Root system architecture (RSA) plays a critical role in the acquisition of water and mineral nutrients. In order to understand the root characteristics that contribute to enhanced crop yield and N accumulation high-yielding and N efficient cultivars under N-stressed conditions. Here, grain yield, N accumulation and RSA traits of six dominant maize cultivars (CD30, ZH311, ZHg505, CD189, QY9 and RY1210) grown in the Southwestern part of China were investigated in field experiment under three different N regimes in 2019–2020; N300 (300 kg N ha⁻¹), N150 (150 kg N ha⁻¹) and N0 (no N supplied). Using Root Estimator for Shovelomics Traits (REST) for the quantitative analysis of maize root image obtained in the field, RSA traits including total root length (RL), root surface area (RA), root angle opening (RO), and root maximal width (RMW) were quantified in this study. The results showed that Yield, N accumulation and RSA were significantly affected by N rates, cultivars and their interactions. Grain yield, N accumulation and root weight showed a similar trend under N300 and N150 conditions compared to N0 conditions. With the input of N fertilizer, the root length, surface area, and angle increase, but root width does not increase. Under the N300 and N150 condition, RL, RA, RO and RMW increased by 17.96%, 17.74%, 18.27%, 9.22%, and 20.39%, 18.58%, 19.92%, 16.79%, respectively, compared to N0 condition. CD30, ZH505 and RY1210 have similar RO and RMW, larger than other cultivars. However, ZH505 and RY1210 have 13.22% and 19.99% longer RL, and 11.41% and 5.17% larger RA than CD30. Additionally, the grain yield of ZH505 and RY1210 is 17.57% and 13.97% higher compared with CD30. The N accumulation of ZH505 and RY1210 also shows 4.55% and 9.60% higher than CD30. Correlation analysis shows that RL, RA, RO and RMW have a significant positive correlation with grain yield while RO and RMW have a significant positive correlation with N accumulation. Linear plus plateau model analysis revealed that when the RO reaches 99.53°, and the RMW reaches 15.18 cm, the N accumulation reaches its maximum value under 0–300 kg N ha⁻¹ conditions. Therefore, selecting maize cultivars with efficient RSA suitable for different soil N inputs can achieve higher grain yield and N use efficiency.

Main conclusion: Integrated root phenotypes and transcriptome analysis have revealed key candidate genes responsible for maize root growth and development in potassium deficiency. Potassium (K) is a vital macronutrient for plant growth, but our understanding of its regulatory mechanisms in maize root system architecture (RSA) and K⁺ uptake remains limited. To address this, we conducted hydroponic and field trials at different growth stages. K⁺ deficiency significantly inhibited maize root growth, with metrics like total root length, primary root length, width and maximum root number reduced by 50% to 80% during early seedling stages. In the field, RSA traits exhibited maximum values at the silking stage but continued to decline thereafter. Furthermore, K deprivation had a pronounced negative impact on root morphology and RSA growth and grain yield. RNA-Seq analysis identified 5972 differentially expressed genes (DEGs), including 17 associated with K⁺ signaling, transcription factors, and transporters. Weighted gene co-expression network analysis revealed 23 co-expressed modules, with enrichment of transcription factors at different developmental stages under K deficiency. Several DEGs and transcription factors were predicted as potential candidate genes responsible for maize root growth and development. Interestingly, some of these genes exhibited homology to well-known regulators of root architecture or development in Arabidopsis, such as Zm00001d014467 (AtRCI3), Zm00001d011237 (AtWRKY9), and Zm00001d030862 (AtAP2/ERF). Identifying these key genes helps to provide a deeper understanding of the molecular mechanisms governing maize root growth and development under nutrient deficient conditions offering potential benefits for enhancing maize production and improving stress resistance through targeted manipulation of RSA traits in modern breeding efforts.

A growing leaf can be divided into three sections: division zone, elongation zone, and maturation zone. In previous studies, low nitrogen (LN) inhibited maize growth and development, especially leaf growth; however, the gene expression in response to LN in different regions in leaf were not clear. Here, using hydroponics and a transcriptome approach, we systematically analyzed the molecular responses of those zones and differentially expressed genes (DEG) in response to LN supply. Developmental stage-specific genes (SGs) were highly stage-specific and involved in distinct biological processes. SGs from division (SGs–DZ) and elongation zones (SGs–EZ) were more related to developmentally dependent processes, whereas SGs of the maturation zone (SGs–MZ) were more related to metabolic processes. The common genes (CGs) were overrepresented in carbon and N metabolism, suggesting that rebalancing carbon and N metabolism in maize leaves under LN condition was independent of developmental stage. Coexpression modules (CMs) were also constructed in our experiment and a total of eight CMs were detected. Most of SGs–DZ and SGs–EZ were classified into a set termed CM turquoise, which was mainly enriched in ribosome and DNA replication, whereas several genes from SGs–MZ and CGs were clustered into CM blue, which mainly focused on photosynthesis and carbon metabolism. Finally, a comprehensive coexpression network was extracted from CM blue, and several maize CONSTANS-LIKE(ZmCOL) genes seemed to participate in regulating photosynthesis in maize leaves under LN condition in a developmental stage-specific manner. With this study, we uncovered the LN-responsive CGs and SGs that are important for promoting plant growth and development under insufficient nitrogen supply.

With growing concerns about global warming, it is crucial to adopt agronomic practices that enhance rice yields from paddy fields while reducing greenhouse gas (GHG) emissions for sustainable agriculture. An optimal nitrogen (N) fertilization rate and planting density are vital to ensure high rice yields, minimize GHG emissions, and understand emission behavior for better field management. We hypothesized that optimizing N application rates and planting density to improve nitrogen use efficiency (NUE) in rice cultivation would reduce resource losses and GHG emissions. To test this hypothesis, we implemented five treatments with a rice straw return cultural system: two planting densities (16 hills m⁻² (traditional density, D1) and 20 hills m⁻² (25% higher density, D2)) and three N application rates (no N fertilizer (N0), 180 kg N ha⁻¹ (N1), and 144 kg N ha⁻¹ (N2)). The control treatment (CK) was traditional planting density with no N fertilizer. The four new cropping modes were N1D1, N1D2, N2D1, and N2D2. We investigated the effects of N application rates and planting density on rice grain yield, NUE, and GHG emissions in multiple rice-growing seasons. The N1D2 treatment exhibited the highest grain yield over the three years, with a value of 10,452 kg ha⁻¹, representing an increase of 12.2% compared to CK. Moreover, N uptake in N1D2 was the highest, averaging 39.2% (p < 0.05) higher than CK, and 8.5%, 3.5%, and 2.8% (p < 0.05) higher than N1D1, N2D1 and N2D2, respectively. N2D2 exhibited the highest NUE, with a value of 58.99 kg kg⁻¹, surpassing all other treatments over the three years. GHG emissions, global warming potential (GWP), and greenhouse gas intensity (GHGI) in N2D2 were lower than in N1D1, N1D2, and N2D1. Additionally, reducing N application (comparing N1D1 to N2D1) and increasing plant density (comparing N1D1 to N1D2) improved N agronomic efficiency (NAE) and N partial productivity (PFP_N). The negative correlation between the NAE and PFP_N with GWP and GHG emissions further supports the potential for optimized N management and denser planting density to reduce environmental impact. These findings have important implications for sustainable rice cultivation practices in Southwest China and similar agroecosystems, emphasizing the need for integrated nutrient management strategies to achieve food security and climate change mitigation goals.