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Abstract
The two independent domestication events in the genus Oryza that led to African and
Asian rice offer an extremely useful system for studying the genetic basis of parallel
evolution. This system is also characterized by parallel de-domestication events,
with two genetically distinct weedy rice biotypes in the US derived from the Asian
domesticate. One important trait that has been altered by rice domestication and de-domestication
is hull colour. The wild progenitors of the two cultivated rice species have predominantly
black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species
and one of the US weedy biotypes are characterized by straw-coloured hulls. Using
Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation
at this locus to study the parallel evolution of hull colour variation in the domesticated
and weedy rice system. We find that independent Bh4-coding mutations have arisen in
African and Asian rice that are correlated with the straw hull phenotype, suggesting
that the same gene is responsible for parallel trait evolution. For the U.S. weeds,
Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship
between the two biotypes and domesticated Asian rice; straw hull weeds are most similar
to indica crops, and black hull weeds are most similar to aus crops. Tests for selection
indicate that Asian crops and straw hull weeds deviate from neutrality at this gene,
suggesting possible selection on Bh4 during both rice domestication and de-domestication.