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Figure 1 | BMC Genomics

Figure 1

From: SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

Figure 1

Examples of seven SNP loci validated by the Illumina GoldenGate genotyping assay showing homozygous and heterozygous cluster separation for 91 rice genotypes based on plotting of normalized R [sum of intensities of the two channels (Cy3 and Cy5)] on the y axis vs. normalized theta [(2/π)Tan-1(Cy5/Cy3)] on the x axis. A normalized theta value nearest to 0 is homozygous for allele A (japonica “Nipponbare” type), a theta value nearest to 0.5 is heterozygote AB and a theta value nearest to 1 is homozygous for allele B (indica “93–11” type). Two graphs demonstrate the monomorphic SNP loci (plots A and C), while five others (plots B, D, E, F and G) show polymorphic SNP loci with clear separation between the three genotypic classes.

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