Collaborative Research: Mechanisms of differentiation and morphogenesis of the ligule/auricle hinge

植物生物学的一个基本问题是植物细胞如何形成特定的形态和功能，从而构成植物器官。该合作项目将研究叶边界细胞获得其特殊细胞命运的细胞和发育遗传机制，这是一个农学上重要的过程，有助于光捕获和作物产量。该项目将培养一名研究生和两名博士后，研究显微镜、基因表达和基因组结构方面的最新技术。机器学习方法将用于分析这些补充数据。该项目还将对这些技术的本科生暑期实习生进行培训，并将每年赞助有关大生物数据计算分析的实践性教育网络研讨会和讲习班。此外，在这个项目中产生的数据将为一个新课程中的团队学习项目提供种子，该课程是nsf资助的研究生培训补助金的一部分，该补助金还将为植物科学家提供一个免费的机器学习在线培训课程。细胞命运获取如何受基因调控是植物器官发生的基本问题。多细胞生物的一个共同特征是在一个器官的发育不同的组织之间形成明显的边界。舌叶/耳廓构成玉米叶片的发育边界，在近端支持鞘组织和远端光合叶片之间形成一个特殊的铰链状结构。舌瓣/耳廓形态表现出自然变异，是一种遗传上易受控制的性状；由此产生的叶片角度差异与玉米改良有关。舌叶/耳廓生长的细胞参数将在三个不同的个体发育阶段被表征。单细胞RNA-seq将鉴定舌叶/耳廓生长过程中的细胞特异性遗传网络，单细胞ATAC-seq将鉴定这三个阶段的关键转录因子和顺式调控特征。机器学习策略将综合和关联这些细胞生物学、转录组学和染色质数据，以识别基因组网络和参与舌叶/耳廓分化的候选基因。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。

A fundamental question in plant biology is how plant cells are patterned to develop the specific forms and functions that comprise plant organs. This collaborative project will investigate the cellular and developmental genetic mechanisms whereby leaf boundary cells acquire their specialized cell fates, an agronomically important process that contributes to light capture and crop yield. This project will train a graduate student and two postdoctoral scientists in state-of-the-art techniques in microscopy, gene expression and genome structure. Machine learning approaches will be used to analyze these complementary data. The project will also train undergraduate summer interns in these techniques and will sponsor yearly, hands-on, educational webinars and workshops on computational analyses of big biological data. In addition, the data generated during this project will seed team-learning projects in a new course developed as part of a separate NSF-funded graduate student training grant, which will also sponsor a free, online training course on machine learning for plant scientists. How cell-fate acquisition is genetically regulated is the fundamental question in plant organogenesis. A common feature of multicellular organisms is the formation of distinct boundaries between developmentally distinct tissues of an organ. The ligule/auricle comprises the developmental boundary within maize leaves, forming a specialized hinge-like structure between the proximal, supportive sheath tissue and the distal, photosynthetic blade. Ligule/auricle morphology shows natural variation and is a genetically tractable trait; the resultant difference in leaf blade angle are relevant to maize improvement. The cellular parameters of ligule/auricle outgrowth will be characterized during three distinct ontogenetic stages. Single-cell RNA-seq will identify cell-specific genetic networks during ligule/auricle outgrowth, and single-cell ATAC-seq will identify key transcription factors and cis-regulatory features during these same three stages. Machine learning strategies will synthesize and correlate these cell-biological, transcriptomic, and chromatin data, to identify genomic networks and candidate genes involved in ligule/auricle differentiation.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.