Rice OsLHT1 Functions in Leaf-to-Panicle Nitrogen Allocation for Grain Yield and Quality

Empowering rice breeding with NextGen genomics tools for rapid enhancement nitrogen use efficiency

As rice has no physiological capacity of fixing nitrogen in the soil, its production had always been reliant on the external application of nitrogen (N) to ensure enhanced productivity. In the light of improving nitrogen use efficiency (NUE) in rice, several advanced agronomic strategies have been proposed. However, the soared increase of the prices of N fertilizers and subsequent environmental downfalls caused by the excessive use of N fertilizers, reinforces the prerequisite adaptation of other sustainable, affordable, and globally acceptable strategies. An appropriate alternative approach would be to develop rice cultivars with better NUE. Conventional breeding techniques, however, have had only sporadic success in improving NUE, and hence, this paper proposes a new schema that employs the wholesome benefits of the recent advancements in omics technologies. The suggested approach promotes multidisciplinary research, since such cooperation enables the synthesis of many viewpoints, approaches, and data that result in a comprehensive understanding of NUE in rice. Such collaboration also encourages innovation that leads to developing rice varieties that use nitrogen more effectively, facilitate smart technology transfer, and promotes the adoption of NUE practices by farmers and stakeholders to minimize ecological impact and contribute to a sustainable agricultural future.

Amino acid permease OsAAP12 negatively regulates rice tillers and grain yield by transporting specific amino acids to affect nitrogen and cytokinin pathways

Amino acids are necessary nutrients for the growth of Oryza sativa (rice), which can be mediated by amino acid transporter; however, our understanding of these transporters is still limited. This study found that the expression levels of amino acid permease gene OsAAP12 differed between indica and japonica rice. Altered expression of OsAAP12 negatively regulated tillering and yield in transgenic rice lines. Subcellular localization revealed that OsAAP12 was primarily localized to the plasma membrane. Moreover, it was indicated that OsAAP12 transported polar neutral amino acids asparagine (Asn), threonine (Thr), and serine (Ser) through experiments involving yeast heterologous complementation, fluorescence amino acid uptake, and amino acid content determination. Additionally, exogenous application of amino acids Asn, Thr, and Ser suppressed axillary buds outgrowth in OsAAP12 overexpression lines compared with wild-type ZH11. Conversely, the opposite trend was observed in CRISPR mutant lines. RNA-seq analysis showed that the expression patterns of genes involved in the nitrogen and cytokinin pathways were generally altered in OsAAP12 modified lines. Hormone assays indicated that OsAAP12 mutant lines accumulated cytokinins in the basal part of rice, whereas overexpression lines had the opposite effect. In summary, CRISPR mutant of OsAAP12 boosted rice tillering and grain yield by coordinating the content of amino acids and cytokinins, which has potential application value in high-yield rice breeding.

Role of reactive nitrogen species in changing climate and future concerns of environmental sustainability

The nitrogen (N) cycle is an intricate biogeochemical process that encompasses the conversion of several chemical forms of N. Given its role in food production, the need for N for life on Earth is obvious. However, the release of reactive nitrogen (Nr) species throughout different biogeochemical processes contributes to atmospheric pollution. Several human activities generate many species, including ammonia, nitrous oxide (N2O), nitric oxide, and nitrate. The primary reasons for this change are the use of nitrogen-based fertilizers, industrial activities, and the burning of fossil fuels. N2O poses a significant threat to environmental sustainability on our planet, with its global warming potential approximately 298 times greater than that of CO2. It has direct or indirect impacts on the environment, agroecosystem, and human life on earth. Solar, hydroelectric, geothermal, and wind turbines must be used to reduce Nr emissions. In addition, enterprises should install catalytic converters to minimize nitrogen gas emissions. To reduce Nr emissions, strategic interventions like fertilizer balancing are needed. This work will serve as a comprehensive guide for researchers, academics, and policymakers. Additionally, it will also assist social workers in emphasizing the Nr issue to the public in order to raise awareness within worldwide society.

