Higher nitrogen use efficiency (NUE) in hybrid "super rice" links to improved morphological and physiological traits in seedling roots

Post-heading dry-matter transport and nutrient uptake differentiate hybrid and inbred indica rice in the double-cropping system in South China

Introduction

Hybrid rice demonstrated superior performance in enhancing yield and efficiency in rice production compared to inbred rice. Nevertheless, the underlying mechanism responsible for the increased yield and efficiency of hybrid rice in South China's double-cropping rice region remains understudied.

Methods

Field experiments over two consecutive years were conducted. Firstly, yield variations among 20 inbred and 15 hybrid rice cultivars prevalent in South China's double-cropping rice system were examined. Secondly, selecting representative hybrid and inbred rice cultivars with significant yield disparities were carried out on further analyzing dry-matter production, source-sink relationships, and nutrient absorption and utilization in both rice types.

Results

Hybrid rice displayed an average grain yield of 8.07 and 7.22 t hm-2 in the early and late seasons, respectively, which corresponds to a 12.29% and 13.75% increase over inbred rice with statistically significant differences. In comparison to inbred rice, hybrid rice exhibited enhanced nitrogen concentration in leaves at the heading stage (15.48-16.20%), post-heading dry matter accumulation (52.62-73.21%), post-heading dry matter conversion rate (29.23-34.12%), and harvest index (17.31-18.37%). Additionally, grain nitrogen and phosphorus uptake in hybrid rice increased by 11.88-22.50% and 16.38-19.90%. Hybrid rice mainly improved post-heading nitrogen and phosphorus uptake and transport, while not total nitrogen and phosphorus uptake. Internal nitrogen and phosphorus use efficiency enhanced by 9.83%-14.31% and 10.15%-13.66%, respectively. Post-heading dry matter accumulation, harvest index, grain nitrogen and phosphorus uptake, and internal nitrogen and phosphorus use efficiency exhibited significant positive linear correlations with grain yield.

Discussion

The period from heading to maturity is critical for enhancing hybrid rice yield and efficiency. Improving photosynthetic capacity during this period and promoting nutrient transport to grains serve as crucial pathways for increasing grain yield and efficiency. This study is of great significance for further improvement grain yield and breeding rice cultivars with high-yield and high nutrients use efficiency for South China's double-cropped rice system.

Identification of the mechanistic basis of nitrogen responsiveness in two contrasting Setaria italica accessions

Nitrogen (N) is a macronutrient limiting crop productivity with varied requirements across species and genotypes. Understanding the mechanistic basis of N responsiveness by comparing contrasting genotypes could inform the development and selection of varieties with lower N demands, or inform agronomic practices to sustain yields with lower N inputs. Given the established role of millets in ensuring climate-resilient food and nutrition security, we investigated the physiological and genetic basis of nitrogen responsiveness in foxtail millet (Setaria italica L.). We had previously identified genotypic variants linked to N responsiveness, and here we dissect the mechanistic basis of the trait by examining the physiological and molecular behaviour of N responsive (NRp-SI58) and non-responsive (NNRp-SI114) accessions at high and low N. Under high N, NRp-SI58 allocates significantly more biomass to nodes, internodes and roots, more N to developing grains, and is more effective at remobilizing flag leaf N compared with NNRp-SI114. Post-anthesis flag leaf gene expression suggests that differences in N induce much higher transcript abundance in NNRp-SI114 than NRp-SI58, a large proportion of which is potentially regulated by APETALA2 (AP2) transcription factors. Overall, the study provides novel insights into the regulation and manipulation of N responsiveness in S. italica.

Plant iron status regulates ammonium-use efficiency through protein N-glycosylation

