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

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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.