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Background  During the Neolithic revolution, early farmers altered plant development to domesticate crops. Similar traits were often selected independently in different wild species; yet the genetic basis of this parallel phenotypic evolution remains elusive. Plant architecture ranks among these target traits composing the domestication syndrome. We focused on the reduction of branching which occurred in several cereals, an adaptation known to rely on the major gene  Teosinte-branched1  ( Tb1 ) in maize. We investigate the role of the  Tb1  orthologue ( Pgtb1 ) in the domestication of pearl millet ( Pennisetum glaucum ), an African outcrossing cereal.    Methodology/Principal Findings  Gene cloning, expression profiling, QTL mapping and molecular evolution analysis were combined in a comparative approach between pearl millet and maize. Our results in pearl millet support a role for  PgTb1  in domestication despite important differences in the genetic basis of branching adaptation in that species compared to maize (e.g. weaker effects of Pg Tb1 ). Genetic maps suggest this pattern to be consistent in other cereals with reduced branching ( e.g.  sorghum, foxtail millet). Moreover, although the adaptive sites underlying domestication were not formerly identified, signatures of selection pointed to putative regulatory regions upstream of both  Tb1  orthologues in maize and pearl millet. However, the signature of human selection in the pearl millet  Tb1  is much weaker in pearl millet than in maize.    Conclusions/Significance  Our results suggest that some level of parallel evolution involved at least regions directly upstream of  Tb1  for the domestication of pearl millet and maize. This was unanticipated given the multigenic basis of domestication traits and the divergence of wild progenitor species for over 30 million years prior to human selection. We also hypothesized that regular introgression of domestic pearl millet phenotypes by genes from the wild gene pool could explain why the selective sweep in pearl millet is softer than in maize.

Cereal Domestication and Evolution of Branching: Evidence for Soft Selection in the Tb1 Orthologue of Pearl Millet (Pennisetum glaucum [L.] R. Br.)