Improving nitrogen-use efficiency is an important path toward enhancing crop yield and alleviating the environmental impacts of fertilizer use. Ammonium (NH4+) is the energetically preferred inorganic N source for plants. The interaction of NH4+ with other nutrients is a chief determinant of ammonium-use efficiency (AUE) and of the tipping point toward ammonium toxicity, but these interactions have remained ill-defined. Here, we report that iron (Fe) accumulation is a critical factor determining AUE and have identified a substance that can enhance AUE by manipulating Fe availability. Fe accumulation under NH4+ nutrition induces NH4+ efflux in the root system, reducing both growth and AUE in Arabidopsis (Arabidopsis thaliana). Low external availability of Fe and a low plant Fe status substantially enhance protein N-glycosylation through a Vitamin C1-independent pathway, thereby reducing NH4+ efflux to increase AUE during the vegetative stage in Arabidopsis under elevated NH4+ supply. We confirm the validity of the iron-ammonium interaction in the important crop species lettuce (Lactuca sativa). We further show that dolomite can act as an effective substrate to subdue Fe accumulation under NH4+ nutrition by reducing the expression of Low Phosphate Root 2 and acidification of the rhizosphere. Our findings present a strategy to improve AUE and reveal the underlying molecular-physiological mechanism.

Microplastic Has No Effect on Rice Yield and Gaseous N Emission from an Infertile Soil with High Inorganic N Inputs

Microplastic might affect the crop yield, nitrogen (N) use efficiency and reactive N losses from agricultural soil systems. However, evaluation of these effects in infertile soil planted with different rice cultivars is lacking. We conducted a soil column experiment to determine the influence of a typical microplastic polyethylene (PE) input into an infertile soil with 270 kg N ha-1 and planted with two rice cultivars, i.e., a common rice Nangeng 5055 (NG) and a hybrid rice Jiafengyou 6 (JFY). The results showed that JFY produced a significantly (p < 0.05) greater grain yield than NG (61.6-66.2 vs. 48.2-52.5 g pot-1) but was not influenced by PE. Overall, PE hardly changed the N use efficiency of NG and JFY. Unexpectedly, PE significantly (p < 0.05) increased the total amino acid content of NG. Compared with JFY, NG volatilized significantly (p < 0.05) more ammonia (NH3) (0.84-0.92 vs. 0.64-0.67 g N pot-1) but emitted equal nitrous oxide (N2O). PE exerted no effect on either NH3 volatilization or the N2O emission flux pattern and cumulative losses of the rice growth cycle, whether with NG or JFY. Some properties of tested soils changed after planting with different rice cultivars and incorporating with microplastic. In conclusion, the rice production, N use efficiency, NH3 volatilization and N2O emission from the N-fertilized infertile soil were pronouncedly influenced by the rice cultivar, but not the PE. However, PE influenced the grain quality of common rice and some properties of tested soils with both rice cultivars.

Nitrate-responsive transcriptome analysis of rice RGA1 mutant reveals the role of G-protein alpha subunit in negative regulation of nitrogen-sensitivity and use efficiency

KEY MESSAGE

Nitrate-responsive transcriptomic, phenotypic and physiological analyses of rice RGA1 mutant revealed many novel RGA1-regulated genes/processes/traits related to nitrogen use efficiency, and provided robust genetic evidence of RGA1-regulation of NUE. Nitrogen (N) use efficiency (NUE) is important for sustainable agriculture. G-protein signalling was implicated in N-response/NUE in rice, but needed firm genetic characterization of the role of alpha subunit (RGA1). The knock-out mutant of RGA1 in japonica rice exhibited lesser nitrate-dose sensitivity than the wild type (WT), in yield and NUE. We, therefore, investigated its genomewide nitrate-response relative to WT. It revealed 3416 differentially expressed genes (DEGs), including 719 associated with development, grain yield and phenotypic traits for NUE. The upregulated DEGs were related to photosynthesis, chlorophyll, tetrapyrrole and porphyrin biosynthesis, while the downregulated DEGs belonged to cellular protein metabolism and transport, small GTPase signalling, cell redox homeostasis, etc. We validated 26 nitrate-responsive DEGs across functional categories by RT-qPCR. Physiological validation of nitrate-response in the mutant and the WT at 1.5 and 15 mM doses revealed higher chlorophyll and stomatal length but decreased stomatal density, conductance and transpiration. The consequent increase in photosynthesis and water use efficiency may have contributed to better yield and NUE in the mutant, whereas the WT was N-dose sensitive. The mutant was not as N-dose-responsive as the WT in shoot/root growth, productive tillers and heading date, but equally responsive as WT in total N and protein content. The RGA1 mutant was less impacted by higher N-dose or salt stress in terms of yield, protein content, photosynthetic performance, relative water content, water use efficiency and catalase activity. PPI network analyses revealed known NUE-related proteins as RGA1 interactors. Therefore, RGA1 negatively regulates N-dose sensitivity and NUE in rice.

