Abstract
Nitrogen (N) is an essential nutrient for plants, and it directly affects grain yield and protein content in cereal crops. Plant root systems are not only critical for anchorage in the soil, but also for N acquisition. Therefore, genes controlling root development might also affect N uptake by plants. In this study, the responses of nitrogen on root architecture of mutant rtcs and wild-type of maize were investigated by morphological and physiological analysis. Subsequently, we performed a comparative RNA-Seq analysis to compare gene expression profiles between mutant rtcs roots and wild-type roots under different N conditions. We identified 786 co-modulated differentially expressed genes (DEGs) related to root development. These genes participated in various metabolic processes. A co-expression cluster analysis and a cis-regulatory motifs analysis revealed the importance of the AP2-EREBP transcription factor family in the rtcs-dependent regulatory network. Some genotype-specific DEGs contained at least one LBD motif in their promoter region. Further analyses of the differences in gene transcript levels between rtcs and wild-type under different N conditions revealed 403 co-modulated DEGs with distinct functions. A comparative analysis revealed that the regulatory network controlling root development also controlled gene expression in response to N-deficiency. Several AP2-EREBP family members involved in multiple hormone signaling pathways were among the DEGs. These transcription factors might play important roles in the rtcs-dependent regulatory network related to root development and the N-deficiency response. Genes encoding the nitrate transporters NRT2-1, NAR2.1, NAR2.2, and NAR2.3 showed much higher transcript levels in rtcs than in wild-type under normal-N conditions. This result indicated that the LBD gene family mainly functions as transcriptional repressors, as noted in other studies. In summary, using a comparative RNA-Seq-based approach, we identified DEGs related to root development that also participated in the N-deficiency response in maize. These findings will increase our understanding of the molecular regulatory networks controlling root development and N-stress responses.
Highlights
Nitrogen (N) is one of the most important nutrients for plants, and it directly affects grain yield and protein content in cereal crops [1]
Longer of PRL and lateral root on primary root (LRL) were observed in rtcs than wild-type on normal-N condition, and the difference in LRL was continuously increased with increasing time (Fig 1B)
The increase in PRL and LRL was fairly smooth over time in both genotypes after low-N treatment, while larger changes of LRL were detected in rtcs (Fig 1B)
Summary
Nitrogen (N) is one of the most important nutrients for plants, and it directly affects grain yield and protein content in cereal crops [1]. Agricultural productivity is limited by N, as it is an essential macronutrient. Both low- and high-N supply can negatively affect plant growth. Previous studies have shown that excess N can negatively affect plant growth [4, 5]. To optimize the use of fertilizers and decrease their environmental impacts, it is very important to improve the N use efficiency (NUE) of plants. Understanding of the molecular mechanisms of N metabolism such as N uptake, assimilation, and recycling during plant growth and development will contribute to increasing the NUE of crop plants
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