Figure 3.

Structural variation in the NAM founders. A) Pairwise alignments between Ki11, B73, Il14H on chromosome 8. Grey links represent syntenic aligned regions; gaps of unknown size (scaffold gaps) are marked by dashed lines. B) Large (>100 kbp) structural variants, centromeres, and knobs across the NAM lines versus the B73 reference. The subset of SVs larger than 1 Mbp were manually curated, and only those containing genes are represented. Features 1-5 highlight major SVs: 1) Multiple centromere movement events; 2) A major inversion previously hypothesized based on suppressed recombination; 3) A large deletion in the Ms71 inbred; 4) Knob polymorphism; 5) Reciprocal translocation between chromosome 9 and 10 in the Oh7B inbred (both segments placed in their standard positions for display).