BackgroundDuring 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 FindingsGene 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 PgTb1). 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/SignificanceOur 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.

Weedy plants with intermediate (domesticated x wild) phenotypes occur in most pearl millet fields in West Africa, even in the absence of wild populations. They are usually found, in high numbers, both inside and outside of drills. Questions pertaining to the evolutionary dynamics of diversity within the pearl millet complex (domesticated-weedy-wild forms) were addressed in this study. The diversity of the different components of this complex sampled in two pearl millet fields in two villages of southwestern Niger was assessed at both molecular (AFLP) and morphological levels. Results show that, in both fields, weedy plants found outside of drills are morphologically distinct from weedy plants found inside drills, despite their close similarity at AFLP markers. The data suggest some introgression from the wild to the weedy population but nevertheless that the gene flow between the parapatric wild and domesticated populations is very low. This challenges the traditional view that regular hybridization between domesticated and wild pearl millets explains the abundance of these weedy plants despite farmers' seed selection. The level of genetic differentiation between fields from the two villages was low when considering domesticated and weedy plants. This could be explained by high gene flow resulting from substantial seed exchanges between farmers. The fact that it is very difficult for farmers to keep their own selected seeds, and the consequent substantial seed exchanges between them, is probably the main factor accounting for the maintenance and dispersal of weedy pearl millets in the region, even in areas where no wild forms have been observed.