Figure 4: B73 or Mo17 specific HAKmers.

(a) Genome-wide distributions of all rDNA-related k-mers, B73- and Mo17-specific k-mers that can be perfectly aligned to the B73Ref3 reference genome. Alignment counts (e.g., 100 was used to represent alignments of 10 k-mers and 10 hits per k-mer) per bin (100 kb) were plotted versus bin physical locations at the B73Ref3. (b) Counts of a Mo17-specific k-mer in IBM DH lines were treated as a trait and the genomic loci (or locus) contributing the levels of counts in DH lines were mapped. (c) Principal component analysis (PCA) was performed using normalized counts of each B73- or Mo17-specific k-mer in multiple teosinte, landrace, and improved maize lines. Numbers in parentheses are percentages of variation in normalized counts explained by principal component (PC) 1 and 2. (d) Sum of normalized counts of all B73-specific k-mers (blue) or Mo17-specific k-mers (green) in different lines from HapMap2 WGS sequencing data without error correction. Bars were sorted in the subspecies order, teosinte (first Parviglumis then Mexicana), landrace, and improved maize lines. Within each subspecies, bars were sorted by total counts of B73-specific k-mers first and then by total counts of Mo17-specific k-mers.