TRTech-PGR: Comprehensive identification and functional characterization of cis-regulatory elements in legumes

该项目将产生一个大型、高质量和统一的数据集，其中包括几种互补类型的数据，以解决经济上重要的豆科植物家族中的一些悬而未决的问题，包括大豆、菜豆和花生。这些数据对于研究不同的发育途径，如叶、根和种子发育，以及根瘤的形成和功能是非常有价值的，根瘤是固定大气氮的专门植物结构。这些数据集还将导致识别控制基因表达的关键DNA序列，使其能够更准确地表征，并导致对这些序列进行工程设计，以用于作物改良。在质量控制之后，这里产生的数据集和基因组资源将通过一个互动网站和联邦数据库立即公开发布。除了科学和农业方面的影响，该项目还继续与西南部的主要是西班牙裔和美洲原住民部落大学建立合作伙伴关系。圣达菲社区学院将举办一个研讨会，介绍探索DNA序列的现代计算生物学方法。这一活动是让公众和有兴趣的本科生参与研究活动的渠道，也是每年招募实习生和他们的教师导师在我们的研究机构进行暑期培训的一种方式。近年来，在植物基因组组装和基因注释方面取得了重大进展。然而，植物顺式调控DNA元件的系统鉴定和功能表征仍然是一个挑战，因为在动物身上高效的方法还没有推广到植物上。一个全面和精心挑选的植物顺式调控DNA元件数据集有助于理解发育过程中和/或对外部刺激的反应过程中的转录调控。此外，顺式调控的DNA元件也是重要农艺性状和进化性状遗传变异的研究热点。该研究小组最近优化了几种高通量方法，通过染色质签名、它们结合的转录因子、它们通过直接物理染色质相互作用的目标基因以及它们在高通量报告分析中的调节活性来识别顺式调节元件。本项目的目标是利用这些方法系统地鉴定、分析和功能验证重要的豆科植物包括大豆、菜豆、菜豆、花生、花生和花生中的顺式调控元件。这一奖项反映了NSF的法定使命，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，被认为值得支持。

This project will produce a large, high-quality and uniform dataset that includes several, complementary types of data to address a number of outstanding questions in the economically important legume family of plants, which includes soybean, common bean and peanut. These data are highly valuable for studying diverse developmental pathways such as leaf, root and seed development, as well as the formation and function of root nodules, specialized plant structures that fix atmospheric nitrogen. The datasets will also lead to the identification of critical DNA sequences that control gene expression and will allow their more accurate characterization as well as lead to engineering of these sequences for crop improvement. The datasets and genomic resources generated here will be released publicly and immediately following quality control through an interactive website and federal data repositories. In addition to the scientific and agricultural impact, the project continues a partnership with primarily Hispanic and Native American tribal colleges in the Southwest. A workshop that presents modern-day computational biology approaches to explore DNA sequences will be hosted at Santa Fe Community College. This event serves as a conduit to engage the public and interested undergraduates in research activities and also serves as a means to recruit interns and their faculty mentors for summer training at our research institutions annually. Significant progress has been made in recent years in plant genome assembly and gene annotation. However, the systematic identification and functional characterization of plant cis-regulatory DNA elements remain a challenge, as methods that are highly effective in animals have not translated to plants. A comprehensive and well-curated data set of plant cis-regulatory DNA elements is instrumental to understanding transcriptional regulation during development and/or in response to external stimuli. In addition, cis-regulatory DNA elements are hotspots for genetic variations underlying agronomically and evolutionarily important traits. The research team has recently optimized several high-throughput methods to identify cis-regulatory elements by chromatin signatures, their bound transcription factors, their target genes by direct physical chromatin interactions, and their regulatory activities in high-throughput reporter assays. The goal of this project is to use these methods to systematically identify, analyze and functionally validate cis-regulatory elements in important legume species including Glycine max (soybean), Phaseolus vulgaris (common bean), Phaseolus coccineus (runner bean), Arachis ipaensis, Arachis duranensis and Arachis hypogea (peanut). The results will be used to address a number of mechanistic, developmental and evolutionary questions.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.