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Functional characterization of the maize lateralrootless 1 gene

Subject Area Plant Genetics and Genomics
Plant Breeding and Plant Pathology
Term from 2016 to 2023
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 317530843
 
Final Report Year 2023

Final Report Abstract

Lateral roots substantially increase the absorbing surface of cereal root systems. In maize (Zea mays L.), lateral roots are initiated from phloem pole pericycle cells. The maize mutant lateralrootless 1 (lrt1) is defective in lateral root formation in primary and seminal roots. The overall goal of this project was to clone and characterize the lrt1 gene. We cloned the lrt1 gene by mapping in combination with bulk segregant analysis-sequencing (BSA-seq) and subsequent validation by CRISPR/Cas9. The lrt1 gene encodes a homolog of the DDB1-CUL4-ASSOCIATED FACTOR (DCAF) subunit of the CUL4-based E3 ubiquitin ligase (CRL4) complex localized in the nucleus. DCAF proteins bind substrate proteins and promote their ubiquitylation, thus marking them for subsequent degradation in the 26S proteasome. The lrt1 gene is preferentially expressed in the meristematic zone of all root types. Genetic analyses suggest that lrt1 acts upstream of the lateral root regulator rum1. Beneficial interactions between plant roots and rhizosphere microorganisms are pivotal for plant fitness. We have established that root-derived flavones promote the enrichment of bacteria of the taxa Oxalobacteraceae in the rhizosphere, which in turn promote maize growth and nitrogen acquisition and that this process is coordinated by the LRT1-mediated formation of lateral roots. For the first time, we were able to elucidate the genetic basis of the mutual interactions between root architecture and specific microbial taxa in the rhizosphere that lead to improved plant performance. Furthermore, we studied the transcriptomic networks of xylem pole and phloem pole pericycle cells in maize during the early stages of lateral root development by combining the isolation of these cells by laser capture microdissction (LCM) with cell type-specific RNAseq experiments in wild type and lrt1 roots. In a weighted gene co-expression network analysis (WGCNA) in combination with an enrichment analysis of transcription factor families, the ERF (ETHYLENE RESPONSE FACTOR) family was the only transcription factor family that was significantly overrepresented. Four of the six members of this family were significantly upregulated in stage 3 phloem pole pericycle cells of wild-type primary roots. In order to explore the role of those ethylene response factors in lateral root formation, we created mutants of two of these ethylene response factor genes by CRISPR/Cas9 and established that lateral root density was significantly reduced in both mutants in comparison to wild-type. Finally, we followed up on previous work which demonstrated that the arbuscular mycorrhiza fungus (AMF) Glomus mosseae can induce lateral root formation in the lrt1 mutant and performed a RNAseq analysis in which we compared lrt1 mutant primary roots treated with this AMF with untreated roots. We demonstrated that five of six ERFs we induced by this fungus suggesting that AMF are able to induce ethylene response factor genes in the lrt1 mutant, thus contributing to the formation of lateral roots.

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