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是如何形成模式以发展组成植物器官的特定形式和功能的。这个合作项目将研究叶片边界细胞获得其特殊细胞命运的细胞和发育遗传机制，这是一个重要的农学过程，有助于光捕获和作物产量。该项目将培训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先进技术。将使用机器学习方法来分析这些互补数据。该项目还将培训本科生暑期实习生掌握这些技术，并将赞助每年一次的动手教育网络研讨会和关于大生物数据计算分析的研讨会。此外，在这个项目期间产生的数据将在一个新课程中为团队学习项目提供种子，该课程是由美国国家科学基金会单独资助的研究生培训基金的一部分，该基金还将为植物科学家赞助一个免费的在线机器学习培训课程。细胞命运的获得如何受到遗传调控是植物器官发生中的基本问题。多细胞生物体的一个共同特征是在发育不同的器官组织之间形成明显的边界。叶舌/叶耳构成玉米叶片内的发育边界，在近端的支持鞘组织和远端的光合作用叶片之间形成一种特殊的铰链状结构。叶舌/叶耳形态表现出自然变异，是一种遗传易控性状；由此产生的叶片角度差异与玉米改良有关。舌叶/耳廓突起的细胞参数将在三个不同的个体发育阶段进行表征。单细胞RNA-SEQ将在舌叶/耳廓生长过程中识别细胞特有的遗传网络，单细胞ATAC-SEQ将在这三个相同的阶段识别关键转录因子和顺式调节功能。机器学习策略将综合和关联这些细胞生物学、转录和染色质数据，以确定涉及舌叶/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，并通过使用基金会的智力优势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.