Low Nitrogen Conditions Research Articles

Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed (Brassica napus L.).

Plants rely on root systems for nutrient uptake from soils. Marker-assisted selection helps breeders to select desirable root traits for effective nutrient uptake. Here, 12 root and biomass traits were investigated at the seedling stage under low nitrogen (LN), low phosphorus (LP), and low potassium (LK) conditions, respectively, in a recombinant inbred line (RIL) population, which was generated from Brassica napus L. Zhongshuang11 and 4D122 with significant differences in root traits and nutrient efficiency. Significant differences for all the investigated traits were observed among RILs, with high heritabilities (0.43–0.74) and high correlations between the different treatments. Quantitative trait loci (QTL) mapping identified 57, 27, and 36 loci, explaining 4.1–10.9, 4.6–10.8, and 4.9–17.4% phenotypic variances under LN, LP, and LK, respectively. Through QTL-meta analysis, these loci were integrated into 18 significant QTL clusters. Four major QTL clusters involved 25 QTLs that could be repeatedly detected and explained more than 10% phenotypic variances, including two NPK-common and two specific QTL clusters (K and NK-specific), indicating their critical role in cooperative nutrients uptake of N, P, and K. Moreover, 264 genes within the four major QTL clusters having high expressions in roots and SNP/InDel variations between two parents were identified as potential candidate genes. Thirty-eight of them have been reported to be associated with root growth and development and/or nutrient stress tolerance. These key loci and candidate genes lay the foundation for deeper dissection of the NPK starvation response mechanisms in B. napus.

GWAS and Transcriptome Analysis Reveal Key Genes Affecting Root Growth under Low Nitrogen Supply in Maize.

Nitrogen (N) is one of the most important factors affecting crop production. Root morphology exhibits a high degree of plasticity to nitrogen deficiency. However, the mechanisms underlying the root foraging response under low-N conditions remain poorly understood. In this study, we analyzed 213 maize inbred lines using hydroponic systems and regarding their natural variations in 22 root traits and 6 shoot traits under normal (2 mM nitrate) and low-N (0 mM nitrate) conditions. Substantial phenotypic variations were detected for all traits. N deficiency increased the root length and decreased the root diameter and shoot related traits. A total of 297 significant marker-trait associations were identified by a genome-wide association study involving different N levels and the N response value. A total of 51 candidate genes with amino acid variations in coding regions or differentially expressed under low nitrogen conditions were identified. Furthermore, a candidate gene ZmNAC36 was resequenced in all tested lines. A total of 38 single nucleotide polymorphisms and 12 insertions and deletions were significantly associated with lateral root length of primary root, primary root length between 0 and 0.5 mm in diameter, primary root surface area, and total length of primary root under a low-N condition. These findings help us to improve our understanding of the genetic mechanism of root plasticity to N deficiency, and the identified loci and candidate genes will be useful for the genetic improvement of maize tolerance cultivars to N deficiency.

A 3' UTR-derived small RNA connecting nitrogen and carbon metabolism in enteric bacteria.

Increasing numbers of small, regulatory RNAs (sRNAs) corresponding to 3' untranslated regions (UTR) are being discovered in bacteria. One such sRNA, denoted GlnZ, corresponds to the 3' UTR of the Escherichia coli glnA mRNA encoding glutamine synthetase. Several forms of GlnZ, processed from the glnA mRNA, are detected in cells growing with limiting ammonium. GlnZ levels are regulated transcriptionally by the NtrC transcription factor and post-transcriptionally by RNase III. Consistent with the expression, E. coli cells lacking glnZ show delayed outgrowth from nitrogen starvation compared to wild type cells. Transcriptome-wide RNA-RNA interactome datasets indicated that GlnZ binds to multiple target RNAs. Immunoblots and assays of fusions confirmed GlnZ-mediated repression of glnP and sucA, encoding proteins that contribute to glutamine transport and the citric acid cycle, respectively. Although the overall sequences of GlnZ from E. coli K-12, Enterohemorrhagic E. coli and Salmonella enterica have significant differences due to various sequence insertions, all forms of the sRNA were able to regulate the two targets characterized. Together our data show that GlnZ impacts growth of E. coli under low nitrogen conditions by modulating genes that affect carbon and nitrogen flux.