OsNLP3 enhances grain weight and reduces grain chalkiness in rice

Grain weight, a key determinant of yield in rice (Oryza sativa L.), is governed primarily by genetic factors, whereas grain chalkiness, a detriment to grain quality, is intertwined with environmental factors such as mineral nutrients. Nitrogen (N) is recognized for its effect on grain chalkiness, but the underlying molecular mechanisms remain to be clarified. This study revealed the pivotal role of rice NODULE INCEPTION-LIKE PROTEIN 3 (OsNLP3) in simultaneously regulating grain weight and grain chalkiness. Our investigation showed that loss of OsNLP3 leads to a reduction in both grain weight and dimension, in contrast to the enhancement observed with OsNLP3 overexpression. OsNLP3 directly suppresses the expression of OsCEP6.1 and OsNF-YA8, which were identified as negative regulators associated with grain weight. Consequently, two novel regulatory modules, OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8, were identified as key players in grain weight regulation. Notably, the OsNLP3-OsNF-YA8 module not only increases grain weight but also mitigates grain chalkiness in response to N. This research clarifies the molecular mechanisms that orchestrate grain weight through the OsNLP3-OsCEP6.1 and OsNLP3-OsNF-YA8 modules, highlighting the pivotal role of the OsNLP3-OsNF-YA8 module in alleviating grain chalkiness. These findings reveal potential targets for simultaneous enhancement of rice yield and quality.

Blocking of amino acid transporter OsAAP7 promoted tillering and yield by determining basic and neutral amino acids accumulation in rice

BACKGROUND

Amino acids are not only the main form of N in rice, but also are vital for its growth and development. These processes are facilitated by amino acid transporters within the plant. Despite their significance, only a few AAP amino acid transporters have been reported.

RESULTS

In this study, we observed that there were differences in the expression of amino acid transporter OsAAP7 among 521 wild cultivated rice varieties, and it directly negatively correlated with tillering and grain yield per plant. We revealed that OsAAP7 protein was localized to the endoplasmic reticulum and had absorption and transport affinity for amino acids such as phenylalanine (Phe), lysine (Lys), leucine (Leu), and arginine (Arg) using subcellular localization, yeast substrate testing, fluorescent amino acid uptake, and amino acid content determination. Further hydroponic studies showed that exogenous application of amino acids Phe, Lys and Arg inhibited the growth of axillary buds in the overexpression lines, and promoted the elongation of axillary buds in the mutant lines. Finally, RNA-seq analysis showed that the expression patterns of genes related to nitrogen, auxin and cytokinin pathways were changed in axillary buds of OsAAP7 transgenic plants.

CONCLUSIONS

This study revealed the gene function of OsAAP7, and found that blocking of amino acid transporter OsAAP7 with CRISPR/Cas9 technology promoted tillering and yield by determining basic and neutral amino acids accumulation in rice.

Genomic variation in weedy and cultivated broomcorn millet accessions uncovers the genetic architecture of agronomic traits

Large-scale genomic variations are fundamental resources for crop genetics and breeding. Here we sequenced 1,904 genomes of broomcorn millet to an average of 40× sequencing depth and constructed a comprehensive variation map of weedy and cultivated accessions. Being one of the oldest cultivated crops, broomcorn millet has extremely low nucleotide diversity and remarkably rapid decay of linkage disequilibrium. Genome-wide association studies identified 186 loci for 12 agronomic traits. Many causative candidate genes, such as PmGW8 for grain size and PmLG1 for panicle shape, showed strong selection signatures during domestication. Weedy accessions contained many beneficial variations for the grain traits that are largely lost in cultivated accessions. Weedy and cultivated broomcorn millet have adopted different loci controlling flowering time for regional adaptation in parallel. Our study uncovers the unique population genomic features of broomcorn millet and provides an agronomically important resource for cereal crops.

