Fig. 6

Structural variation and genetic analysis of the Wc1 locus. a Duplication alignments between A188 and a B73 region identified as A188plus by CGRD. b Tandem repeats of 13 intact copies of 27.4-kb sequences. Two DLE-1 restriction patterns in repeat units: Types A and B were identified. c The QTL result of kernel color using the DH population. Arrows point at locations of known causal genes. d A simplified carotenoid pathway. GGPP stands for geranylgeranyl diphosphate. e Seeds at 16 days after pollination (DAP16) were collected and used for quantifying gene expression (exp) of y1 and ccd1. Three biological replicates were used. Bars are color-coded based on the colors of mature seeds. Error bars represent standard deviation (SD). Letters on top of bars are statistical groups determined by Tukey tests. Y1 (wc1) and y1 (Wc1) stand for B73 and A188 alleles, respectively. Mature seeds from the same lines show slightly different colors from seeds of DAP16. Total carotenoids of mature seeds were measured and the values of mean ± SD are listed. Superscript letters are statistical groups determined by Tukey tests