High Resolution Functional Genomics of Fleshy Fruit Development and Environmental Responses

PI：Jocelyn K.C. Rose（康奈尔大学）CoPI：Carmen Catala和Zhangjun Fei（博伊斯汤普森植物研究所）和James J. Giovannoni（USDA-ARS/博伊斯汤普森植物研究所）肉质水果是独特的植物发育系统，为人类和动物提供重要的饮食成分。番茄是一种重要的经济作物，已成为肉质果实发育、成熟、货架期和营养品质研究的主要模式。然而，与肉质果实的发育、生理、品质性状和环境响应的关键方面相关的许多基本问题仍然没有答案。该项目将破译植物生物学中的复杂问题，这些问题也是肉质果实发育和质量的核心：（i）影响果实生长和成熟的调节过程;（ii）相关的激素生物合成和信号传导途径;（iii）导致细胞壁形成和重组的分子事件，并提供保护免受环境胁迫。该项目的一个重要内容是发展一个强有力的教育和培训组成部分。这将采取两个方案的形式：（1）年度植物基因组学和系统生物学研讨会，包括一系列综合的“技术模块”与研讨会和实验室为基础的实践培训“组学学科”;（2）在科学传播的多层次培训课程，提供口头和书面陈述技巧的指导。这些将与本科生，高中生和高中教师联系，特别强调通过现有康奈尔计划网络的支持，代表性不足的群体的参与。迄今为止的研究提供了宝贵的初步见解的身份和时间表达模式的一些基因，调节水果的发展，然而，他们几乎完全使用总番茄果皮（“肉”），并在很大程度上忽略了空间变化的全球基因表达的不同组成细胞类型。该项目的目标是利用尖端基因组学技术，将这些研究扩展到表征番茄果实对干旱的反应，干旱是作物生产中日益严重的问题。这些研究将扩展到番茄的两种不同的野生亲缘植物，它们对水分胁迫表现出很高的耐受性，因此可能为作物改良提供机会。预期成果是：A）番茄表达图谱（TEA），栽培番茄和野生亲缘植物的基因表达数据库，以及在细胞/组织类型分辨率水平上对控制果实发育和对干旱反应的调控电路的新见解; B）关于番茄和野生近缘种果实发育期间激素生物合成和信号传导途径的组织特异性以及细胞壁生物合成和重塑的详细信息，干旱处理后。 公众将通过番茄表达图谱（TEA）网站和长期公共存储库访问所有数据和生物材料。所有DNA序列将在生成后立即通过Genbank（http：//www.example.com）和SGN（http：solgenomics.net）进行质量控制并发布到公共领域。ncbi.nlm.nih.gov在本项目下生成的原始RNA-Seq、sRNA-seq和BS-seq数据集将提交给NCBI SRA（http：//www.ncbi.nlm.nih.gov/sra）进行长期储存和公众访问，而处理后的表达和甲基化图谱将通过TEA和番茄功能基因组学数据库（http：//solgenomics.net/ted）和番茄表观基因组数据库（http：//ted.bti.cornell.edu/epigenome）存档和访问。

PI: Jocelyn K.C. Rose (Cornell University) CoPIs: Carmen Catala and Zhangjun Fei (Boyce Thompson Institute for Plant Research) and James J. Giovannoni (USDA-ARS/Boyce Thompson Institute for Plant Research) Fleshy fruit are unique plant developmental systems and provide important components of human and animal diets. Tomato (Solanum lycopersicum), an economically important crop, has emerged as the principal model for studies of fleshy fruit development, ripening, shelf life and nutritional quality. However, many fundamental questions related to key aspects of the development, physiology, quality traits and environmental responses of fleshy fruit remain unanswered. This project will decipher complex problems in plant biology that are also central to fleshy fruit development and quality: (i) the regulatory processes that influence fruit growth and ripening; (ii) the associated hormone biosynthesis and signaling pathways; and (iii) molecular events that result in cell wall formation and restructuring, and that provide protection from environmental stresses. An important element of this project is the development of a strong education and training component. This will take the form of two programs: (1) an annual Plant Genomics and Systems Biology Workshop, comprising a series of integrated 'technology modules' with both seminars and lab-based practical training in 'omics disciplines'; (2) a multi-level training course in Scientific Communication, providing guidance in both oral and written presentation skills. These will be affiliated with undergraduate students, high school students and high school teachers, with particular emphasis on the participation of under-represented groups through the support of a network of existing Cornell programs. Studies to date have provided valuable initial insights into the identity and temporal expression patterns of some of the genes that regulate fruit development; however, they have almost exclusively used total tomato fruit pericarp ('flesh') and have largely ignored spatial variation in global gene expression in the different constituent cell types. The goal of this project is to extend these studies to characterize the responses of fruits to drought, an increasing problem in crop production, in tomato using cutting edge genomics technologies. These studies will be extended to two diverse wild relatives of tomato that show a high tolerance of water stress, and so may provide opportunities for crop improvement. The expected outcomes are: A) the Tomato Expression Atlas (TEA), a gene expression database for cultivated tomato and wild relatives, and new insights into the regulatory circuitry that controls fruit development and responses to drought, at a cell/tissue type level of resolution; B) detailed information about the tissue specificity of hormone biosynthesis and signaling pathways, and cell wall biosynthesis and remodeling during fruit development in tomato and wild relatives, and following drought treatments. Public access to all data and biological materials will be through the Tomato Expression Atlas (TEA) website and long-term public repositories. All DNA sequences will be released to the public domain immediately after generation and quality control through Genbank (http://ncbi.nlm.nih.gov) and SGN (http://solgenomics.net). Raw RNA-Seq, sRNA-seq and BS-seq datasets generated under this project will be submitted to NCBI SRA (http://www.ncbi.nlm.nih.gov/sra) for long term storage and public access while processed expression and methylation profiles will be archived and accessed through the TEA and through the Tomato Functional Genomics Database (http://solgenomics.net/ted) and the Tomato Epigenome database (http://ted.bti.cornell.edu/epigenome).