The mechanisms of plant defense against pathogen attack in plant leaves have been extensively studied. However, our understanding of plant defense mechanisms in plant roots is still limited. In this study, a semi-dominant mutant nrtp1-D (necrotic root tip 1), with a short-root phenotype, was characterized in rice. Map-based cloning revealed that NRTP1 encoded a typical coiled-coil nucleotide binding leucine rich repeat (CC-NB-LRR) type protein and the mutation caused an amino acid substitution in the Nucleotide-Binding adaptor shared by Apaf1, certain R genes and CED4 (NB-ARC) domain, which may cause constitutive auto-activation of the NRTP1 protein. Gene expression analysis revealed that NRTP1 was preferentially expressed in rice roots. Expression of mutant nrtp1-D in tobacco leaves induced necrotic lesions, which indicated a common mechanism of plant defense response between leaves and roots. Transcriptome analysis revealed that many typical defense-response genes were differentially expressed in homozygous nrtp1-D. In addition, we also found differential expression of genes in pathways which had not previously been described as being associated with pathogen response. Histochemical analysis showed that the level of nitric oxide (NO), but not reactive oxygen species (ROS), was increased in homozygous nrtp1-D mutant roots. These results indicate that, in addition to the mechanism of defense response common to both roots and shoots, a novel pathway may also exist in rice roots, which does not operate in shoots.

Leaf colour is a valuable morphological phenotype for studying plant metabolism and physiology. To elucidate the mutation mechanism of leaf colour variation in maize, we compared the ethyl methylsulfonate (EMS)-induced maize mutant zmpgl, which has light green leaves, with the wild-type maize line B73. At the seedling stage, the zmpgl mutant presented distinct light green leaf colouration. Comprehensive analyses revealed that both the photosynthetic parameters and pigment contents of the mutant seedlings were significantly lower than those of the wild-type seedlings. Transmission electron microscopy of the mutant leaves revealed alterations in the chloroplast structure, which consequently impaired the photosynthetic efficiency and accumulation of organic matter. Through integrated transcriptomic and metabolomic profiling, we identified differentially expressed genes (DEGs) and differentially abundant metabolites associated with the zmpgl phenotype. These molecular components were associated with pathways related to plant metabolism, chloroplast structure-associated hormone signalling, and redox homeostasis. Further investigation revealed a significant differential expression of genes involved in several critical biological processes, including tetrapyrrole synthesis, lipid metabolism (related to leaf photosynthesis), amino acid metabolism (associated with chlorophyll synthesis and the light response), and abscisic acid (ABA) biosynthesis. These processes are crucial for plant photosynthesis, respiration, and catalytic functions. This study not only provides a valuable resource for further investigation of plant photosynthetic systems but also establishes a foundational framework for the comprehensive functional characterisation of genes involved in the leaf colour change in the zmpgl mutant. These findings contribute to our understanding of the molecular basis of leaf colour variation and its impact on photosynthetic performance in maize.

Sorghum is an important cereal crop. The maintenance of leaf color significantly influences sorghum growth and development. Although the mechanisms of leaf color mutation have been well studied in many plants, those in sorghum remain largely unclear. Here, we identified a sorghum gradient-pale-green leaf mutant (sbgpgl1) from the ethyl methanesulfonate (EMS) mutagenesis mutant library. Phenotypic, photosynthesis-related parameter, ion content, transcriptome, and metabolome analyses were performed on wild-type BTx623 and the sbgpgl1 mutant at the heading stage, revealing changes in several agronomic traits and physiological indicators. Compared with BTx623, sbgpgl1 showed less height, with a smaller length and width of leaf and panicle. The overall Chl a and Chl b contents in sbgpgl1 were lower than those in BTx623. The net photosynthetic rate, stomatal conductance, and transpiration rate were significantly reduced in sbgpgl1 compared to BTx623. The content of copper (Cu), zinc (Zn), and manganese (Mn) was considerably lower in sbgpgl1 leaves than in BTx623. A total of 4469 differentially expressed genes (DEGs) and 775 differentially accumulated metabolites (DAMs) were identified by RNA-seq and UPLC-MS/MS. The results showed that sbgpgl1 primarily influenced sorghum metabolism by regulating metabolic pathways and the biosynthesis of secondary metabolites, especially flavonoids and phenolic acids, resulting in the gradient-pale-green leaf phenotype. These findings reveal key genes and metabolites involved on a molecular basis in physiological variations of the sorghum leaf color mutant.

Nitrogen (N) is an essential macronutrient for plant growth. NIN–like protein (NLP) transcription factors play important roles in nitrate signaling and response in plants. However, a comprehensive analysis of the NLP gene family in sorghum is still lacking. In this study, we identified five NLP genes in sorghum, and a high collinearity of NLP was detected in sorghum, rice and maize. N deficiency decreased SbNLP3 and SbNLP4 expression levels in roots, and the expression of SbNLP1 and SbNLP2 declined in roots during nitrate resupply. Subcellular localization analysis revealed that SbNLP1 was mostly detected in nuclei and cytoplasm. Compared with wild–type rice ZH11 plants, SbNLP1 overexpression plants showed improved low nitrogen (LN) tolerance, with longer roots and shoots under LN conditions. Transcriptome analysis between overexpression lines OE1–5 and ZH11 showed that 773 and 967 differentially expressed genes (DEGs) were identified in roots and shoots under LN conditions, respectively. In contrast, 674 and 1283 DEGs were identified in roots and shoots under normal nitrogen (NN) conditions, respectively. Thirty–seven N–related DEGs were identified in roots through GO enrichment under LN conditions, and terms of plant hormone signal transduction, biosynthesis of secondary metabolites and plant–pathogen interaction were identified through KEGG enrichment. WGCNA analysis also revealed plant hormone signal transduction pathways and plant pathogen interaction pathways in OE1–5 under LN conditions. These results provide a basis for N use efficiency (NUE) improvement in sorghum and functional analysis of SbNLPs.