Genetic Dissection of Root Morphological Traits Related to Nitrogen Use Efficiency in Brassica napus L. under Two Contrasting Nitrogen Conditions

Genome-wide association studies of root system architecture traits in a broad collection of Brassica genotypes

The root systems of Brassica species are complex. Eight root system architecture (RSA) traits, including total root length, total root surface area, root average diameter, number of tips, total primary root length, total lateral root length, total tertiary root length, and basal link length, were phenotyped across 379 accessions representing six Brassica species (B. napus, B. juncea, B. carinata, B. oleracea, B. nigra, and B. rapa) using a semi-hydroponic system and image analysis software. The results suggest that, among the assessed species, B. napus and B. oleracea had the most intricate and largest root systems, while B. nigra exhibited the smallest roots. The two species B. juncea and B. carinata shared comparable root system complexity and had root systems with larger root diameters. In addition, 313 of the Brassica accessions were genotyped using a 19K Brassica single nucleotide polymorphism (SNP) array. After filtering by TASSEL 5.0, 6,213 SNP markers, comprising 5,103 markers on the A-genome (covering 302,504 kb) and 1,110 markers on the C-genome (covering 452,764 kb), were selected for genome-wide association studies (GWAS). Two general linear models were tested to identify the genomic regions and SNPs associated with the RSA traits. GWAS identified 79 significant SNP markers associated with the eight RSA traits investigated. These markers were distributed across the 18 chromosomes of B. napus, except for chromosome C06. Sixty-five markers were located on the A-genome, and 14 on the C-genome. Furthermore, the major marker-trait associations (MTAs)/quantitative trait loci (QTLs) associated with root traits were located on chromosomes A02, A03, and A06. Brassica accessions with distinct RSA traits were identified, which could hold functional, adaptive, evolutionary, environmental, pathological, and breeding significance.

Genetic control of root morphology in response to nitrogen across rapeseed diversity

Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.

Molecular dissection of heterosis in cereal roots and their rhizosphere

Heterosis is already manifested early in root development. Consistent with the dominance model of heterosis, gene expression complementation is a general mechanism that contributes to phenotypic heterosis in maize hybrids. Highly heterozygous F1-hybrids outperform their parental inbred lines, a phenomenon known as heterosis. Utilization of heterosis is of paramount agricultural importance and has been widely applied to increase yield in many crop cultivars. Plant roots display heterosis for many traits and are an important target for further crop improvement. To explain the molecular basis of heterosis, several genetic hypotheses have been proposed. In recent years, high-throughput gene expression profiling techniques have been applied to investigate hybrid vigor. Consistent with the classical genetic dominance model, gene expression complementation has been demonstrated to be a general mechanism to contribute to phenotypic heterosis in diverse maize hybrids. Functional classification of these genes supported the notion that gene expression complementation can dynamically promote hybrid vigor under fluctuating environmental conditions. Hybrids tend to respond differently to available nutrients in the soil. It was hypothesized that hybrid vigor is promoted through a higher nutrient use efficiency which is linked to an improved root system performance of hybrids in comparison to their inbred parents. Recently, the interaction between soil microbes and their plant host was added as further dimension to disentangle heterosis in the belowground part of plants. Soil microbes influenced the performance of maize hybrids as illustrated in comparisons of sterile soil and soil inhabited by beneficial microorganisms.

Root system architecture for abiotic stress tolerance in potato: Lessons from plants

The root is an important plant organ, which uptakes nutrients and water from the soil, and provides anchorage for the plant. Abiotic stresses like heat, drought, nutrients, salinity, and cold are the major problems of potato cultivation. Substantial research advances have been achieved in cereals and model plants on root system architecture (RSA), and so root ideotype (e.g., maize) have been developed for efficient nutrient capture to enhance nutrient use efficiency along with genes regulating root architecture in plants. However, limited work is available on potatoes, with a few illustrations on root morphology in drought and nitrogen stress. The role of root architecture in potatoes has been investigated to some extent under heat, drought, and nitrogen stresses. Hence, this mini-review aims to update knowledge and prospects of strengthening RSA research by applying multi-disciplinary physiological, biochemical, and molecular approaches to abiotic stress tolerance to potatoes with lessons learned from model plants, cereals, and other plants.

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.

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

An excellent root system is responsible for crops with high nitrogen-use efficiency (NUE). The current study evaluated the natural variations in 13 root- and biomass-related traits under a low nitrogen (LN) treatment in a rapeseed association panel. The studied traits exhibited significant phenotypic differences with heritabilities ranging from 0.53 to 0.66, and most of the traits showed significant correlations with each other. The genome-wide association study (GWAS) found 51 significant and 30 suggestive trait–SNP associations that integrated into 14 valid quantitative trait loci (QTL) clusters and explained 5.7–21.2% phenotypic variance. In addition, RNA sequencing was performed at two time points to examine the differential expression of genes (DEGs) between high and low NUE lines. In total, 245, 540, and 399 DEGs were identified as LN stress-specific, high nitrogen (HN) condition-specific, and HNLN common DEGs, respectively. An integrated analysis of GWAS, weighted gene co-expression network, and DEGs revealed 16 genes involved in rapeseed root development under LN stress. Previous studies have reported that the homologs of seven out of sixteen potential genes control root growth and NUE. These findings revealed the genetic basis underlying nitrogen stress and provided worthwhile SNPs/genes information for the genetic improvement of NUE in rapeseed.

