Fig. 2

Schematic representation of verifying the homologous haplotype origin in Saccharum hybrid R570 based on homo(oe)ologous gene allele sequence comparison with two progenitor Saccharum species as references. Notes: Similar analyses as Garsmeur et al. (2011) [18] were performed for the schematic. Each gene allele is represented by a square. For each locus, the most divergent allele is marked in black and its theoretical divergence time (highest estimate observed in Myr) is indicated in italics. All alleles that fall into groups (of at least three) with all values lower than one-third of this maximum divergence time are marked by white squares. When the phylogenetic trees were not degenerate, the alleles (loci 6, 7, 8, and 11b) of the same branch (relating to the same internal node) were placed in vertical dotted boxes. But for five alleles of loci 7, the alleles from the same phylogenetic tree branch were placed in the transparent blue boxes due to they distribute separately in the figure. The white triangle in the black square for locus 11a indicates an insertion. The ‘x’ mark indicates absence of the gene