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

植物生物学中的一个基本问题是植物细胞如何形成特定的形式和功能，包括植物器官。该合作项目将研究叶边界细胞获得其专门细胞命运的细胞和发育遗传机制，这是一个有助于光捕获和作物产量的重要农学过程。该项目将培养一名研究生和两名博士后科学家，掌握显微镜、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。该项目还将对本科生暑期实习生进行这些技术的培训，并将每年赞助关于大生物数据计算分析的实践教育网络研讨会和讲习班。 此外，该项目产生的数据将在一个新课程中为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免费的机器学习在线培训课程。细胞命运的获得是如何受遗传调控的，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器官的发育不同组织之间形成明显的边界。叶舌/叶耳包括玉米叶片内的发育边界，在近端的支持性鞘组织和远端的光合叶片之间形成专门的铰链状结构。叶舌/叶耳形态表现出自然变异，是一个遗传上易处理的性状;叶片角度的差异与玉米改良有关。叶舌/耳廓生长的细胞参数将在三个不同的个体发育阶段的特点。单细胞RNA-seq将在叶舌/耳廓生长期间鉴定细胞特异性遗传网络，单细胞ATAC-seq将在这三个相同阶段鉴定关键转录因子和顺式调控特征。机器学习策略将综合并关联这些细胞生物学、转录组学和染色质数据，以识别涉及叶舌/耳廓分化的基因组网络和候选基因。该奖项反映了NSF的法定使命，并被认为值得通过使用基金会的智力价值和更广泛的影响审查标准进行评估来支持。

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.