The beneficial effect of Epichloë endophytes on the growth of host grasses was affected by arbuscular mycorrhizal fungi, pathogenic fungi and nitrogen addition

Native grasslands are often limited by nitrogen, so even a low level of nitrogen deposition may significantly impact the growth of plants as well as plant-associated microbes. Epichloë endophytes inhabit the aboveground tissues of healthy plants, and their beneficial effects on the growth of host grasses have been widely reported. In this study, the abundance of the endophyte and its effect on the host Achnatherum sibiricum when cooccurring with arbuscular mycorrhizal fungi (AMF) or pathogens was investigated with increasing nitrogen supply. The results demonstrated that endophyte abundance increased significantly with increasing leaf nitrogen concentration and plant biomass under low nitrogen conditions, but there was no such correlation for AMF or pathogen abundance. The individual effect of endophytes on plant performance was positive under both low ( P = 0.002) and high ( P = 0.013) nitrogen conditions; only the promotion degree was even greater under low nitrogen conditions ( P = 0.004). When endophytes and AMF were both present, the combined effects of the two symbionts on plant growth were antagonistic under low nitrogen levels ( P = 0.048), while the combined effects of the two symbionts on plant growth were independent under high nitrogen levels ( P = 0.109). When endophytes and pathogens were both present, the net effect on plants was greater than the sum of the separate effects of the two microbes and was not affected by environmental nitrogen. Endophytes could inhibit pathogen abundance by increasing total phenolic content of the host A. sibiricum . Overall, the impact of endophytes on host plants was affected not only by abiotic environmental nitrogen but also by biotic factors AMF and pathogens. Therefore, clarifying the impact factors of endophytes on host growth is important for predicting the population dynamics and community diversity of host plants. • Host plant biomass increased with increasing abundance of endophytes only under low nitrogen treatment. • When present alone, endophytes promoted host growth under both low and high nitrogen conditions. • When present with AMF, the net effect on plants was antagonistic under low nitrogen while independent under high nitrogen. • When present with pathogens, the net effect on plants was greater than the sum of the separate effects of the two microbes.

Estimation of chlorophyll, macronutrients and water content in maize from hyperspectral data using machine learning and explainable artificial intelligence techniques

ABSTRACT We used the secondary hyperspectral data set (leaf reflectance of maize) taken in the spectral range from 350 to 2500 nm in a field (under low and high nitrogen conditions) and glasshouse experiment. Water, chlorophyll, nitrogen (N), phosphorus (P) and potassium (K) contents of maize leaves taken from these experiments were measured using the standard methods. Six machine learning regression algorithms (Random Forest, Support Vector Regression, k-Nearest Neighbours, Multilayer Perceptron, Gradient Boosting Regression and Partial Least Square Regression) were used for development of the models to predict these parameters from leaf reflectance data. Each plant parameter was estimated with a different machine learning algorithm. Explainable artificial intelligence methods were used to identify the optimum wavelengths for each parameter. The wavelengths in the short-wave infrared (SWIR) region were found optimum for estimating the water content across the three N regimes, and the red-edge band for chlorophyll. The optimum wavelengths for estimating N content in leaves were in the green spectral region under low N status, near-infrared (NIR) and SWIR regions under greenhouse and SWIR region under high N status. The important wavelengths for estimating P in maize leaves were 1088, 1262 and 1263 nm under low N status and the SWIR range under high N status and greenhouse conditions. The SWIR band was useful for estimating the K content in leaves.