Polylactic acid microplastics have stronger positive effects on the qualitative traits of rice (Oryza sativa L.) than polyethylene microplastics: Evidence from a simulated field experiment

Soil pollution by microplastics (MPs) from different types of agricultural films has received substantial attention due to its potential effects on crop quality. To date, the effects of different types of MPs on rice grain quality and their underlying molecular mechanisms have not been clarified. In this study, we examined the effects of polyethylene MPs (PE-MPs) and biodegradable polylactic acid MPs (PLA-MPs) on rice grain quality at the environmental level (0.5 %) and evaluated the molecular mechanism through transcriptome analysis. PE- and PLA-MPs increased the number of rice grains per plant by 19.83 % and 24.66 %, respectively, and decreased the rice empty-shell rate by 55.89 % and 26.53 %, respectively. However, PLA-MPs increased the 1000-seed weight by 11.37 %, whereas PE-MPs had no obvious impact in this respect. Furthermore, MP exposure, especially that of PE-MPs, affected the content of mineral elements, fatty acids, and amino acids of rice grains by disturbing the expression of genes related to these functions and metabolism. Our findings provide insights into the response of rice grains to the stress caused by different MPs.

Mapping of Candidate Genes for Nitrogen Uptake and Utilization in Japonica Rice at Seedling Stage

Nitrogen (N) is one of the essential nutrients for the growth and development of crops. The adequate application of N not only increases the yield of crops but also improves the quality of agricultural products, but the excessive application of N can cause many adverse effects on ecology and the environment. In this study, genome-wide association analysis (GWAS) was performed under low- and high-N conditions based on 788,396 SNPs and phenotypic traits relevant to N uptake and utilization (N content and N accumulation). A total of 75 QTLs were obtained using GWAS, which contained 811 genes. Of 811 genes, 281 genes showed different haplotypes, and 40 genes had significant phenotypic differences among different haplotypes. Of these 40 genes, 5 differentially expressed genes (Os01g0159250, Os02g0618200, Os02g0618400, Os02g0630300, and Os06g0619000) were finally identified as the more valuable candidate genes based on the transcriptome data sequenced from Longjing31 (low-N-tolerant variety) and Songjing 10 (low-N-sensitive variety) under low- and high-N treatments. These new findings enrich the genetic resources for N uptake and utilization in rice, as well as lay a theoretical foundation for improving the efficiency of N uptake and utilization in rice.

Uncovering the Genomic Regions Associated with Yield Maintenance in Rice Under Drought Stress Using an Integrated Meta-Analysis Approach

The complex trait of yield is controlled by several quantitative trait loci (QTLs). Given the global water deficit issue, the development of rice varieties suitable for non-flooded cultivation holds significant importance in breeding programs. The powerful approach of Meta-QTL (MQTL) analysis can be used for the genetic dissection of complicated quantitative traits. In the current study, a comprehensive MQTL analysis was conducted to identify consistent QTL regions associated with drought tolerance and yield-related traits under water deficit conditions in rice. In total, 1087 QTLs from 134 rice populations, published between 2000 to 2021, were utilized in the analysis. Distinct MQTL analysis of the relevant traits resulted in the identification of 213 stable MQTLs. The confidence interval (CI) for the detected MQTLs was between 0.12 and 19.7 cM. The average CI of the identified MQTLs (4.68 cM) was 2.74 times narrower compared to the average CI of the initial QTLs. Interestingly, 63 MQTLs coincided with SNP peak positions detected by genome-wide association studies for yield and drought tolerance-associated traits under water deficit conditions in rice. Considering the genes located both in the QTL-overview peaks and the SNP peak positions, 19 novel candidate genes were introduced, which are associated with drought response index, plant height, panicle number, biomass, and grain yield. Moreover, an inclusive MQTL analysis was performed on all the traits to obtain "Breeding MQTLs". This analysis resulted in the identification of 96 MQTLs with a CI ranging from 0.01 to 9.0 cM. The mean CI of the obtained MQTLs (2.33 cM) was 4.66 times less than the mean CI of the original QTLs. Thirteen MQTLs fulfilling the criteria of having more than 10 initial QTLs, CI < 1 cM, and an average phenotypic variance explained greater than 10%, were designated as "Breeding MQTLs". These findings hold promise for assisting breeders in enhancing rice yield under drought stress conditions.

