title: Comparative RNA-Seq Analysis Reveals That Regulatory Network of Maize Root Development Controls the Expression of Genes in Response to N Stress.
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.
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Xiujing
authors.initials: X
authors.lastname: He
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Haixia
authors.initials: H
authors.lastname: Ma
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Xiongwei
authors.initials: X
authors.lastname: Zhao
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Shujun
authors.initials: S
authors.lastname: Nie
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Yuhua
authors.initials: Y
authors.lastname: Li
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Zhiming
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Yaou
authors.initials: Y
authors.lastname: Shen
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Chen
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Hai
authors.initials: H
authors.lastname: Lan
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Shufeng
authors.initials: S
authors.lastname: Zhou
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Shibin
authors.initials: S
authors.lastname: Gao
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Guangtang
authors.initials: G
authors.lastname: Pan
authors.affiliation: Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture; Maize Research Institute of Sichuan Agricultural University, Wenjiang, Sichuan, China.
authors.forename: Haijian
authors.initials: H
authors.lastname: Lin
mesh_terms: D001483:Base Sequence; D001692:Biological Transport / Q000235:genetics; D004268:DNA-Binding Proteins / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics* / Q000502:physiology; D009584:Nitrogen / Q000172:deficiency* / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics; D018517:Plant Roots / Q000254:growth & development*; D018520:Plant Shoots / Q000254:growth & development; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000502:physiology; D014157:Transcription Factors / Q000378:metabolism; D059467:Transcriptome / Q000235:genetics; D003313:Zea mays / Q000254:growth & development*
chemical_list: D004268:DNA-Binding Proteins; D010940:Plant Proteins; D014157:Transcription Factors; C093680:ethylene-responsive element binding protein; D009584:Nitrogen