Genome-Wide Association Studies of Root-Related Traits in Brassica napus L. under Low-Potassium Conditions

Roots are essential organs for a plant’s ability to absorb water and obtain mineral nutrients, hence they are critical to its development. Plants use root architectural alterations to improve their chances of absorbing nutrients when their supply is low. Nine root traits of a Brassica napus association panel were explored in hydroponic-system studies under low potassium (K) stress to unravel the genetic basis of root growth in rapeseed. The quantitative trait loci (QTL) and candidate genes for root development were discovered using a multilocus genome-wide association study (ML-GWAS). For the nine traits, a total of 453 significant associated single-nucleotide polymorphism (SNP) loci were discovered, which were then integrated into 206 QTL clusters. There were 45 pleiotropic clusters, and qRTA04-4 and qRTC04-7 were linked to TRL, TSA, and TRV at the same time, contributing 5.25–11.48% of the phenotypic variance explained (PVE) to the root traits. Additionally, 1360 annotated genes were discovered by examining genomic regions within 100 kb upstream and downstream of lead SNPs within the 45 loci. Thirty-five genes were identified as possibly regulating root-system development. As per protein–protein interaction analyses, homologs of three genes (BnaC08g29120D, BnaA07g10150D, and BnaC04g45700D) have been shown to influence root growth in earlier investigations. The QTL clusters and candidate genes identified in this work will help us better understand the genetics of root growth traits and could be employed in marker-assisted breeding for rapeseed adaptable to various conditions with low K levels.

Transformation of Plant to Resource Acquisition Under High Nitrogen Addition Will Reduce Green Roof Ecosystem Functioning

Ecosystem engineering, such as green roof, provides numerous key ecosystem functions dependent on both plants and environmental changes. In the recent years, global nitrogen (N) deposition has become a hot topic with the intensification of anthropogenic disturbance. However, the response of green roof ecosystems to N deposition is still not clear. To explore the effects of N addition on plant ecological strategy and ecosystem functioning (biomass), we conducted a 3-month N addition simulation experiment using 12 common green roof species from different growth forms on an extensive green roof in Tianjin, China. The experiment included three different N addition treatments (0, 3.5, and 10.5 gN m^-2 year^-1). We found that plants with the resource-acquisitive strategy were more suitable to survive in a high N environment, since both aboveground and belowground traits exhibited synergistic effects. Moreover, N addition indirectly decreased plant biomass, indicating that ecosystem functioning was impaired. We highlight that there is a trade-off between the survival of green roof species and keeping the ecosystem functioning well in the future N deposition. Meanwhile, these findings also provide insights into how green roof species respond to global climate change and offer important information for better managing and protecting similar ecosystem engineering in the background of high N deposition.

Recent Advances in Agronomic and Physio-Molecular Approaches for Improving Nitrogen Use Efficiency in Crop Plants

The efficiency with which plants use nutrients to create biomass and/or grain is determined by the interaction of environmental and plant intrinsic factors. The major macronutrients, especially nitrogen (N), limit plant growth and development (1.5-2% of dry biomass) and have a direct impact on global food supply, fertilizer demand, and concern with environmental health. In the present time, the global consumption of N fertilizer is nearly 120 MT (million tons), and the N efficiency ranges from 25 to 50% of applied N. The dynamic range of ideal internal N concentrations is extremely large, necessitating stringent management to ensure that its requirements are met across various categories of developmental and environmental situations. Furthermore, approximately 60 percent of arable land is mineral deficient and/or mineral toxic around the world. The use of chemical fertilizers adds to the cost of production for the farmers and also increases environmental pollution. Therefore, the present study focused on the advancement in fertilizer approaches, comprising the use of biochar, zeolite, and customized nano and bio-fertilizers which had shown to be effective in improving nitrogen use efficiency (NUE) with lower soil degradation. Consequently, adopting precision farming, crop modeling, and the use of remote sensing technologies such as chlorophyll meters, leaf color charts, etc. assist in reducing the application of N fertilizer. This study also discussed the role of crucial plant attributes such as root structure architecture in improving the uptake and transport of N efficiency. The crosstalk of N with other soil nutrients plays a crucial role in nutrient homeostasis, which is also discussed thoroughly in this analysis. At the end, this review highlights the more efficient and accurate molecular strategies and techniques such as N transporters, transgenes, and omics, which are opening up intriguing possibilities for the detailed investigation of the molecular components that contribute to nitrogen utilization efficiency, thus expanding our knowledge of plant nutrition for future global food security.

