High Resolution Functional Genomics of Fleshy Fruit Development and Environmental Responses

PI: Jocelyn K.C. Rose（康奈尔大学）CoPIs: 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）肉质果实是植物独特的发育系统，是人类和动物饮食的重要组成部分。番茄（Solanum lycopersicum）是一种重要的经济作物，已成为研究肉质果实发育、成熟、保质期和营养品质的主要模型。然而，有关肉质果实发育、生理、品质性状和环境反应等关键方面的许多基本问题仍未得到解答。该项目将破译植物生物学中的复杂问题，这些问题也对肉质果实的发育和质量至关重要：(i)影响果实生长和成熟的调控过程；（ii）相关的激素生物合成和信号通路；（iii）导致细胞壁形成和重组的分子事件，并提供对环境压力的保护。这个项目的一个重要因素是发展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)每年一次的植物基因组学和系统生物学研讨会，包括一系列集成的“技术模块”，包括“组学学科”的研讨会和实验室实践培训；(2)科学传播的多层次培训课程，提供口头和书面表达技巧的指导。这些项目将隶属于本科生、高中生和高中教师，特别强调通过康奈尔大学现有项目网络的支持，让代表性不足的群体参与进来。迄今为止的研究已经为一些调节果实发育的基因的身份和时间表达模式提供了有价值的初步见解；然而，他们几乎完全使用了整个番茄果皮（“果肉”），并且在很大程度上忽略了不同组成细胞类型中全局基因表达的空间差异。该项目的目标是扩展这些研究，以表征水果对干旱的反应，这是作物生产中日益严重的问题，在番茄中使用尖端的基因组技术。这些研究将扩展到番茄的两个不同的野生近缘品种，它们对水分胁迫表现出较高的耐受性，因此可能为作物改良提供机会。预期的结果是：A)番茄表达图谱（TEA），一个栽培番茄和野生近缘番茄的基因表达数据库，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回路的新见解；B)关于番茄及其野生近缘种在果实发育过程中以及干旱处理后的激素合成和信号通路、细胞壁生物合成和重塑的组织特异性的详细信息。公众可以通过番茄表达图谱（TEA）网站和长期公共资源库访问所有数据和生物材料。所有DNA序列将在生成和质量控制后立即通过Genbank （http://ncbi.nlm.nih.gov）和SGN （http://solgenomics.net）发布到公共领域。本项目生成的原始RNA-Seq、sRNA-seq和BS-seq数据集将提交给NCBI SRA （http://www.ncbi.nlm.nih.gov/sra）进行长期存储和公众访问，而处理后的表达和甲基化谱将通过TEA、番茄功能基因组数据库（http://solgenomics.net/ted）和番茄表观基因组数据库（http://ted.bti.cornell.edu/epigenome）进行存档和访问。

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).