Genomic constrains on domestication: Why are so few species domesticated?

Gaining an understanding of the molecular basis of crop domestication allows researchers to pinpoint 'domestication genes' - those involved in larger fruit, more seeds or enhanced germination. It is assumed that selection at these genes involved a novel mutation arising (e.g. fruit elongation in tomato) or through selection on standing genetic variation (e.g. branching in maize). A third understudied mechanism could be that phenotypic plasticity 'pushed' the crop progenitor in the direction that humans then selected for. For example, wild Brassicas grown in cultivation exhibit significantly larger roots; could this have been the first step towards domestication of turnips?
In this project, not only will phenotypic plasticity be assessed, but gene expression plasticity too. Therefore, we are not limited to a handful of morphological traits, but we have the potential to test this hypothesis from data derived from thousands of expression traits. We therefore can answer whether plasticity in the wild progenitors of crops was selected upon by humans. Further, using existing genomic data we can investigate the molecular basis of gene expression divergence and genome evolution during domestication, how these correlate to protein sequence evolution and whether they depend on transposable element integration.
The student will (1) assess phenotypic and gene expression plasticity in crops and their wild relatives; (2) identify genes, networks and pathways that have experienced selection; and (3) answer the question whether phenotypic plasticity plays an important role in domestication.
We anticipate that this new way to investigate domestication will uncover novel domestication genes in our chosen crops. These genes have the potential to underlie important phenotypes and could be the basis for future crop improvement in changing climate. As such this project has significant impact potential from basic and applied angles, ranging from understand how evolution canalises plasticity, to discovering the genetic basis of adaptive traits in crops.