Varietal responses of root characteristics to low nitrogen application explain the differing nitrogen uptake and grain yield in two rice varieties

Rice root characteristics are tightly associated with high-efficient nitrogen uptake. To understand the relationship of root plastic responses with nitrogen uptake when reducing nitrogen application for green rice production, a hydroponic experiment and a soil pot experiment were conducted under high (HN) and low (LN) nitrogen applications, using two rice (Oryza sativa L.) varieties, NK57 and YD6, three nitrogen absorption traits (total nitrogen accumulation, net NH4 + influx on root surface, nitrogen uptake via apoplasmic pathway) and root characteristics were investigated. In comparison with HN, LN significantly reduced nitrogen absorption and grain yield in both varieties. Concomitantly, there was a decrease in total root length, root surface area, root number, root volume, and root cortical area under LN, while single root length, root aerenchyma area, and root lignin content increased. The expression of OsAMT1;1 and OsAMT1;2 down-regulated in both varieties. The findings revealed that YD6 had smaller reduction degree for the three nitrogen absorption traits and grain yield, accompanied by smaller reduction degree in total root length, root surface area, root cortical area, and expression of the two genes under LN. These root characteristics were significantly and positively correlated with the three nitrogen absorption traits and grain yield, especially under LN. These results indicate that a large root system, lower reduction degree in several root characters, and high expression of OsAMT genes in YD6 explains its high nitrogen accumulation and grain yield under reduced nitrogen application. The study may provide rationale for developing varieties with low nitrogen fertilizer requirements for enabling green rice production.

Expression levels of nitrogen assimilation-related genes, physiological responses, and morphological adaptations of three indica rice (Oryza sativa L. ssp. indica) genotypes subjected to nitrogen starvation conditions

Nitrogen (N) is an essential nutrient available to the plants in form of nitrate and ammonium. It is a macronutrient important for the plant growth and development, especially in cereal crops, which consume it for the production of amino acids, proteins/enzymes, nucleic acids, cell wall complexes, plant hormones, and vitamins. In rice production, 17 kg N uptake is required to produce 1 ton of rice. Considering this, many techniques have been developed to evaluate leaf greenness or SPAD value for assessing the amount of N application in the rice cultivar to maximize the grain yield. The aim of the present study was to investigate the morpho-physiological characteristics and relative expression level of N assimilation in three different rice genotypes (MT2, RD31, KDML105) under 1.00 × (full N), 0.50 × , 0.25 × (N depletion), and 0.00 × (N deficiency) at seedling stage and the morpho-physiological traits and the grain yield attributes under 1.00 × (full N) and 0.25 × (N depletion) were compared. Leaf chlorosis and growth inhibition in rice seedlings under N deficiency were evidently observed. Shoot height, number of leaves, shoot fresh weight, shoot dry weight, and root fresh weight in KDML105 under N deficiency were decreased by 27.65%, 42.11%, 65.44%, 47.90%, and 54.09% over the control (full N). Likewise, leaf greenness was lowest in KDML105 under N deficiency (78.57% reduction over the full N), leading to low photosynthetic abilities. In addition, expression of nitrogen assimilation-related genes, OsNR1, OsGln1;1, and OsGln2, in KDML105 under N depletion were increased within 3 h and then declined after the long incubation period, whereas those were unchanged in cvs. MT2 and RD31. Similarly, relative expression level of OsNADH-GOGAT, OsFd-GOGAT, and OsAspAt1 in KDML105 was peaked when subjected to 0.50 × N for 6 h and then declined after the long incubation period. Moreover, overall growth characters and physiological changes in cv. RD31 at vegetative stage under 0.25 × N were retained better than those in cvs. KDML105 and MT2, resulting in high yield at the harvesting process. In summary, N assimilated-related genes in rice seedlings under N depletion were rapidly regulated within 3-6 h, especially cv. KDML105 and MT2, then downregulated, resulting in physiological changes, growth inhibition, and yield reduction.

