Figure 1From: SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structureExamples 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.Back to article page