Molecular mechanisms underlying seminal root formation during domestication and improvement of maize

植物根系是全球粮食安全的关键，因为它们从土壤中提取几乎所有人类消耗的矿物质营养素。谷物已经进化出由不同根类型组成的复杂的三维根系，这些根系可以在发育过程中不断调整其结构以适应环境变化。玉米的早期根系包括单个初生根和在盾片节处形成的可变数量的种子根。种子根是玉米的一个新的创新，并不存在于密切相关的物种高粱。它们有助于从表层土壤中提取矿物质营养素和水分，因此有助于早期活力。种子根的出现及其数量的增加是玉米从其祖先大刍草驯化过程中最重要的地下创新。在初步工作中，我们对玉米US艾姆斯小组的2444个玉米自交系进行了表型分析，这些自交系平均显示4个种子根。我们观察到本小组中包括的五个种质组之间的种子根数量的实质性变化。相比之下，我们表型鉴定的玉米祖先大刍草的大多数加入物不形成任何种子根。本项目的总体目标是确定从大刍草到玉米种子根数量增加的分子机制以及现代玉米种子根数量的变异性。为此，我们将通过RNA-seq分析选定基因型的盾片节的转录组。这些基因型将被分成四类，具有不同的种子根平均数，范围从0（I类）到9-10（IV类）。此外，我们将包括单基因玉米突变体rtcs和rum 1，它们不形成任何种子根和bige 1，在这些分析中表现出过多的种子根形成。利用加权基因共表达网络分析（WGCNA）寻找与种子根数表型变异高度相关的基因模块。随后，在这些分析中确定的选定候选基因将进行原位杂交实验，以证明它们的盾片结特异性表达。这些基因的突变体将在我们内部的反向遗传学知识库中进行鉴定。最后，我们将通过CRISPR/Cas9进行基因组编辑来验证这些突变体。我们计划在该项目的第二个资助期内更详细地描述这些候选基因的功能和突变表型。

Plant roots are a key to global food security because they extract virtually all mineral nutrients from soil that are consumed by humans. Cereals have evolved elaborate three-dimensional root systems composed of different root types that can continuously adjust their architecture to environmental changes during development. The early root system of maize comprises a single primary root and a variable number of seminal roots formed at the scutellar node. Seminal roots are a novel innovation of maize and are not present in the closely related species Sorghum. They facilitate the extraction of mineral nutrients and water from top-soil layers and are therefore instrumental for early vigor. The emergence of seminal roots and their increase in number is the most important belowground innovation during the domestication of maize from its ancestor teosinte.In preliminary work, we phenotyped the 2444 maize inbred lines of the maize US Ames panel, which display on average four seminal roots. We observed substantial variablity in seminal root number between the five germplasm groups included in this panel. In contrast, most accessions of the maize progenitor teosinte that we phenotyped do not form any seminal roots. The overall goal of this project is to identify the molecular mechanisms underlying the increase of seminal root number from teosinte to maize and the variability of seminal root number in modern maize. To this end, we will profile the transcriptomes of scutellar nodes of selected genotypes by RNA-seq. These genotypes will by grouped in four classes with distinct average numbers of seminal roots ranging from zero (class I) to 9-10 (class IV). Moreover, we will include the monogenic maize mutants rtcs and rum1, which do not form any seminal roots and bige1, which displays excessive seminal root formation in these analyses. Weighted gene co-expression network analysis (WGCNA) will be used to find modules of genes, whose expression pattern is highly correlated with the phenotypic variations of seminal root number. Subsequently, selected candidate genes identified in these analyses will be subjected to in situ hybridization experiments to demonstrate their scutellar node specific expression. Mutants of these genes will be identified in our in-house reverse genetics repository. Finally, we will apply genome editing by CRISPR/Cas9 to validate these mutants. We plan to characterize the functions of these candidate genes and the mutant phenotypes in more detail in the second funding period of this project.