Fig. 2

Genomic features of the MM population. In panel a, heterozygosity and allele call failure rate from the Illumina MaizeSNP50 BeadChip in the MM panel. The middle graph reports individual MM lines as gray dots and replicas of founder inbred lines as colored squares. CML91 (seldom present in the MM) and W153R have higher heterozygosity than expected. The other inbreds have residual heterozygosity close to 0.5%. The two replicas of B73, and one each for Mo17 and H99 are not visible because of exceedingly small heterozygosity (0.02%). The observed heterozygosity for the MM (top histogram; mean 3.43%; mode 1.4%) is skewed to the left. The MM lines showing high heterozygosity also show higher failure rate (right histogram), likely due to artifacts in allele calls. In panel b, MAF distribution in the MM founders (gray) and MM lines (red) on a subset of SNP fully genotyped and homozygous in the founder lines. MAF distribution in founders is skewed towards rare alleles, confirming founders’ diversity. This is partially contributed by residual heterozygosity. MAF 0.5 is not reached because nine founders are considered in this calculation. The breeding design successfully shuffled alleles, leveling MAF distribution around founders’ frequency classes