Microplastics have rice cultivar-dependent impacts on grain yield and quality, and nitrogenous gas losses from paddy, but not on soil properties

Microplastics might affect the nitrogen (N)-use efficiency, crop production, and reactive N losses in agricultural system. However, it remains unclear whether the effects are dependent on crop cultivar. Here, a pot experiment was conducted to evaluate the effects of a typical polyethylene (PE) microplastics addition on grain yield and amino acid content, N-use efficiency, ammonia (NH₃) volatilization and nitrous oxide (N₂O) emission, and properties of paddy soil planted with common rice Nangeng 5055 (NG) and hybrid rice Jiafengyou 6 (JFY). The results showed that PE addition significantly reduced the grain yield and total grain amino acid content of hybrid rice by 23% and 1.7%, respectively. In addition, PE addition significantly decreased the N agronomic and recovery efficiencies of hybrid rice by 30% and 27%, respectively. For paddy soil in which hybrid rice was grown, PE addition significantly increased NH₃ volatilization by 72%, but exerted no influence on N₂O emission. Interestingly, the N₂O emission from NG+PE treatment was 15% significantly lower than that from NG treatment, which was associated with decreased gene copies of nirK (by 50%) and nirS (by 84%) in NG+PE treatment. Generally, no significant change in soil properties was found as result of microplastics addition regardless of the cultivar. In conclusion, the impacts of microplastics on rice production and quality, N-use efficiency and nitrogenous gas losses from paddy soil are cultivar-dependent.

Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development

Two regions located at chromosome A05 and D04 were found to be significantly associated with 0-0.5 mm and 0.5-2 mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0-0.5 mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24 Mb). For SNPs associated with root surface area, root volume and 0.5-2 mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70 Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT-PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties.

OsEIL1 protects rice growth under NH4+ nutrition by regulating OsVTC1-3-dependent N-glycosylation and root NH4+ efflux

Rice is known for its superior adaptation to ammonium (NH₄⁺ ) as a nitrogen source. Compared to many other cereals, it displays lower NH₄⁺ efflux in roots and higher nitrogen-use efficiency on NH₄⁺ . A critical role for GDP-mannose pyrophosphorylase (VTC1) in controlling root NH₄⁺ fluxes was previously documented in Arabidopsis, but the molecular pathways involved in regulating VTC1-dependent NH₄⁺ efflux remain unclear. Here, we report that ETHYLENE-INSENSITIVE3-LIKE1 (OsEIL1) acts as a key transcription factor regulating OsVTC1-3-dependent NH₄⁺ efflux and protein N-glycosylation in rice grown under NH₄⁺ nutrition. We show that OsEIL1 in rice plays a contrasting role to Arabidopsis-homologous ETHYLENE-INSENSITIVE3 (AtEIN3) and maintains rice growth under NH₄⁺ by stabilizing protein N-glycosylation and reducing root NH₄⁺ efflux. OsEIL1 constrains NH₄⁺ efflux by activation of OsVTC1-3, but not OsVTC1-1 or OsVTC1-8. OsEIL1 binds directly to the promoter EIN3-binding site (EBS) of OsVTC1-3 in vitro and in vivo and acts to increase the transcription of OsVTC1-3. Our work demonstrates an important link between excessive root NH₄⁺ efflux and OsVTC1-3-mediated protein N-glycosylation in rice grown under NH₄⁺ nutrition and identifies OsEIL1 as a direct genetic regulator of OsVTC1-3 expression.

OsGF14b is involved in regulating coarse root and fine root biomass partitioning in response to elevated [CO2] in rice

Elevated [CO₂] can increase rice biomass and yield, but the degree of this increase varies substantially among cultivars. Little is known about the gene loci involved in the acclimation and adaptation to elevated [CO₂] in rice. Here, we report on a T-DNA insertion mutant in japonica rice exhibiting a significantly enhanced response to elevated [CO₂] compared with the wild type (WT). The root biomass response of the mutant was higher than that of the WT, and this manifested in the number of adventitious roots, the average diameter of roots, and total root length. Furthermore, coarse roots (>0.6 mm) and thin lateral roots (<0.2 mm) were more responsive to elevated [CO₂] in the mutant. When exposed to lower light intensity, however, the response of the mutant to elevated [CO₂] was not superior to that of the WT, indicating that the high response of the mutant under elevated [CO₂] was dependent on light intensity. The T-DNA insertion site was located in the promoter region of the OsGF14b gene, and insertion resulted in a significant decrease in OsGF14b expression. Our results indicate that knockout of OsGF14b may improve the response to elevated [CO₂] in rice by enhancing carbon allocation to coarse roots and to fine lateral roots.

