Figure 4

Haplotype analysis of trees exhibiting recombination in the chromosome 4 segment associated with pod color. (a) Recombinant trees from population T4 Type 1; (b) recombinant trees from population T4 Type 2; (c) recombinant trees from population MP01. Maternal and paternal haplotypes are shown at the top of each figure. Tree names are colored according to pod-color phenotype. Red represents haplotypes associated with red pod color, and green represents haplotypes associated with green pod color from the two parents, while the yellow marker values represent uncertainty in the haplotype assignment. The black vertical bars surround the most likely region regulating pod-color variation according to the haplotypes of the recombinants (that is, if a recombinant shows only haplotypes for a given marker associated with green pods, but its phenotype is red, this indicates that the marker is not associated with pod color; this is the case for CATIE 1-63 at marker 22,053,861 in (a). The P-values from the Fisher's exact test are shown above each marker for each parent. The P-values are colored by parental phenotype, with the father always being bright red. The location of three candidate genes is indicated by colored dots above the closest markers.