The difference method is not necessarily reliable for comparing the nitrogen use efficiency of hybrid rice cultivars with different tolerance to low nitrogen conditions

The difference method is one of the most commonly used methods to measure crop nitrogen (N) use efficiency. This study aimed to test the reliability of using this method to evaluate the N use efficiency of low-N tolerant hybrid rice. Two years of N fertilization experiments were conducted to compare yield attributes and N use efficiency measured by the difference method between two hybrid rice cultivars with contrasting tolerance to low N conditions, i.e. Deyou 4727 (D4727) with higher tolerance and Y-liangyou 900 (Y900) with relatively lower tolerance. Results showed that D4727 produced 17–24% higher grain yield than Y900 under zero-N fertilization conditions, confirming the higher tolerance of D4727 to low N conditions. Higher grain weight, harvest index, and internal N use efficiency were responsible for the higher grain yield in D4727 than in Y900. However, recovery efficiency of N determined by the difference method was not consistently different between D4727 and Y900, and physiological N use efficiency (PEN) and agronomic N use efficiency (AEN) determined by the difference method were 31–68% lower in D4727 compared to Y900. The lower PEN and AEN in D4727 than in Y900 were mainly due to a higher grain yield in D4727 than in Y900 under unfertilized conditions. This study suggests that the difference method is not necessarily reliable for comparing the N use efficiency of rice cultivars with different tolerance to low-N conditions, and both crop performance under unfertilized conditions and N responses under fertilized conditions should be considered when using this method to evaluate the N use efficiency of rice.

Lipidomics Analysis of Tea Leaves Cultured in Hydroponics Reveals That High Nitrogen Application Decreases Tea Plant Resistance to Ultraviolet Radiation

Lipid composition in tea leaves is significantly affected by ultraviolet (UV) radiation and nitrogen levels. Here, to reveal the response of lipids in tea plants (Camellia sinensis L.) to the interaction between nitrogen and UV radiation, we treated tea plants with three gradients of UV radiation under two nitrogen levels by the hydroponic method. Lipidomics results show that ultraviolet radiation can decrease neutral lipid (TAG) and increase membrane lipids (including PC, PE, and PG) under hydroponic conditions, indicating that tea plants could survive UV radiation by decomposing TAG to avoid damaging cells. In addition, the accumulation of phospholipids and galactolipids may be related to avoiding UV damage and enhancing photosynthesis in tea plants under UV radiation. Furthermore, the response of lipid components to UV radiation in tea plants under low nitrogen conditions is significantly lower than that under high nitrogen conditions, which suggests that excessive nitrogen application may reduce the resistance of tea plants to UV radiation. This study provides a theoretical basis for optimizing cultivation measures based on tea UV resistance.

Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight).

Protistan algae (phytoplankton) dominate coastal upwelling ecosystems where they form massive blooms that support the world's most important fisheries and constitute an important sink for atmospheric CO2 . Bloom initiation is well understood, but the biotic and abiotic forces that shape short-term dynamics in community composition are still poorly characterized. Here, high-frequency (daily) changes in relative abundance dynamics of the metabolically active protistan community were followed via expressed 18S V4 rRNA genes (RNA) throughout two algal blooms during the spring of 2018 and 2019 in Santa Monica Bay (central Southern California Bight). A diatom bloom formed after wind-driven, nutrient upwelling events in both years, but different taxa dominated each year. Whereas diatoms bloomed following elevated nutrients and declined after depletion each year, a massive dinoflagellate bloom manifested under relatively low inorganic nitrogen conditions following diatom bloom senescence in 2019 but not 2018. Network analysis revealed associations between diatoms and cercozoan putative parasitic taxa and syndinean parasites during 2019 that may have influenced the demise of the diatoms, and the transition to a dinoflagellate-dominated bloom.

Comparative genomic and transcriptomic analyses uncover the molecular basis of high nitrogen-use efficiency in the wheat cultivar Kenong 9204