Transcriptome Analysis of Two Near-Isogenic Lines with Different NUE under Normal Nitrogen Conditions in Wheat

Simple Summary

High nitrogen use efficiency (NUE) in wheat (Triticum aestivum L.) is the key to ensure high yield and reduce pollution. Understanding the physiological and molecular changes that regulate NUE is important for the breeding of high-NUE wheat varieties. Carbon and nitrogen metabolism are the basic metabolic pathways in plants. It becomes important to reveal the underlying molecular mechanisms related to carbon and nitrogen metabolism, which may be helpful to improve NUE. In this paper, two wheat near-isogenic lines (NILs) with contrasting NUE were performed RNA-Sequencing (RNA-Seq) to identify candidate genes associated with carbon/nitrogen metabolism under normal nitrogen conditions. Our research may provide new insights into the comprehensive understanding of the molecular mechanism underlying NUE.

Abstract

Nitrogen (N) is an essential nutrient element for crop productivity. Unfortunately, the nitrogen use efficiency (NUE) of crop plants gradually decreases with the increase of the N application rate. Nevertheless, little has been known about the molecular mechanisms of differences in NUE among genotypes of wheat. In this study, we used RNA-Sequencing (RNA-Seq) to compare the transcriptome profiling of flag leaves at the stage of anthesis in wheat NILs (1Y, high-NUE, and 1W, low-NUE) under normal nitrogen conditions (300 kg N ha⁻¹, corresponding to 1.6 g N pot⁻¹). We identified 7023 DEGs (4738 upregulated and 2285 downregulated) in the comparison between lines 1Y and 1W. The responses of 1Y and 1W to normal N differed in the transcriptional regulatory mechanisms. Several genes belonging to the GS and GOGAT gene families were upregulated in 1Y compared with 1W, and the enhanced carbon metabolism might lead 1Y to produce more C skeletons, metabolic energy, and reductants for nitrogen metabolism. A subset of transcription factors (TFs) family members, such as ERF, WRKY, NAC, and MYB, were also identified. Collectively, these identified candidate genes provided new information for a further understanding of the genotypic difference in NUE.

Integrative Transcriptomic and Proteomic Analysis Reveals an Alternative Molecular Network of Glutamine Synthetase 2 Corresponding to Nitrogen Deficiency in Rice (Oryza sativa L.)

Nitrogen (N) is an essential nutrient for plant growth and development. The root system architecture is a highly regulated morphological system, which is sensitive to the availability of nutrients, such as N. Phenotypic characterization of roots from LY9348 (a rice variety with high nitrogen use efficiency (NUE)) treated with 0.725 mM NH₄NO₃ (1/4N) was remarkable, especially primary root (PR) elongation, which was the highest. A comprehensive analysis was performed for transcriptome and proteome profiling of LY9348 roots between 1/4N and 2.9 mM NH₄NO₃ (1N) treatments. The results indicated 3908 differential expression genes (DEGs; 2569 upregulated and 1339 downregulated) and 411 differential abundance proteins (DAPs; 192 upregulated and 219 downregulated). Among all DAPs in the proteome, glutamine synthetase (GS2), a chloroplastic ammonium assimilation protein, was the most upregulated protein identified. The unexpected concentration of GS2 from the shoot to the root in the 1/4N treatment indicated that the presence of an alternative pathway of N assimilation regulated by GS2 in LY9348 corresponded to the low N signal, which was supported by GS enzyme activity and glutamine/glutamate (Gln/Glu) contents analysis. In addition, N transporters (NRT2.1, NRT2.2, NRT2.3, NRT2.4, NAR2.1, AMT1.3, AMT1.2, and putative AMT3.3) and N assimilators (NR2, GS1;1, GS1;2, GS1;3, NADH-GOGAT2, and AS2) were significantly induced during the long-term N-deficiency response at the transcription level (14 days). Moreover, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that phenylpropanoid biosynthesis and glutathione metabolism were significantly modulated by N deficiency. Notably, many transcription factors and plant hormones were found to participate in root morphological adaptation. In conclusion, our study provides valuable information to further understand the response of rice roots to N-deficiency stress.