw PM probes intensity data.The data are in log2 scale and the biological replicate arrays for rice varieties CP, LG and RT are shown in black, red and green color respectively. CP = Cypress, LG = LaGrue, RT = RT0034 and PM = perfect match.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1808426&req=5

pone-0000284-g001: Density plots for the raw PM probes intensity data.The data are in log2 scale and the biological replicate arrays for rice varieties CP, LG and RT are shown in black, red and green color respectively. CP = Cypress, LG = LaGrue, RT = RT0034 and PM = perfect match.
Mentions: The biotin labeled probes generated from labeling of g-DNA was hybridized to Affymetrix rice expression array (see experimental procedure). Following hybridization the preliminary data quality was assessed from GCOS1.3 software (Affymetrix) generated expression report according to guidelines (see Affymetrix manual) set for such experiments. The average background, noise (RawQ) and the call rate was comparable among all the three rice varieties viz. Cypress (CP), LaGrue (LG) and RT0034 (RT) and also among their biological replicates (data not shown). However to get better assessment of data quality the raw intensity data of only perfect match (PM) probes/features of rice varieties viz. CP, LG and RT were log2 transformed and studied by density plots (Figure 1) and pair-wise scatter plots (Figure 2) respectively. The results obtained from density plot indicated no major deviations as replicates of rice varieties were correlated to each other. For scatter plot study 12000 randomly chosen features were plotted against each other for all pair-wise combinations (Figure 2) as suggested in Borevitz's methods paper [12]. No major variation was observed among biological replicates of each variety as most of the features were falling along the diagonal. The features falling above or below diagonal lines indicate their differential hybridization intensity and thus qualify for SFPs. The number of such features showing differential hybridization in CP&LG (blue box) was much less than those in CP&RT (red box) or LG&RT (green box) pairs respectively as one would expect between varieties of same than to different genetic background.

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