Discovery of Genomic Regions and Candidate Genes Controlling Root Development Using a Recombinant Inbred Line Population in Rapeseed (Brassica napus L.)

Marker-assisted selection enables breeders to quickly select excellent root architectural variations, which play an essential role in plant productivity. Here, ten root-related and shoot biomass traits of a new F₆ recombinant inbred line (RIL) population were investigated under hydroponics and resulted in high heritabilities from 0.61 to 0.83. A high-density linkage map of the RIL population was constructed using a Brassica napus 50k Illumina single nucleotide polymorphism (SNP) array. A total of 86 quantitative trait loci (QTLs) explaining 4.16–14.1% of the phenotypic variances were detected and integrated into eight stable QTL clusters, which were repeatedly detected in different experiments. The codominant markers were developed to be tightly linked with three major QTL clusters, qcA09-2, qcC08-2, and qcC08-3, which controlled both root-related and shoot biomass traits and had phenotypic contributions greater than 10%. Among these, qcA09-2, renamed RT.A09, was further fine-mapped to a 129-kb interval with 19 annotated genes in the B. napus reference genome. By integrating the results of real-time PCR and comparative sequencing, five genes with expression differences and/or amino acid differences were identified as important candidate genes for RT.A09. Our findings laid the foundation for revealing the molecular mechanism of root development and developed valuable markers for root genetic improvement in rapeseed.

Genotypic variation in root architectural traits under contrasting phosphorus levels in Mediterranean and Indian origin lentil genotypes

The development of phosphorus-efficient crop cultivars boosts productivity while lowering eutrophication in the environment. It is feasible to improve the efficiency of phosphorus (P) absorption in lentils by enhancing phosphorus absorption through root architectural traits. The root architectural traits of 110 diverse lentil genotypes of Indian and Mediterranean origin were assessed, and the relationships between traits were investigated. In a hydroponics experiment, the lentil lines were examined at the seedling stage under two conditions: adequate P supply and deficient P supply. The Pearson correlation coefficients between root architectural traits and genetic diversity among lentil lines were assessed. To estimate variance components, a model (fixed factor) was used. In this experiment, both phosphorus (P) and genotype were fixed variables. Our lentil lines showed significant genetic variability and considerable genetic diversity for all traits under both treatments. The TRL (total root length) and PRL (primary root length) showed strong positive associations with all other characteristics excluding root average diameter (RAD) in both P treatments. In both P treatments, the RAD revealed a negative significant association with Total Root Tips (TRT), as well as total root volume (TRV) and total root forks (TRF) in the deficit conditions of P. Total root volume (TRV), total surface area (TSA), and total root tips had higher coefficient variance values. The first two principal components represented 67.88% and 66.19% of the overall variance in the adequate and deficit P treatments respectively. The Shannon-Weaver diversity index (H') revealed that RAD, PRL, and TSA had more variability than TRT and TRF under both treatments. According to the Comprehensive Phosphorus Efficiency Measure (CPEM), the best five highly efficient genotypes are PLL 18-09, PLS 18-01, PLL 18-25, PLS 18-23, and PLL 18-07, while IG112131, P560206, IG334, L11-231, and PLS18-67 are highly inefficient genotypes. The above contrasting diverse lentil genotypes can be utilized to produce P-efficient lentil cultivars. The lentil germplasm with potentially favorable root traits can be suggested to evaluated for other abiotic stress to use them in crop improvement programme. The scientific breakthroughs in root trait phenotyping have improved the chances of establishing trait-allele relationships. As a result, genotype-to-phenotype connections can be predicted and verified with exceptional accuracy, making it easier to find and incorporate favourable nutrition-related genes/QTLs in to breeding programme.

Enriching Urea with Nitrogen Inhibitors Improves Growth, N Uptake and Seed Yield in Quinoa (Chenopodium quinoa Willd) Affecting Photochemical Efficiency and Nitrate Reductase Activity

Quinoa is a climate resilience potential crop for food security due to high nutritive value. However, crop variable response to nitrogen (N) use efficiency may lead to affect grain quality and yield. This study compared the performance of contrasting quinoa genotypes (UAF Q-7, EMS-line and JQH1) to fertilizer urea enriched with urease and nitrification inhibitors (NIs; 1% (w/w) thiourea + boric acid + sodium thiosulphate), ordinary urea and with no N as control. Application of NIs-enriched urea improved plant growth, N uptake and chlorophyll values in quinoa genotype UAF-Q7 and JHQ1, however, highest nitrate reductase (NR) activity was observed in EMS-line. Quinoa plants supplied with NIs-enriched urea also completed true and multiple leaf stage, bud formation, flowering, and maturity stages earlier than ordinary urea and control, nevertheless, all quinoa genotypes reached true and multiple leaf stage, flowering and maturity stages at same time. Among photosynthetic efficiency traits, application of NIs-enriched urea expressed highest photosynthetic active radiations (PAR), electron transport rate (ETR), current fluorescence (Ft) and reduced quantum yield (Y) in EMS line. Nitrogen treatments had no significant difference for panicle length, however, among genotypes, UAF-Q7 showed highest length of panicle followed by others. Among yield attributes, NIs-enriched urea expressed maximum 1000-seed weight and seed yield per plant in JQH-1 hybrid and EMS-line. Likely, an increase in quinoa grain protein contents was observed in JQH-1 hybrid for NIs-enriched urea. In conclusion, NIs-enriched urea with urease and nitrification inhibitors simultaneously can be used to improve the N uptake, seed yield and grain protein contents in quinoa, however, better crop response was attributed to enhanced plant growth and photosynthetic efficiency.

