Skip to main content
. 2017 Feb 3;206(1):135–150. doi: 10.1534/genetics.116.198911

Figure 2.

Figure 2

Structure of the Wc locus and Ccd1r haplotypes of maize and teosinte. (a) Sequencing and assembly of a bac clone containing one border of the Wc locus revealed two complete and one partial copy of a 28-kb repeat that included copies of Ccd1 (red) and nearby Tglu (purple) and P450 (turquoise) genes. The repeats are punctuated by a composite Tam3L-like sequence (Tam3Lc), which is shown in greater detail in part d. The rightmost copy of Ccd1 is bordered by an intact Tam3L transposon (Tam3Lb) with a flanking 8-bp host site duplication. The 10-kb segment between Tam3Lb and a second Tam3L transposon (Tam3La) is colinear with the region upstream of Ccd1r in the B73 reference and teosinte genomes that includes Rpl21 (blue, see part c). The 13.5-kb sequence that extends from Tam3La to the right end of the bac clone (abridged for clarity) aligns to sequence located 1.9 Mb proximal to Ccd1r in the B73 reference. Consequently, Tam3La is not flanked by an 8-bp host site duplication. (b) Location of Wc relative to the Ccd1r progenitor locus on the long arm of chromosome 9 (see Figure 1b). (c) Comparison of Ccd1r haplotypes found in maize (B73 reference) and teosinte (data on distributions of Ccd1r haplotypes in maize and teosinte are summarized in Table 3). The teosinte structure was determined by sequencing a 12-kb region containing Ccd1r in Z. mays spp. parviglumis. Gray box with arrow inset, position and orientation of P450 5′-flanking sequence included in Tam3Lc. (d). Structure of Tam3Lc, a composite transposon-like element that punctuates the Wc 28-kb repeats. Numbers in parts a and d indicate coordinates of sequence alignments to the B73 genome (version 3).