Studying the regulatory mechanisms that drive nitrogen-use efficiency (NUE) in crops is important for sustainable agriculture and environmental protection. In this study, we generated a high-quality genome assembly for the high-NUE wheat cultivar Kenong 9204 and systematically analyzed genes related to nitrogen uptake and metabolism. By comparative analyses, we found that the high-affinity nitrate transporter gene family had expanded in Triticeae. Further studies showed that subsequent functional differentiation endowed the expanded family members with saline inducibility, providing a genetic basis for improving the adaptability of wheat to nitrogen deficiency in various habitats. To explore the genetic and molecular mechanisms of high NUE, we compared genomic and transcriptomic data from the high-NUE cultivar Kenong 9204 (KN9204) and the low-NUE cultivar Jing 411 and quantified their nitrogen accumulation under high- and low-nitrogen conditions. Compared with Jing 411, KN9204 absorbed significantly more nitrogen at the reproductive stage after shooting and accumulated it in the shoots and seeds. Transcriptome data analysis revealed that nitrogen deficiency clearly suppressed the expression of genes related to cell division in the young spike of Jing 411, whereas this suppression of gene expression was much lower in KN9204. In addition, KN9204 maintained relatively high expression of NPF genes for a longer time than Jing 411 during seed maturity. Physiological and transcriptome data revealed that KN9204 was more tolerant of nitrogen deficiency than Jing 411, especially at the reproductive stage. The high NUE of KN9204 is an integrated effect controlled at different levels. Taken together, our data provide new insights into the molecular mechanisms of NUE and important gene resources for improving wheat cultivars with a higher NUE trait.

GmNAC181 promotes symbiotic nodulation and salt tolerance of nodulation by directly regulating GmNINa expression in soybean.

Soybean (Glycine max) is one of the most important crops world-wide. Under low nitrogen (N) condition, soybean can form a symbiotic relationship with rhizobia to acquire sufficient N for their growth and production. Nodulation signaling controls soybean symbiosis with rhizobia. The soybean Nodule Inception (GmNINa) gene is a central regulator of soybean nodulation. However, the transcriptional regulation of GmNINa remains largely unknown. Nodulation is sensitive to salt stress, but the underlying mechanisms are unclear. Here, we identified an NAC transcription factor designated GmNAC181 (also known as GmNAC11) as the interacting protein of GmNSP1a. GmNAC181 overexpression or knockdown in soybean resulted in increased or decreased numbers of nodules, respectively. Accordingly, the expression of GmNINa was greatly up- and downregulated, respectively. Furthermore, we showed that GmNAC181 can directly bind to the GmNINa promoter to activate its gene expression. Intriguingly, GmNAC181 was highly induced by salt stress during nodulation and promoted symbiotic nodulation under salt stress. We identified a new transcriptional activator of GmNINa in the nodulation pathway and revealed a mechanism by which GmNAC181 acts as a network node orchestrating the expression of GmNINa and symbiotic nodulation under salt stress conditions.

Genome-Wide Identification of TaSAUR Gene Family Members in Hexaploid Wheat and Functional Characterization of TaSAUR66-5B in Improving Nitrogen Use Efficiency.

Excessive input of nitrogen fertilizer not only causes a great waste of resources but brings about a series of ecological and environmental problems. Although Small Auxin Up-regulated RNAs (SAURs) participate in diverse biological processes, the function of SAURs in the nitrogen starvation response has not been well-studied. Here, we identified 308 TaSAURs in wheat and divided them into 10 subfamilies. The promoter regions of most TaSAURs contain hormone responsive elements, and their expression levels change under the treatment of different hormones, such as IAA, MeJA, and ABA. Interestingly, overexpression of one of the TaSAUR family members, a nitrogen starvation responsive gene, TaSAUR66-5B, can promote the growth of Arabidopsis and wheat roots. In addition, overexpression of TaSAUR66-5B in Arabidopsis up-regulates the expression levels of auxin biosynthesis related genes, suggesting that overexpression TaSAUR66-5B may promote root growth by increasing the biosynthesis of auxin. Furthermore, overexpression of TaSAUR66-5B in wheat can increase the biomass and grain yields of transgenic plants, as well as the nitrogen concentration and accumulation of both shoots and grains, especially under low nitrogen conditions. This study provides important genomic information of the TaSAUR gene family and lays a foundation for elucidating the functions of TaSAURs in improving nitrogen utilization efficiency in wheat.

Superior Haplotypes for Early Root Vigor Traits in Rice Under Dry Direct Seeded Low Nitrogen Condition Through Genome Wide Association Mapping.

