Evolution of Duplicated Pathways and Networks Following Genome Doubling

智力优势。现代植物生物学的一个重要发现是，植物谱系通常起源于物种之间的杂交和随后的杂交基因组加倍。两个不同基因组之间的这种生物团聚启动了广泛的遗传和基因组现象，这些现象通过未知的机制发生，并具有很大程度上未知的功能和进化后果。为了进一步了解基因组倍增的动态和结果，该项目将研究基因组合并和倍增对途径和网络的影响。利用棉花属（Gossypium）作为全基因组加倍研究的成熟模型，本研究将重点关注两种不同的途径和网络。对于花青素的生物合成途径，突变过程，基因表达的变化和代谢物积累之间的多重关系将得到澄清。使用第二个更复杂的网络，涉及开花时间，实验将解决网络对早期棉花驯化者进行的强烈定向选择的反应，因为野生物种被人类从野生，光周期敏感，多年生植物转化为昼长中性，年化行作物。值得注意的是，这一过程在两个不同的物种中得到了复制，这为测试选择性育种反应的可重复性提供了一个独特的机会。这项研究需要三种互补的实验方法。首先，使用新技术，将从祖先基因组以及两种不同栽培棉花的驯化和野生形式中分离和测序核心花青素生物合成途径中涉及的关键蛋白质和开花时间网络中涉及的大约70种蛋白质的所有基因。第二，基因表达的变化将详细的过程中的每个进化阶段，包括杂交，基因组加倍，和人类选择在作物改良。第三，将研究花青素苷途径基因组加倍对代谢物积累的影响。这三个数据源的综合将揭示在物种分化、基因组间杂交和基因组加倍的进化过程中，突变、基因表达和代谢物积累之间的相互关系。总的来说，这些研究将为植物生物学中的一个重要过程提供一个新的视角，具有广泛的概念性和适用性。更广泛的影响：计划开展多项活动，以包容和培训代表性不足的群体的学生，并为学生和K-12教育工作者提供研究经验。该项目特别关注为期七周的教师暑期研究体验计划，该计划为7 - 12年级的生物教师提供了一个机会，以提高他们对科学探究的理解，同时向他们介绍尖端科学。教师将在研讨会上学习理论和方法，并进行与大型正在进行的项目相关的独立项目。他们将接受现代实验室技术的实践培训，包括与基因序列和基因表达分析，代谢物积累和生物信息学相关的技术。此外，教师们将每周在选定的经验丰富的名师指导下开会，讨论将他们的研究经验转移到7 - 12年级的科学课堂上。为了让教师更深入地理解和欣赏进化生物学，Wendel每年夏天都会领导一个教师培训研究小组，重点是将分子遗传学的观点纳入进化生物学的教学。在每个夏季课程结束时，教师将准备在课堂上实施基于研究的教育模块的计划。

Intellectual Merit. A central finding of modern plant biology is that plant lineages often originate from and diversify following hybridization between species and subsequent doubling of the hybrid genome. This biological reunion among two different genomes sets in motion a wide spectrum of genetic and genomic phenomena with that occur through unknown mechanisms and have largely unknown functional and evolutionary consequences. To advance understanding of the dynamics and outcomes of genome doubling, this project will study the consequences of genome merger and doubling on pathways and networks. Using the cotton genus (Gossypium) as a well-developed model for studies of whole-genome doubling, this study will focus on two different pathways and networks. For the anthocyanin biosynthetic pathway, multiple relationships among mutational processes, changes in gene expression, and metabolite accumulation will be clarified. Using a second, more complex network involving flowering time, experiments will address responses of a network to the intense directional selection practiced by early cotton domesticators as the wild species was transformed by humans from a wild, photoperiod-sensitive, perennial plant into a day-length neutral, annualized row crop. Remarkably, this process was replicated for two different species, providing a unique opportunity to test the repeatability of the response to selective breeding. The research entails three complementary experimental approaches. First, using novel technologies, all genes for the key proteins involved in the core anthocyanin biosynthetic pathway and the approximately 70 proteins involved in the flowering time network will be isolated and sequenced from the progenitor genomes, as well as from domesticated and wild forms of two different cultivated species of cotton. Second, changes in gene expression will be detailed for each evolutionary stage in the process, including hybridization, genome doubling, and human selection during crop improvement. Third, the consequences of genome doubling on metabolite accumulation will be studied for the anthocyanin pathway. Synthesis of these three data sources will reveal the interrelationships among mutations, gene expression, and metabolite accumulation, during the evolutionary processes of species divergence, inter-genomic hybridization, and genome doubling. Collectively, these studies will provide a novel perspective on an important process in plant biology, with broad conceptual generality and applicability. Broader Impacts: Multiple activities are planned that target inclusion and training of students from underrepresented groups and provide research experiences for students and K-12 educators. The project has a special focus on a seven-week summer research experience for teachers program, which provides 7th -12th grade biology teachers with an opportunity to enhance their understanding of scientific inquiry while introducing them to cutting-edge science. Teachers will learn theory and methods in workshops and conduct independent projects associated with larger on-going projects. They will receive hands-on training in modern laboratory techniques, including those associated with gene sequence and gene expression analysis, metabolite accumulation, and bioinformatics. Also, teachers will meet weekly under the guidance of selected experienced master teachers to discuss transfer of their research experiences into the 7th -12th grade science classroom. To provide teachers with a deeper understanding and appreciation evolutionary biology, Wendel will lead a teacher training study group each summer, with the explicit focus of incorporating molecular genetics perspectives into the teaching of evolutionary biology. At the end of each summer session, teachers will prepare a plan for implementing research-based education modules in the classroom.