Mutations that cause amino acid substitutions at the invariant positions in homeodomain of OSH3 KNOX protein suggest artificial selection during rice domestication.

KNOX homeodomain (HD) proteins encoded by KNOTTED1-like homeobox genes (KNOX genes) are considered to work as important regulators for plant developmental and morphogenetic events. We found that OSH3, one of the KNOX genes isolated from a cultivar of Oryza sativa (Nipponbare), encodes a novel HD, which has two amino acid substitutions at invariant positions. Sequence analysis of OSH3 from various domesticated and wild species of rice has revealed that these substitutions are distributed only in Japonica and Javanica type of O. sativa, two groups of domesticated rice in Asia. Surprisingly, nucleotide sequences in the first intron are almost conserved in the rice strains that have the substitutions at the invariant amino acids. Overexpression studies revealed that these invariant amino acids are critical for the function of OSH3 in vivo. The facts that these substitutions occurred specifically at the functionally important amino acids and the sequences are conserved in intron where neutral mutations accumulate suggest the substitutions at the invariant positions of OSH3 have been fixed by artificial selections during domestication. Based on these observations, we hypothesize that OSH3 is responsible for one of the traits that are selectively introduced during the domestication of most of Japonica and a part of Javanica type of rice.