Polyploidy and Plasticity in the Crop Brassicas

快速的全球变化给农业和自然景观中的植物带来了前所未有的压力。该项目探索了植物生物学中一个鲜为人知的领域：基因组和生物复杂性是如何相关的，以及如何操纵这种关系来设计诸如提高农业应用对非生物和生物胁迫的耐受性等反应。如果下一代科学家得到适当的培训，未来将有丰富的合成生物学应用。为了解决这一差距，该项目将为博士后、研究生和本科生提供系统生物学和预测建模方面的研究培训。该团队将与计算机科学家、建模专家和新闻系学生合作，为新世纪提供综合系统生物学的愿景。所有拟议的研究和推广活动都与招募和指导来自代表性不足群体的学生相结合。该项目将通过日常对话、联合研讨会、团队授课课程和其他场所来展示学员和其他学生。此外，该项目将开发新的计算和基因组方法，将开始整合基因型和表型，从而改变比较生物学。本项目产生的所有数据、计算工具和资源将通过长期存储库和白菜：芸苔生物和基因组进化社区资产提供给更广泛的研究社区，白菜是一个门户网站，将与nsf支持的iPlant协作开发的网络基础设施集成。芸苔属作物具有巨大的形态和化学多样性，是研究驯化和其他经济上重要的植物过程的理想选择。本项目的目的是探索多倍性（两个基因组的合并和加倍）与油菜可塑性之间的关系。通过整合比较基因组学、网络和遗传模型，该项目面临着一个关键问题：“芸苔属作物的全基因组三倍复制是否促进了它们的驯化和适应性？”本项目利用拟南芥的系统生物学和组学资源，重点研究了关于全基因组三倍复制（WGT）如何影响芸苔属植物的两个假设。第一个问题是，芸苔属作物的多倍体是否与代谢和基因表达网络的整体改变有关，是否可能通过复制核心高通量酶来实现更快的生长。第二个是多倍体和随后人类农民的驯化是否改变了芸苔类作物中与生物胁迫相关的网络。具体目标是：(1)利用比较基因组学（跨芸苔和拟南芥种）绘制多倍体后复制基因图谱，并确定多倍体后基因共表达和代谢的变化；(2)在甘蓝（花椰菜、卷心菜、花椰菜、球芽甘蓝和大头菜）和甘蓝（芜菁、白菜、白菜和油籽）的平行驯化过程中，寻找选择和最近对生物胁迫的适应特征；(3)通过对甘蓝F1型杂种基因表达和硫代葡萄糖苷水平的研究，确定基因响应胁迫的功能因子。基因组组织和基因表达的分析将提高目前对代谢创新的遗传基础的理解。转录组和代谢数据的分析将确定驯化过程中选择的变异类型，并描述代谢、生长和生物应激反应的变化。此外，该项目将描述芸苔属植物基因表达模式的进化，并测试芸苔属植物代谢网络的基因组尺度模型，这些模型将通过硫代葡萄糖苷的测量来完善。

Rapid global changes are placing unprecedented pressure on plants in agricultural and natural landscapes. This project explores a poorly understood area of plant biology: how genome and biological complexity are related and how that relationship can be manipulated to design responses such as increased tolerance to abiotic and biotic stresses for agricultural applications. The future promises rich synthetic biology applications, if the next generation of scientists is appropriately trained. To address this gap, this project will provide research training in systems biology and predictive modeling for postdoctoral fellows, and graduate and undergraduate students. This team will partner with computer scientists, modeling experts, and journalism students to provide a vision of integrated systems biology for the new century. All research and outreach activities proposed are integrated with recruiting and mentoring students from underrepresented groups. This project will expose trainees and other students through daily dialogues, joint seminars, team-taught courses, and other venues. In addition, this project will develop novel computational and genomic methods that will start to integrate genotype with phenotype, thus transforming comparative biology. Access to all data, computational tools and resources generated in this project will be provided to the broader research community through long-term repositories and through CABBAGE: Community Assets for Brassica Biology And Genome Evolution, a web portal that will be integrated with the cyberinfrastructure developed by the NSF-supported iPlant Collaborative. Brassica crops have tremendous morphological and chemical diversity and are ideal for studying domestication and other economically important plant processes. The goal of this project is to explore the relationship between polyploidy (the merger and doubling of two genomes) and plasticity using the crop Brassicas. By integrating comparative genomics, networks, and genetic models, this project confronts the key question "Did a whole genome triplication in the crop Brassicas facilitate their domestication and adaptability?". This project leverages the systems biology and -omics resources of Arabidopsis to focus on two hypotheses regarding how whole genome triplication (WGT) affected the Brassicas. The first is whether polyploidy in the crop Brassicas are associated with global alterations to the metabolic and gene expression networks, possibly allowing faster growth through duplication of core, high-flux, enzymes. The second is whether polyploidy and subsequent domestication by human farmers altered the networks related to biotic stress in the crop Brassicas. The specific objectives are to: (1) map post-polyploid duplicated genes using comparative genomics (across species of Brassica and Arabidopsis) and identify post-polyploid changes in gene co-expression and metabolism; (2) search for signatures of selection and recent adaptations to biotic stress during the parallel domestications of Brassica oleracea (broccoli, cabbage, cauliflower, Brussels sprouts, and kohlrabi) and B. rapa (turnips, Chinese cabbage, Pak Choi, and oilseeds); and (3) survey gene expression and glucosinolate levels in F1 hybrids of B. oleracea morphotypes to identify functional elements in genetic response to stress. Analyses of genome organization and gene expression will improve the current understanding of the genetic basis of metabolic innovation. Analyses of transcriptome and metabolic data will identify the types of variation selected during domestication and describe the resulting changes to metabolism, growth, and biotic stress response. Further, this project will describe the evolution of gene expression patterns in Brassica and test genome-scale models of metabolic networks in Brassica, which will be refined with glucosinolate measurements.