Whole-plant phenotypic engineering: moving beyond ratios for multi-objective optimization of nutrient use efficiency

Nutrient use efficiency (NUE) is typically measured as the ratio of yield to soil nutrient availability but ignores contributions of underlying plant traits. Relevant plant traits can be grouped as root acquisition efficiency, shoot radiation use efficiency, and plant metabolic efficiency. The intentional integration of these traits will lead to synergistic improvements of NUE. Recent progress in trait-focused research includes phenotyping root nutrient uptake rates and respiration, engineering reduced photorespiration, and identification of nutrient assimilation pathways. Traits need to be conceptualized in agricultural systems contexts to improve synchrony of plant demand and soil supply of nutrients, including consideration of crop mixtures. Use of simulation modeling and multi-objective optimization will allow accelerating NUE gains beyond selection for a single ratio.

Oilseed Rape Cultivars Show Diversity of Root Morphologies with the Potential for Better Capture of Nitrogen

The worldwide demand for vegetable oils is rising. Oilseed rape (Brassica napus) diversifies cereal dominated crop rotations but requires important nitrogen input. Yet, the root organ is offering an untapped opportunity to improve the nitrogen capture in soil. This study evaluates three culture systems in controlled environment, to observe root morphology and to identify root attributes for superior biomass production and nitrogen use. The phenotypic diversity in a panel of 55 modern winter oilseed rape cultivars was screened in response to two divergent nitrate supplies. Upon in vitro and hydroponic cultures, a large variability for root morphologies was observed. Root biomass and morphological traits positively correlated with shoot biomass or leaf area. The activities of high-affinity nitrate transport systems correlated negatively with the leaf area, while the combined high- and low-affinity systems positively with the total root length. The X-ray computed tomography permitted to visualize the root system in pipes filled with soil. The in vitro root phenotype at germination stage was indicative of lateral root deployment in soil-grown plants. This study highlights great genetic potential in oilseed rape, which could be manipulated to optimize crop root characteristics and nitrogen capture with substantial implications for agricultural production.

Genetic Dissection of Mature Root Characteristics by Genome-Wide Association Studies in Rapeseed (Brassica napus L.)

Roots are complicated quantitative characteristics that play an essential role in absorbing water and nutrients. To uncover the genetic variations for root-related traits in rapeseed, twelve mature root traits of a Brassica napus association panel were investigated in the field within three environments. All traits showed significant phenotypic variation among genotypes, with heritabilities ranging from 55.18% to 79.68%. Genome-wide association studies (GWAS) using 20,131 SNPs discovered 172 marker-trait associations, including 103 significant SNPs (-log10 (p) > 4.30) that explained 5.24-20.31% of the phenotypic variance. With the linkage disequilibrium r² > 0.2, these significant associations were binned into 40 quantitative trait loci (QTL) clusters. Among them, 14 important QTL clusters were discovered in two environments and/or with phenotypic contributions greater than 10%. By analyzing the genomic regions within 100 kb upstream and downstream of the peak SNPs within the 14 loci, 334 annotated genes were found. Among these, 32 genes were potentially associated with root development according to their expression analysis. Furthermore, the protein interaction network using the 334 annotated genes gave nine genes involved in a substantial number of interactions, including a key gene associated with root development, BnaC09g36350D. This research provides the groundwork for deciphering B. napus' genetic variations and improving its root system architecture.

Comparison of different selection traits for identification of phosphorus use efficient lines in mungbean

Phosphorus (P) is one of the major constraints for crop growth and development, owing to low availability and least mobility in many tropical soil conditions. Categorization of existing germplasm under P deficient conditions is a prerequisite for the selection and development of P efficient genotypes in the mungbean. In the present investigation, 36 diverse genotypes were categorized for phosphorus use efficiency traits using four different techniques for identification of phosphorus use efficient mungbean genotypes. The studied genotypes were categorized for P efficiency based on efficiency, responsiveness, and stress tolerance score of genotypes under normal and low P conditions. The mean values of traits, root dry mass, root to shoot ratio, and P utilization efficiency are significantly higher under low P conditions indicating the high responsiveness of traits to P deficiency. The presence of significant interaction between genotypes and P treatment indicates the evaluated genotypes were significantly affected by P treatment for studied traits. The total P uptake showed significant and positive correlations with root dry mass, shoot dry mass, total dry mass,and P concentration under both P regimes. Out of the four techniques used for the categorization of genotypes for P efficiency, three techniques revealed that the genotype PUSA 1333, followed by Pusa Vishal, PUSA 1031, and Pusa Ratna is efficient. The categorization based on stress tolerance score is the finest way to study variation and for the selection of contrasting genotypes for P efficiency. The identified P efficient genotypes would be valuable resources for genetic enhancement of P use efficiency in mungbean breeding.