Water and land resources have been aggressively exploited in the recent decades to meet the growing demands for food. The changing climate has prompted rice scientists and farmers of the tropics and subtropics to adopt the direct seeded rice (DSR) system. DSR system of rice cultivation significantly reduces freshwater consumption and labor requirements, while increasing system productivity, resource use efficiency, and reducing greenhouse gas emissions. Early root vigor is an essential trait required in an ideal DSR system of rice cultivation to ensure a good crop stand, adequate uptake of water, nutrients and compete with weeds. The aus subpopulation which is adapted for DSR was evaluated to understand the biology of early root growth under limited nitrogen conditions over two seasons under two-time points (14 and 28 days). The correlation study identified a positive association between shoot dry weight and root dry weight. The genome-wide association study was conducted on root traits of 14 and 28 days with 2 million single-nucleotide polymorphisms (SNPs) using an efficient mixed model. QTLs over a significant threshold of p < 0.0001 and a 10% false discovery rate were selected to identify genes involved in root growth related to root architecture and nutrient acquisition from 97 QTLs. Candidate genes under these QTLs were explored. On chromosome 4, around 30 Mbp are two important peptide transporters (PTR5 and PTR6) involved in mobilizing nitrogen in the root during the early vegetative stage. In addition, several P transporters and expansin genes with superior haplotypes are discussed. A novel QTL from 21.12 to 21.46 Mb on chromosome 7 with two linkage disequilibrium (LD) blocks governing root length at 14 days were identified. The QTLs/candidate genes with superior haplotype for early root vigor reported here could be explored further to develop genotypes for DSR conditions.

A Koshihikari X Oryza rufipogon Introgression Line with a High Capacity to Take up Nitrogen to Maintain Growth and Panicle Development under Low Nitrogen Conditions.

Nitrogen (N) is an important macronutrient for plant growth and development. Currently, N fertilizers are required for the efficient production of modern crops such as rice due to their limited capacity to take up N when present at low concentrations. Wild rice represents a useful genetic resource for improving crop responses to low nutrient stress. Here, we describe the isolation and characterization of an introgression line, KRIL37, that carries a small region of the Oryza rufipogon genome in the Oryza sativa L. cv Koshihikari (KH) background. This line was found to grow better under low N conditions and have similar or lower C/N ratios in aerial portions compared to those in the parental KH cultivar, suggesting that KRIL37 has a higher capacity to take up and assimilate N when present at low concentrations. KRIL37 performance in the field was also better than that of KH cultivated without N and fertilizer (-F). Transcriptome analyses of 3-week-old seedlings based on RNA-sequencing revealed that KH induced a wider suite of genes than the tolerant line KRIL37 in response to low N conditions. Some ammonium transporters and N assimilation genes were found to be induced under low N in KRIL37, but not in KH. Our findings suggest that the superior growth performance of KRIL37 under limited N conditions could be due to the expression of wild alleles influencing N uptake and assimilation. Our study demonstrates the potential to use wild rice genomes to improve modern crops for low nutrient tolerance.

The pho1;2a'-m1.1 allele of Phosphate1 conditions misregulation of the phosphorus starvation response in maize (Zea mays ssp. mays L.).

