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

通过了解作物驯化的分子基础，研究人员可以精确定位“驯化基因”--那些与果实更大、种子更多或发芽增强有关的基因。假设在这些基因上的选择涉及到一个新的突变(例如番茄的果实伸长)或通过对现有遗传变异的选择(例如玉米的分枝)。第三个未被研究的机制可能是表型可塑性将作物祖先推向人类随后选择的方向。例如，栽培中种植的野生甘蓝表现出明显更大的根；这是否可能是驯化萝卜的第一步？在这个项目中，不仅将评估表型可塑性，还将评估基因表达可塑性。因此，我们并不局限于少数几个形态特征，但我们有可能从来自数千个表达特征的数据中检验这一假设。因此，我们可以回答作物野生祖先的可塑性是否是人类所选择的。此外，利用现有的基因组数据，我们可以研究驯化过程中基因表达差异和基因组进化的分子基础，它们如何与蛋白质序列进化相关，以及它们是否依赖于转座元件整合。学生将(1)评估作物及其野生近亲的表型和基因表达可塑性；(2)识别经历过选择的基因、网络和途径；(3)回答表型可塑性是否在驯化中起重要作用的问题。我们预计，这种研究驯化的新方法将在我们选择的作物中发现新的驯化基因。这些基因有可能成为重要表型的基础，并可能成为未来在气候变化中改良作物的基础。因此，该项目从基础和应用角度具有重大影响潜力，从了解进化如何引导可塑性，到发现作物适应性特征的遗传基础。

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.