PDF1.5 Enhances Adaptation to Low Nitrogen Levels and Cadmium Stress

Environmental acclimation ability plays a key role in plant growth, although the mechanism remains unclear. Here, we determined the involvement of Arabidopsis thaliana PLANT DEFENSIN 1 gene AtPDF1.5 in the adaptation to low nitrogen (LN) levels and cadmium (Cd) stress. Histochemical analysis revealed that AtPDF1.5 was mainly expressed in the nodes and carpopodium and was significantly induced in plants exposed to LN conditions and Cd stress. Subcellular localization analysis revealed that AtPDF1.5 was cell wall- and cytoplasm-localized. AtPDF1.5 overexpression significantly enhanced adaptation to LN and Cd stress and enhanced the distribution of metallic elements. The functional disruption of AtPDF1.5 reduced adaptations to LN and Cd stress and impaired metal distribution. Under LN conditions, the nitrate transporter AtNRT1.5 expression was upregulated. Nitrate transporter AtNRT1.8 expression was downregulated when AtPDF1.5 was overexpressed, resulting in enhanced transport of NO₃^- to shoots. In response to Cd treatment, AtPDF1.5 regulated the expression of metal transporter genes AtHMP07, AtNRAMP4, AtNRAMP1, and AtHIPP3, resulting in higher Cd accumulation in the shoots. We conclude that AtPDF1.5 is involved in the processing or transmission of signal substances and plays an important role in the remediation of Cd pollution and LN adaptation.

Nitrogen Uptake Efficiency, Mediated by Fine Root Growth, Early Determines Temporal and Genotypic Variations in Nitrogen Use Efficiency of Winter Oilseed Rape

Maintaining seed yield under low N inputs is a major issue for breeding, which requires thoroughly exploiting the genetic diversity of processes related to Nitrogen Use Efficiency (NUE). However, dynamic analysis of processes underlying genotypic variations in NUE in response to N availability from sowing to harvest are scarce, particularly at the whole-plant scale. This study aimed to dynamically decipher the contributions of Nitrogen Uptake Efficiency (NUpE) and Nitrogen Utilization Efficiency (NUtE) to NUE and to identify traits underlying NUpE genetic variability throughout the growth cycle of rapeseed. Three experiments were conducted under field-like conditions to evaluate seven genotypes under two N conditions. We developed NUE_DM (ratio of total plant biomass to the amount of N available) as a new proxy of NUE at harvest, valid to discriminate genotypes from the end of inflorescence emergence, and N conditions as early as the beginning of stem elongation. During autumn growth, NUpE explained up to 100% of variations in NUE_DM, validating the major role of NUpE in NUE shaping. During this period, under low N conditions, up to 53% of the plant nitrogen was absorbed and NUpE genetic variability resulted not from differences in Specific N Uptake but in fine-root growth. NUtE mainly contributed to NUE_DM genotypic variation during the reproductive phase under high-N conditions, but NUpE contribution still accounted for 50-75% after flowering. Our study highlights for the first time NUpE and fine-root growth as important processes to optimize NUE, which opens new prospects for breeding.

Genome-Wide Differential DNA Methylation and miRNA Expression Profiling Reveals Epigenetic Regulatory Mechanisms Underlying Nitrogen-Limitation-Triggered Adaptation and Use Efficiency Enhancement in Allotetraploid Rapeseed

Improving crop nitrogen (N) limitation adaptation (NLA) is a core approach to enhance N use efficiency (NUE) and reduce N fertilizer application. Rapeseed has a high demand for N nutrients for optimal plant growth and seed production, but it exhibits low NUE. Epigenetic modification, such as DNA methylation and modification from small RNAs, is key to plant adaptive responses to various stresses. However, epigenetic regulatory mechanisms underlying NLA and NUE remain elusive in allotetraploid B. napus. In this study, we identified overaccumulated carbohydrate, and improved primary and lateral roots in rapeseed plants under N limitation, which resulted in decreased plant nitrate concentrations, enhanced root-to-shoot N translocation, and increased NUE. Transcriptomics and RT-qPCR assays revealed that N limitation induced the expression of NRT1.1, NRT1.5, NRT1.7, NRT2.1/NAR2.1, and Gln1;1, and repressed the transcriptional levels of CLCa, NRT1.8, and NIA1. High-resolution whole genome bisulfite sequencing characterized 5094 differentially methylated genes involving ubiquitin-mediated proteolysis, N recycling, and phytohormone metabolism under N limitation. Hypermethylation/hypomethylation in promoter regions or gene bodies of some key N-metabolism genes might be involved in their transcriptional regulation by N limitation. Genome-wide miRNA sequencing identified 224 N limitation-responsive differentially expressed miRNAs regulating leaf development, amino acid metabolism, and plant hormone signal transduction. Furthermore, degradome sequencing and RT-qPCR assays revealed the miR827-NLA pathway regulating limited N-induced leaf senescence as well as the miR171-SCL6 and miR160-ARF17 pathways regulating root growth under N deficiency. Our study provides a comprehensive insight into the epigenetic regulatory mechanisms underlying rapeseed NLA, and it will be helpful for genetic engineering of NUE in crop species through epigenetic modification of some N metabolism-associated genes.

