Developmental Mechanisms Underlying Fleshy Fruit Diversity in Rosaceae

联合负责人：Sridhar Hannenhalli，美国马里兰州大学联合负责人：Chris Dardick，美国农业部阿巴拉契亚水果研究实验室联合负责人：Ann Callahan，美国农业部阿巴拉契亚水果研究实验室联合负责人：人们喜爱的水果也特别适合植物种子传播。即使是关系密切的植物也会表现出不同类型的肉质果实，通过颜色、形状、大小、质地和其他特征的变化来实现传播。植物生物学家和水果作物科学家面临的一个主要问题是，这些不同的水果类型是如何进化的，是什么因素控制了它们的发育。如果科学家能够解释不同水果类型的分子基础，可以使用新的育种工具来提高水果作物的价值，并可以推进基础研究。玫瑰科（蔷薇科）是一个很好的例子，说明水果是如何被选择和适应不同类型的传播的。这个家族的成员，包括我们熟悉的草莓、苹果和玫瑰，都有独特的果实和花朵结构，这些结构是果实的来源。本项目研究这些不同果实在分子水平上是如何发育的。利用比较基因组学和生物信息学方法，该研究将确定玫瑰家族的五个代表：草莓、桃子、李子、苹果和覆盆子之间控制果实发育模式的共享和独特基因。计算方法将用于识别解释不同果实如何以及何时形成的调控基因网络。高中教师将在夏季参与研究项目，学习水果科学和计算数据分析，并将开发用于高中课堂的课程。通过将教师整合到研究中，下一代学生将受到广泛的影响，并将获得基因组学和生物信息学的实际接触。该项目调查分子遗传机制的基础上的肉质果实在蔷薇科表型多样性。通过利用玫瑰科基因组内基因的进化守恒，比较基因组学的力量将用于鉴定肉质果实发育的关键基因和机制。最近公布的蔷薇科基因组序列（苹果、草莓、桃子、覆盆子和李子）为研究这一基本生物学问题提供了前所未有的机会。首先，详细形态学和组织学变化在花和早期果实发育将表征为所选蔷薇科物种。这些知识将指导在特定花组织受精前后立即进行rna测序方法的样品收集。将开发创新的生物信息学工具和策略来识别工具箱基因和调控基因网络，这些基因的空间或时间表达变化可能改变不同物种的肉质果实程序。功能测试包括RNAi、CRISPR和组织特异性异位表达，将在草莓、FasTrack李子和苹果中使用已建立的转化系统来测试预测的工具包基因。最终目的是确定工具包基因表达变化与不同肉质水果类型进化之间的因果关系。这些研究活动将与几个教育和推广项目相结合，包括对基因组学和信息学方面的学生和博士后研究人员的培训，为西弗吉尼亚州农村地区和马里兰州乔治王子县主要少数民族学校的高中教师举办的生物信息学研讨会，以及向公众宣传转基因生物和水果基因组学。所有序列数据将通过NCBI公共数据库和玫瑰科社区数据库提供。

Co-PI: Sridhar Hannenhalli, University of MarylandCo-PI: Chris Dardick, Appalachian Fruit Research Laboratory, USDA-ARSCo-PI: Ann Callahan, Appalachian Fruit Research Laboratory, USDA-ARSFruits that are so enjoyed by people are also especially adapted for plant seed dispersal. Even closely related plants display different types of fleshy fruits that accomplish dispersal through variation in color, shape, size, texture and other traits. A major question for plant biologists and fruit crop scientists is how these diverse fruit types evolved and what factors control their development. If scientists could explain the molecular basis of different fruit types, new breeding tools could be used to increase the value of fruit crops and basic research could be advanced. The Rose family (Rosaceae) is an excellent example of how fruits have been selected and adapted to different types of dispersal. Members of the family, including the familiar strawberries, apples, and roses, all have unique fruits and floral structures from which the fruits are derived. This project investigates how these different fruits develop at the molecular level. Using comparative genomic and bioinformatics methods, the research will identify shared and unique genes that control the pattern of fruit development among five representatives of the Rose family: strawberries, peach, plum, apple and raspberry. Computational methods will be used to identify regulatory gene networks that explain how and when the diverse fruits form. High school teachers will be brought into the research program during the summer to study fruit science and computational data analysis, and curricula will be developed for use in the high school classroom. By integrating teachers into the research, the next generation of students will be impacted broadly and will gain hands-on exposure to genomics and bioinformatics. The project investigates the molecular genetic mechanisms that underlie the phenotypic diversity of fleshy fruits in the Rosaceae. By leveraging the evolutionary conservation of genes within the Rosaceae genome, the power of comparative genomics will be used to identify key genes and mechanisms of fleshy fruit development. The recently published Rosaceae genome sequences (apple, strawberry, peach, raspberry and plum) provide an unprecedented opportunity to investigate this fundamental biological question. First, detail morphological and histological changes during floral and early stage fruit development will be characterized for the chosen Rosaceae species. This knowledge will guide sample collection for RNA-sequencing methods immediately before and after fertilization in specific floral tissues. Innovative bioinformatic tools and strategies will be developed to identify toolkit genes and regulatory gene networks, whose spatial or temporal shifts of expression may alter fleshy fruit programs in different species. Functional tests including RNAi, CRISPR, and tissue-specific ectopic expression will be carried out to test predicted toolkit genes using the established transformation systems in strawberry, FasTrack plum, and apple. The ultimate goal is to identify causal relationships between changes of toolkit gene expression and evolution of distinct fleshy fruit types. The research activities will be integrated with several educational and outreach programs including training of students and postdoctoral researchers in genomics and informatics, bioinformatics workshops for high school teachers from rural West Virginia and predominantly minority-serving schools of Prince Georges County of Maryland, and outreach to the public about Genetically Modified Organisms and fruit genomics. All sequence data will be made available through the public NCBI database and through the community database for the Rosaceae.