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

Abstract

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.

Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

“…Particularly in RL41, one non-synonymous substitution is a parsimony informative site that changes the protein sequence at that codon position. Nevertheless, this kind of changes are frequently seen on inbred lines that were subjected to artificial selection, for instance, missense changes were observed in invariant sites of HD proteins of rice cultivars as a probable consequence of artificial selection during the domestication process [ 54 ].…”

Intragenic diversity and functional conservation of the three homoeologous loci of the KN1-type homeobox gene Wknox1 in common wheat

“…The rice OSH3 locus is only 15-kb apart from that of OSH1 (Sentoku et al, 1999). A number of mutations accumulated in the OSH3 intron regions and two amino acid substitutions were found at invariant positions of its homeodomain region (Sato et al, 2001). Structural mutations within and/or near the Wknox3a locus, which is located at the vicinity of the Wknox1a locus (S. Takumi, R. Morimoto and C. Nakamura, unpublished result), should be further studied to clarify the relationship between the wheat KNOX genes and the Hd mutation.…”

The DROOPING LEAF and OsETTIN2 genes promote awn development in rice

“…OsETT1 (Os05g0563400), OsETT2 (Os01g0670800) and OsETT3 (Os01g0753500) have been described previously (Sato et al ., ; Nagasaki et al ., ; Toriba et al ., ). A fourth gene, Os05g0515400, is designated OsETT4 in this study.…”