Figure 1

Example of graphical display obtained with the Illumina Gene Call Software for 4 different SNPs: (a, c, e, g) germplasm collection genotyping, (b, d, f, h) RIL population genotyping. The 4 SNPs are (a,b) agps1_SNP3, (c,d) cwi2_SNP2, (e,f) TNE003A07_SNP1, (g,h) TE002G22_SNP1. The data points colour codes for the call (red = AA, purple = AB, blue = BB). Genotypes are called for each sample (dots) by their signal intensity (Norm R, y-axis) and Allele Frequency (Norm Theta, x-axis) relative to canonical cluster positions (dark shading) for a given SNP marker. For SNP TNE003A07_SNP1 (e,f), the purple points do not correspond to heterozygous plants but to a third allele. For SNP TE002G22_SNP1 (g,h), the black dots correspond to an additional null allele.