Abstract
The rice orthologue of maize domestication gene Teosinte branched 1 (Tb1) affects tillering. But, unlike maize Tb1 gene, it was not selected during domestication. Here, we report that an OsTb1 duplicate gene (OsTb2) has been artificially selected during upland rice adaptation and that natural variation in OsTb2 is associated with tiller number. Interestingly, transgenic rice overexpressing this gene shows increased rather than decreased tillering, suggesting that OsTb2 gains a regulatory effect opposite to that of OsTb1 following duplication. Functional analyses suggest that the OsTb2 protein positively regulates tillering by interacting with the homologous OsTb1 protein and counteracts the inhibitory effect of OsTb1 on tillering. We further characterize two functional variations within OsTb2 that regulate protein function and gene expression, respectively. These results not only present an example of neo-functionalization that generates an opposite function following duplication but also suggest that the Tb1 homologue has been selected in upland rice.
Highlights
The rice orthologue of maize domestication gene Teosinte branched 1 (Tb1) affects tillering
Our previous analysis of upland rice genomes and irrigated rice genomes revealed that another gene, which is a paralogue of OsTb1 located on rice chromosome 9, is highly differentiated between the two ecotypes[10]
In our previous comparative genomic study[10], we found that Os09g0410500 on chromosome 9, a homologue of the maize Tb1 gene, was highly differentiated between the two ecotypes
Summary
The rice orthologue of maize domestication gene Teosinte branched 1 (Tb1) affects tillering. We further characterize two functional variations within OsTb2 that regulate protein function and gene expression, respectively These results present an example of neofunctionalization that generates an opposite function following duplication and suggest that the Tb1 homologue has been selected in upland rice. We find that a 3 base pair (bp) indel in the coding region of OsTb2 is divergent between the japonica and indica subspecies and that in japonica, the 3 bp insertion enhances the function of OsTb2 in promoting tillering Another functional variation is a T to C mutation that has been selected and fixed in upland rice. Our findings provide another vivid example of gene neo-functionalization and demonstrate that paralogous genes with opposite functions might be selected during domestication and breeding
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