Plant PHO1 proteins play a central role in the translocation and sensing of inorganic phosphate. The maize ( Zea mays ssp. mays ) genome encodes two co‐orthologs of the Arabidopsis PHO1 gene, designated ZmPho1;2a and ZmPho1;2b. Here, we report the characterization of the transposon footprint allele Zmpho1;2a′‐m1.1, which we refer to hereafter as pho1;2a. The pho1;2a allele is a stable derivative formed by excision of an Activator transposable element from the ZmPho1;2a gene. The pho1;2a allele contains an 8‐bp insertion at the point of transposon excision that disrupts the reading frame and is predicted to generate a premature translational stop. We show that the pho1;2a allele is linked to a dosage‐dependent reduction in Pho1;2a transcript accumulation and a mild reduction in seedling growth. Characterization of shoot and root transcriptomes under full nutrient, low nitrogen, low phosphorus, and combined low nitrogen and low phosphorus conditions identified 1100 differentially expressed genes between wild‐type plants and plants carrying the pho1;2a mutation. Of these 1100 genes, 966 were upregulated in plants carrying pho1;2a, indicating the wild‐type PHO1;2a to predominantly impact negative gene regulation. Gene set enrichment analysis of the pho1;2a‐misregulated genes revealed associations with phytohormone signaling and the phosphate starvation response. In roots, differential expression was broadly consistent across all nutrient conditions. In leaves, differential expression was largely specific to low phosphorus and combined low nitrogen and low phosphorus conditions. Of 276 genes upregulated in the leaves of pho1;2a mutants in the low phosphorus condition, 153 were themselves induced in wild‐type plants with respect to the full nutrient condition. Our observations suggest that Pho1;2a functions in the fine‐tuning of the transcriptional response to phosphate starvation through maintenance and/or sensing of plant phosphate status.

Daya Gabung Galur Jagung pada Cekaman Nitrogen Rendah

Reduction of nitrogen in the soil is a problem in corn cultivation that can cause decrease production. The efforts to prevent this problem is to assemble superior maize that is low nitrogen resistance and high production by crossing different corn elders. This study was to analyse the combining ability of five lines (G1, G2, G3, G4 and G5) under normal and low nitrogen conditions used a half diallel cross design using the Griffing’s model I method formula to analyse 10 genotypes. The research design used a split plot design (SPD) with 3 replications, the research location was in the experimental garden of Center for Agricultural Research and Technology in Kebondalem, Mojosari, Mojokerto East Java. The value of the general combining ability (GCA) of the G3 elders significantly affected the weight parameters of the cobs under low nitrogen conditions. The results of the specific combining ability (DGK) on the G7 and G8 crosses had high SCA values on the yield character and weight of 100 seeds under normal conditions and nitrogen stress. Genotype G6 has a high SCA value for cob weight characters.

Cassava (Manihot esculenta) Slow Anion Channel (MeSLAH4) Gene Overexpression Enhances Nitrogen Assimilation, Growth, and Yield in Rice.

Nitrogen is one of the most important nutrient elements required for plant growth and development, which is also immensely related to the efficient use of nitrogen by crop plants. Therefore, plants evolved sophisticated mechanisms and anion channels to extract inorganic nitrogen (nitrate) from the soil or nutrient solutions, assimilate, and recycle the organic nitrogen. Hence, developing crop plants with a greater capability of using nitrogen efficiently is the fundamental research objective for attaining better agricultural productivity and environmental sustainability. In this context, an in-depth investigation has been conducted into the cassava slow type anion channels (SLAHs) gene family, including genome-wide expression analysis, phylogenetic relationships with other related organisms, chromosome localization, and functional analysis. A potential and nitrogen-responsive gene of cassava (MeSLAH4) was identified and selected for overexpression (OE) analysis in rice, which increased the grain yield and root growth related performance. The morpho-physiological response of OE lines was better under low nitrogen (0.01 mm NH4NO3) conditions compared to the wild type (WT) and OE lines under normal nitrogen (0.5 mm NH4NO3) conditions. The relative expression of the MeSLAH4 gene was higher (about 80-fold) in the OE line than in the wild type. The accumulation and flux assay showed higher accumulation of and more expansion of root cells and grain dimension of OE lines compared to the wild type plants. The results of this experiment demonstrated that the MeSLAH4 gene may play a vital role in enhancing the efficient use of nitrogen in rice, which could be utilized for high-yielding crop production.

Effects of Barranca yajiagengensis Powder in the Diet of Trachinotus ovatus on the Growth Performance, Antioxidant Capacity, Immunity and Morphology of the Liver and Intestine.

