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

植物根是全球粮食安全的关键，因为它们几乎从土壤中提取人类消耗的所有矿物质营养。谷物进化出复杂的三维根系，由不同的根型组成，可以在发育过程中不断调整其结构以适应环境的变化。玉米早期的根系由单一的初生根和在盾片节处形成的数量可变的种子根组成。种子根是玉米的一项新创新，在近缘物种高粱中不存在。它们有助于从表土层中提取矿物质养分和水分，因此有助于早期的活力。种子根的出现和数量的增加是玉米从其祖先温州驯化过程中最重要的地下创新。在初步工作中，我们对美国玉米Ames小组的2444个玉米自交系进行了表型鉴定，平均显示4个种子根。我们观察到五个种质组在种子根数上有很大的差异。相反，我们表型的玉米祖先teosinte的大多数材料都没有形成任何种子根。该项目的总体目标是确定种子根数从Teosinte到玉米增加的分子机制以及现代玉米种子根数的变异性。为此，我们将通过RNA-seq对选定的基因型的盾节转录本进行分析。这些基因型将被分成四个类别，具有不同的平均种子根数，范围从0(I类)到9-10(IV类)。此外，我们将包括不形成任何种子根的单基因玉米突变体rtcs和rum1，以及在这些分析中显示出过多的种子根形成的bige1。加权基因共表达网络分析(WGCNA)将被用来寻找基因模块，其表达模式与种子根数的表型变异高度相关。随后，在这些分析中确定的选定候选基因将接受原位杂交实验，以证明其盾节特异性表达。这些基因的突变将在我们内部的反向遗传学储存库中进行鉴定。最后，我们将应用CRISPR/Cas9的基因组编辑来验证这些突变体。我们计划在这个项目的第二个资助期更详细地描述这些候选基因和突变表型的功能。

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.