Genetic variation for root architectural traits in response to phosphorus deficiency in mungbean at the seedling stage

Roots enable the plant to survive in the natural environment by providing anchorage and acquisition of water and nutrients. In this study, root architectural traits of 153 mungbean genotypes were compared under optimum and low phosphorus (P) conditions. Significant variations and medium to high heritability were observed for the root traits. Total root length was positively and significantly correlated with total root surface area, total root volume, total root tips and root forks under both optimum P (r = 0.95, r = 0.85, r = 0.68 and r = 0.82 respectively) and low P (r = 0.95, r = 0.82, r = 0.71 and r = 0.81 respectively). The magnitudes of the coefficient of variations were relatively higher for root forks, total root tips and total root volume. Total root length, total root surface area and total root volume were major contributors of variation and can be utilized for screening of P efficiency at the seedling stage. Released Indian mungbean varieties were found to be superior for root traits than other genotypic groups. Based on comprehensive P efficiency measurement, IPM-288, TM 96–25, TM 96–2, M 1477, PUSA 1342 were found to be the best highly efficient genotypes, whereas M 1131, PS-16, Pusa Vishal, M 831, IC 325828 were highly inefficient. Highly efficient genotypes identified would be valuable genetic resources for P efficiency for utilizing in the mungbean breeding programme.

Identification of QTLs associated with curd architecture in cauliflower

BACKGROUND

Curd architecture is one of the most important characters determining the curd morphology of cauliflower. However, the genetic mechanism dissection of this complex trait at molecular level is lacking. Genes/QTLs responsible for the morphological differences between present-day loose-curd and compact-curd cauliflower haven't been well revealed.

RESULTS

Herein, by using a common compact-curd parent and two loose-curd parents, we developed two double haploid (DH) populations including 122 and 79 lines, respectively. For each population, we decomposed the curd architecture concept into four parameters (basal diameter, stalk length, stalk angle and curd solidity), and collected corresponding phenotypic data for each parameter across two environments. The Kosambi function and composite interval mapping algorithm were conducted to construct the linkage map and analyze the QTLs associated with curd architecture parameters. A total of 20 QTLs were detected with the minimum likelihood of odd (LOD) values ranging from 2.61 to 8.38 and the percentage of the phenotypic variance explained by each QTL (PVE) varying between 7.69 and 25.10%. Of these, two QTLs controlling stalk length (qSL.C6-1, qSL.C6-2) and two QTLs controlling curd solidity (qCS.C6-1 and qCS.C6-2) were steadily expressed in both environments. Further, qSL.C6-1, qSL.C6-2, qCS.C6-1 and qCS.C6-4 fell into the same chromosomal region of the reference genome, indicating that these loci are involved in pleiotropic effects or are tightly linked.

CONCLUSION

The current study identified a series of QTLs associated with curd architecture parameters, which might contribute essentially to the formation of present-day loose-curd cauliflower that is widely cultivated in China. These results may pave the way for intensive deciphering the molecular mechanisms of curd development and for marker-assisted selection of curd morphology in cauliflower breeding.

Root system size response of bzh semi-dwarf oilseed rape hybrids to different nitrogen levels in the field

BACKGROUND AND AIMS

In oilseed rape (Brassica napus) semi-dwarf hybrid varieties from crosses between bzh dwarf and normal-type lines are of increasing interest. They have improved nitrogen (N) uptake, N-utilization and N-use efficiency compared to normal types. This study aimed to elucidate whether these N-related effects can be explained by the bzh shoot growth-type alone or also by differences in root traits.

METHODS

Root system size was measured using root electrical capacitance (EC) in field trials with two N levels in two sets of genotypes segregating for the bzh-locus: (1) 108 doubled haploid (DH) test hybrids in two seasons, 2010-2012, and (2) 16 near-isogenic hybrids in the 2016-17 season. Quantitative trait loci (QTL) for root EC were estimated in DH test hybrids. Seedling root architecture parameters were monitored in vitro.

KEY RESULTS

In vitro root growth showed a higher root: shoot ratio in bzh semi-dwarf hybrids. Root EC in field trials was higher at high N supply than at zero N fertilization. In most trials semi-dwarf hybrids had higher EC than normal-type hybrids, but they reduced root EC in response to N limitation more than normal types. Root EC was more heritable at the end of flowering (h2 = 0.73) than at the beginning of flowering (h2 = 0.36) in near-isogenic hybrids and had a lower heritability in trials of DH test hybrids (h2 = 0.27). A QTL for root EC in the genomic region of the bzh-locus on linkage group A06 was significant at zero N fertilization.