Barranca yajiagengensis, a novel filamentous microalga, can accumulate lutein under high-light and low-nitrogen conditions. It is well known that lutein has antioxidant, anti-inflammatory and immune-modulating properties. The purpose of this study is to evaluate the effects of including lutein-rich B. yajiagengensis powder in the diet of Trachinotus ovatus on the growth performance, antioxidant capacity, immunity, liver, and intestinal morphology. For this aim, three experimental diets containing 0% (BY0), 1% (BY1), and 5% (BY5) B. yajiagengensis powder were formulated for six-week feeding trials. The results indicated that growth performance, feed utilization, and intestinal morphology were not affected by different diet treatments. Fish fed with the BY5 diet promoted antioxidant ability by activating the Nrf2-ARE signal pathway and enhancing antioxidant enzymes activities. Furthermore, the BY5 diet improved non-specific immunity and antibacterial ability by activating lysozymes and the complement system and increasing the nitric oxide (NO) content and total nitric oxide synthase activity. Dietary B. yajiagengensis supplementation improved the liver morphology and exerted hepatoprotective effects. Therefore, as a natural source of lutein, B. yajiagengensis has the potential as a safe and non-toxic immunostimulant for T. ovatus. A diet supplemented with 5% B. yajiagengensis is recommended to improve the growth, antioxidant capacity, immune response, and liver health of T. ovatus.

Insights into nitrogen metabolism in the wild and cultivated lettuce as revealed by transcriptome and weighted gene co-expression network analysis

Large amounts of nitrogen fertilizers applied during lettuce (Lactuca sativa L.) production are lost due to leaching or volatilization, causing severe environmental pollution and increased costs of production. Developing lettuce varieties with high nitrogen use efficiency (NUE) is the eco-friendly solution to reduce nitrogen pollution. Hence, in-depth knowledge of nitrogen metabolism and assimilation genes and their regulation is critical for developing high NUE varieties. In this study, we performed comparative transcriptomic analysis of the cultivated lettuce (L. sativa L.) and its wild progenitor (L. serriola) under high and low nitrogen conditions. A total of 2,704 differentially expressed genes were identified. Key enriched biological processes included photosynthesis, oxidation–reduction process, chlorophyll biosynthetic process, and cell redox homeostasis. The transcription factors (TFs) belonging to the ethylene responsive factor family and basic helix-loop-helix family were among the top differentially expressed TFs. Using weighted gene co-expression network analysis we constructed nine co-expression modules. Among these, two modules were further investigated because of their significant association with total nitrogen content and photosynthetic efficiency of photosystem II. Three highly correlated clusters were identified which included hub genes for nitrogen metabolism, secondary metabolites, and carbon assimilation, and were regulated by cluster specific TFs. We found that the expression of nitrogen transportation and assimilation genes varied significantly between the two lettuce species thereby providing the opportunity of introgressing wild alleles into the cultivated germplasm for developing lettuce cultivars with more efficient use of nitrogen.

Comparative Transcriptome Analysis Reveals Common and Developmental Stage-Specific Genes That Respond to Low Nitrogen in Maize Leaves.

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.

Genome-wide association study identifies novel candidate loci or genes affecting stalk strength in maize

Stalk strength increases resistance to stalk lodging, which causes maize (Zea mays L.) production losses worldwide. The genetic mechanisms regulating stalk strength remain unclear. In this study, three stalk strength-related traits (rind penetrometer resistance, stalk crushing strength, and stalk bending strength) and four plant architecture traits (plant height, ear height, stem diameter, stem length) were measured in three field trials. Substantial phenotypic variation was detected for these traits. A genome-wide association study (GWAS) was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms (SNPs). A total of 94 quantitative trait loci including 241 SNPs were detected. By combining the GWAS data with public gene expression data, 56 candidate genes within 50 kb of the significant SNPs were identified, including genes encoding flavonol synthase (GRMZM2G069298, ZmFLS2), nitrate reductase (GRMZM5G878558, ZmNR2), glucose-1-phosphate adenylyltransferase (GRMZM2G027955), and laccase (GRMZM2G447271). Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR. Comparison of the RPR of the zmnr2 EMS mutant and the wild-type plant under high- and low-nitrogen conditions verified the GRMZM5G878558 function. These findings may be useful for clarifying the genetic basis of stalk strength. The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.