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

驯化的基因组限制：为什么驯化的物种如此之少？

• 批准号: 2441463
• 金额: --
• 依托单位: University of Southampton
• 依托单位国家: 英国
• 项目类别: Studentship
• 财政年份: 2020
• 资助国家: 英国
• 起止时间: 2020 至 无数据
• 项目状态: 未结题
• 来源: https://gtr.ukri.org/projects?ref=studentship-2441463
• 关键词: Genomic; constrains; domestication; Why; so

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.

了解作物驯化的分子基础使研究人员能够查明“驯化基因”——那些与更大的果实、更多的种子或增强的发芽有关的基因。假设这些基因的选择涉及新突变的产生（例如番茄的果实伸长）或通过对固定遗传变异的选择（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，栽培中的野生芸苔属植物表现出明显更大的根；这可能是萝卜驯化的第一步吗？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，我们不仅限于少数形态特征，而且我们有潜力从数千个表达特征得出的数据中检验这一假设。因此，我们可以回答农作物野生祖先的可塑性是否是人类选择的。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缘种的表型和基因表达可塑性； (2) 识别经历选择的基因、网络和通路； (3)回答表型可塑性在驯化过程中是否发挥重要作用的问题。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，并可能成为未来气候变化下作物改良的基础。因此，该项目从基本和应用角度具有重大影响潜力，从了解进化如何发挥可塑性，到发现作物适应性特征的遗传基础。