CONCLUSIONS

Root EC proved to be a meaningful method in oilseed rape breeding programmes targeting root system size. The greater reduction of semi-dwarf root EC compared to the normal type under low N supply with simultaneous increase in N efficiency implies that in roots it is not a question of 'the more the merrier' and that the bzh root system reacts highly economically when N is scarce.

Expression of a cucumber alanine aminotransferase2 gene improves nitrogen use efficiency in transgenic rice

Background

Rice can absorb less than 40% of applied nitrogen fertilizer, whereas the unabsorbed nitrogen fertilizer may cause environmental problems, such as algal blooms in freshwater and increased production of nitrous oxide, a greenhouse gas which is 300 times more potent than carbon dioxide. Development of nitrogen use efficient (NUE) rice is essential for more environmentally friendly rice production. Recently, NUE rice has been developed by root-specific expression of alanine aminotransferase (AlaAT) gene from barley, a monocot plant. Therefore, we tested the efficacy of AlaAT gene from cucumber in transgenic rice, aiming to provide evidence for the conservation of AlaAT gene function in monocot and dicot.

Results

AlaAT gene from cucumber (CsAlaAT2) has been successfully cloned and constructed on pCAMBIA1300 plant expression vectors under the control of tissue-specific promoter OsAnt1. Agrobacterium tumefaciens-mediated transformation of Indonesian rice cv. Fatmawati using this construct produced 14 transgenic events. Pre-screening of T1 seedlings grown in the agar medium containing low nitrogen concentration identified selected events that were superior in the root dry weight. Southern hybridization confirmed the integration of T-DNA in the selected event genomes, each of them carried 1, 2, or 3 T-DNA insertions. Efficacy assay of three lead events in the greenhouse showed that in general transgenic events had increased biomass, tiller number, nitrogen content, and grain yield compared to WT. One event, i.e., FAM13, showed an increase in yield as much as 27.9% and higher plant biomass as much as 27.4% compared to WT under the low nitrogen condition. The lead events also showed higher absorption NUE, agronomical NUE, and grain NUE as compared to WT under the low nitrogen condition.

Conclusions

The results of this study showed that root-specific expression of cucumber alanine aminotransferase2 gene improved nitrogen use efficiency in transgenic rice, which indicate the conservation of function of this gene in monocot and dicot.

Temporal genetic patterns of root growth in Brassica napus L. revealed by a low-cost, high-efficiency hydroponic system

Application of a low-cost and high-efficiency hydroponic system in a rapeseed population verified two types of genetic factors ("persistent" and "stage-specific") that control root development. The root system is a vital plant component for nutrient and water acquisition and is targeted to enhance plant productivity. Genetic dissection of the root system generally focuses on a single stage, but roots grow continuously during plant development. To reveal the temporal genetic patterns of root development, we measured nine root-related traits in a rapeseed recombinant inbred line population at six continuous stages during vegetative growth, using a modified hydroponic system with low-cost and high-efficiency features that could synchronize plant growth under controlled conditions. Phenotypic correlation and growth dynamic analysis suggested the existence of two types of genetic factors ("persistent" and "stage-specific") that control root development. Dynamic (unconditional and conditional) quantitative trait loci (QTL) mapping detected 28 stage-specific and 23 persistent QTLs related to root growth. Among them, 13 early stage-specific, 19 persistent and 8 later stage-specific QTLs were detected at 7 DAS (days after sowing), 16 DAS and 5 EL (expanding leaf stage), respectively, providing efficient and adaptable stages for QTL identification. The effective prediction of biomass accumulation using root morphological traits (up to 96.6% or 92.64% at a specific stage or the final stage, respectively) verified that root growth allocation with maximum root uptake area facilitated biomass accumulation. Furthermore, marker-assistant selection, which combined the "persistent" and "stage-specific" QTLs, proved their effectiveness for root improvement with an excellent uptake area. Our results highlight the potential of high-throughput and precise phenotyping to assess the dynamic genetics of root growth and provide new insights into ideotype root system-based biomass breeding.

Low Nitrogen Enhances Nitrogen Use Efficiency by Triggering NO3- Uptake and Its Long-Distance Translocation

Nitrogen is essential for plant growth and crop productivity; however, nitrogen use efficiency (NUE) decreases with increasing N supply, resulting in a waste of resources. Molecular mechanisms underlying low-nitrogen (LN)-mediated enhancement of NUE are not clear. We used high-NUE Brassica napus genotype H (Xiangyou 15), low-NUE B. napus genotype L (814), and Arabidopsis mutant aux1 to elucidate the mechanism underlying the changes in NUE under different rates of N fertilizer application. NUE of B. napus increased under LN, which enhanced N uptake ability by regulating root system architecture and plasma membrane H⁺-ATPase activity; AUX1 was involved in this process. Additionally, BnNRT1.5 was upregulated and BnNRT1.8 was downregulated under LN, whereby more N was transferred to the shoot through enhanced N transport. Observed changes in photosynthesis under LN were associated with N assimilation efficiency. Our study provides new insights into the mechanisms of plant adaptation to the environment.

