Fig. 1

Genotyping of InDel CNVMAIZE_DEL_12661 using three probe types on 445 individuals. a Schematic distribution of the 9 probes along the sequence of InDel CNVMAIZE_DEL_12661 (green line) and the bordering sequence common between all individuals (blue line) genotyped by the array. Double, dotted, and full arrows represented the probes designing on the forward and reverse flanking sequences of the breakpoint sites (BP), at not polymorphic (MONO) and polymorphic sites (OTV) within internal sequence of InDel. b Schematic distribution of the 8 probes passing Affymetrix® quality control and called by the Affymetrix® pipeline c) Clustering produced by the Affymetrix® algorithm for an OTV, MONO, and BP probe from InDel based on both fluorescence contrast (X axis) and intensity (Y axis) of the 445 inbred lines. Red, blue and yellow dots indicated the presence of the sequence (genotype “present”) either homozygous for allele A (AA) or allele B (BB) or heterozygous (AB), respectively. Cyan and green indicated that the sequence was absent in the individual (OO), or only in one copy of the sequence, e.g. hemizygous for presence/absence (OB or OA). Black dots indicated individuals for which no genotype could be assigned (Missing data) d) Haplotypes displayed by the genotyping using 8 probes (column) on the 445 inbred lines (row). Colors corresponded to the genotype of individuals produced by clustering in c)