Comparative genetics of pigmentation patterns due to multiple alleles at the C gene in cultivated rice

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Diverged phenotypes is often detected in domesticated plants despite invariant phenotypes in their wild forms. One of an example in rice is observed in varying degrees of apiculus coloration due to anthocyanin pigmentation which was previously reported to be caused by a series of alleles in the C locus. The present study revealed, based on their comparative map, that a possible candidate of the C gene is the rice homologue (OsCl) of the maize Cl that belongs to the group of R2R3-Myb factors. Two different types of deletions causing a frameshift were detected in the 3rd exon and both the deleted nucleotides were corresponding to the positions of putative base-contacting residues, suggesting that Indica and Japocia types carries mutations of loss of function with their independent origins. In addition, replacement substitutions were frequently detected in OsCl of strains carrying the previously defined C alleles. Molecular population analysis revealed that 17 haplotypes were found in 39 wild and cultivated rice and haplotypes of cultivated forms were mostly included into one of the three distinct groups, showing few shared haplotypes between taxa including Indica an Japonica types. The genealogy of the OsCl gene suggested that allelic diversification causing phenotypic change possibly resulted from mutations in the coding region rather than from recombination between pre-existing alleles. The changes in amino acids might be associated with selective forces that took places in the lineage of O. sativa as supported by a Ka/Ks ratio higher than 1.0, which gives a significant implication on genetic diversity in landraces.