Genome-wide association study and protein network analysis for understanding candidate genes involved in root development at the rapeseed seedling stage

Root system is essential for plants to absorb water and nutrients. The root related traits are complex quantitative traits and regulated by genetic control. Here, we used two association mapping panels to perform a genome-wide association study (GWAS) on seven root related traits in Brassica napus at the seedling stage and obtained 27 SNP loci significantly associated with the phenotypes. We further conducted a genome-wide LD block analysis of the candidate peak regions and obtained 295 candidate genes with high association peaks across seven phenotypes in LD region. In addition, a protein interaction network using the candidate genes identified here was constructed, and 113 genes were associated. Seven genes, BnaA03g47330D, BnaC09g16810D, BnaA06g22840D, BnaA03g28390D, BnaA08g19920D, BnaA03g28930D and BnaA03g11440D were in a large cluster, and may play important roles in interacting with other related genes. Our data may provide resources for molecular breeding and functional analysis of root growth and development in rapeseed.

Genome-scale characterization of the vacuole nitrate transporter Chloride Channel (CLC) genes and their transcriptional responses to diverse nutrient stresses in allotetraploid rapeseed

The Chloride Channel (CLC) gene family is reported to be involved in vacuolar nitrate (NO₃^-) transport. Nitrate distribution to the cytoplasm is beneficial for enhancing NO₃^- assimilation and plays an important role in the regulation of nitrogen (N) use efficiency (NUE). In this study, genomic information, high-throughput transcriptional profiles, and gene co-expression analysis were integrated to identify the CLCs (BnaCLCs) in Brassica napus. The decreased NO₃^- concentration in the clca-2 mutant up-regulated the activities of nitrate reductase and glutamine synthetase, contributing to increase N assimilation and higher NUE in Arabidopsis thaliana. The genome-wide identification of 22BnaCLC genes experienced strong purifying selection. Segmental duplication was the major driving force in the expansion of the BnaCLC gene family. The most abundant cis-acting regulatory elements in the gene promoters, including DNA-binding One Zinc Finger, W-box, MYB, and GATA-box, might be involved in the transcriptional regulation of BnaCLCs expression. High-throughput transcriptional profiles and quantitative real-time PCR results showed that BnaCLCs responded differentially to distinct NO₃^- regimes. Transcriptomics-assisted gene co-expression network analysis identified BnaA7.CLCa-3 as the core member of the BnaCLC family, and this gene might play a central role in vacuolar NO₃^- transport in crops. The BnaCLC members also showed distinct expression patterns under phosphate depletion and cadmium toxicity. Taken together, our results provide comprehensive insights into the vacuolar BnaCLCs and establish baseline information for future studies on BnaCLCs-mediated vacuolar NO₃^- storage and its effect on NUE.

Genomics-Assisted Identification and Characterization of the Genetic Variants Underlying Differential Nitrogen Use Efficiencies in Allotetraploid Rapeseed Genotypes

Nitrogen (N) is a non-mineral macronutrient essential for plant growth and development. Oilseed rape (A_nA_nC_nC_n, 2n = 4x = 38) has a high requirement for N nutrients whereas showing the lowest N use efficiency (NUE) among crops. The mechanisms underlying NUE regulation in Brassica napus remain unclear because of genome complexity. In this study, we performed high-depth and -coverage whole-genome re-sequencing (WGS) of an N-efficient (higher NUE) genotype “XY15” and an N-inefficient (lower NUE) genotype “814” of rapeseed. More than 687 million 150-bp paired-end reads were generated, which provided about 93% coverage and 50× depth of the rapeseed genome. Applying stringent parameters, we identified a total of 1,449,157 single-nucleotide polymorphisms (SNPs), 335,228 InDels, 175,602 structure variations (SVs) and 86,280 copy number variations (CNVs) between the N-efficient and -inefficient genotypes. The largest proportion of various DNA polymorphisms occurred in the inter-genic regions. Unlike CNVs, the SNP/InDel and SV polymorphisms showed variation bias of the A_n and C_n subgenomes, respectively. Gene ontology analysis showed the genetic variants were mapped onto the genes involving N compound transport and ATPase complex metabolism, but not including N assimilation-related genes. On basis of identification of N-starvation responsive genes through high-throughput expression profiling, we also mapped these variants onto some key NUE-regulating genes, and validated their significantly differential expression between the N-efficient and -inefficient genotypes through qRT-PCR assays. Our data provide genome-wide high resolution DNA variants underlying NUE divergence in allotetraploid rapeseed genotypes, which would expedite the effective identification and functional validation of key NUE-regulating genes through genomics-assisted improvement of crop nutrient efficiency.