Figure 2. The recombination breakpoints identified in 222 recombinant inbred lines (RILs).

A parent dependent 15 bp sliding window approach was used to identify true recombination breakpoints. A total of 53,223 SNPs identified were scored as “A” and “B” representing alleles from the two parents ICC 4958 and ICC 1882 respectively, and for each individual, the ratio of A and B alleles within the window was calculated using a perl script¹⁸. Windows with nine or more alleles from either parent were considered as homozygous for the respective region. The recombination break point was defined at the transition from one genotype to another. The chromosomes are labelled as Ca1 to Ca8 and are separated by vertical lines while each horizontal line represents a single RIL. Green and red bars represent segments from ICC 4958 and ICC 1882 genotypes, respectively. The number of bins per pseudomolecule ranged from 2.75 to 6.12 while an average of 35.71 bins were identified in an individual RIL. The black and white panel at the bottom indicates the consensus 1,610 bins identified in the entire RIL population.