Integrated metabolomic and transcriptomic analyses reveal the molecular mechanism of amino acid transport between source and sink during tea shoot development

KEY MESSAGE

The weighted gene co-expression network analysis and antisense oligonucleotide-mediated transient gene silencing revealed that CsAAP6 plays an important role in amino acid transport during tea shoot development. Nitrogen transport from source to sink is crucial for tea shoot growth and quality formation. Amino acid represents the major transport form of reduced nitrogen in the phloem between source and sink, but the molecular mechanism of amino acid transport from source leaves to new shoots is not yet clear. Therefore, the composition of metabolites in phloem exudates collected by the EDTA-facilitated method was analyzed through widely targeted metabolomics. A total of 326 metabolites were identified in the phloem exudates with the richest variety of amino acids and their derivatives (93), accounting for approximately 39.13% of the total metabolites. Moreover, through targeted metabolomics, it was found that the content of glutamine, glutamic acid, and theanine was the most abundant, and gradually increased with the development of new shoots. Meanwhile, transcriptome analysis suggested that the expression of amino acid transport genes changed significantly. The WGCNA analysis identified that the expression levels of CsAVT1, CsLHTL8, and CsAAP6 genes located in the MEterquoise module were positively correlated with the content of amino acids such as glutamine, glutamic acid, and theanine in phloem exudates. Reducing the CsAAP6 in mature leaves resulted in a significant decrease in the content of glutamic acid, aspartic acid, alanine, leucine, asparagine, glutamine, and arginine in the phloem exudates, indicating that CsAAP6 played an important role in the source to sink transport of amino acids in the phloem. The research results will provide the theoretical basis and genetic resources for the improvement of nitrogen use efficiency and tea quality.

Comparative physiological and transcriptome analysis of leaf nitrogen fluxes in stay-green maize during the vegetative stage

In maize, nitrogen (N) stored in leaves is an important internal source for supporting subsequent growth and development. However, the regulation of N fluxes and photosynthesis and the molecular and genotypic regulations that modify them are less clear in source leaves during the vegetative stage. This knowledge is crucial for improving N use efficiency (NUE). By using 15N labeling and transcriptome methods, an analysis of the physiological and molecular basis of leaf N import and export processes and photosynthetic N use efficiency (PNUE) was conducted in two maize hybrids (XY335 and XY696) with different stay-green characteristics during the vegetative stage. Leaf N import and export in XY696 were 45% and 33% greater than those in XY335. However, the PNUE in XY335 was 17% greater than that in XY696 due to the higher net photosynthetic rate (A) and lower SLN. Correspondingly, the chlorophyll content and photosynthesis-related enzyme (PEPc, PEPck, PPDK) activities increased by 18∼30% in XY335. Transcriptome analysis indicated that the expression levels of several N and carbon metabolism-related genes encoding Rubisco, PEPc, Nir, GS and AS were significantly increased or decreased in XY696 in parallel with enzyme activities. Moreover, there was a large difference in the expression abundance of genes encoding nitrate/nitrite transporters and transmembrane proteins. Our results suggest that two hybrids modulate leaf N fluxes and photosynthesis differently by altering gene expression and enzyme activities. Our study contributes to understanding leaf N fluxes and PNUE regulation and serves as a crucial reference for NUE improvement in maize breeding research.

Knocking Out OsAAP11 to Improve Rice Grain Quality Using CRISPR/Cas9 System

The demand for rice grain quality, particularly in terms of eating and cooking quality, is increasingly concerning at present. However, the limited availability of rice-quality-related gene resources and time-consuming and inefficient traditional breeding methods have severely hindered the pace of rice grain quality improvement. Exploring novel methods for improving rice grain quality and creating new germplasms is an urgent problem that needs to be addressed. In this study, an amino-acid-transporter-encoding gene OsAAP11 (Os11g0195600) mainly expressed in endosperm was selected as the target for gene editing using the CRISPR/Cas9 system in three japonica genetic backgrounds (Wuyungeng30, Nangeng9108, and Yanggeng158, hereafter referred to as WYG30, NG9108, and YG158). We successfully obtained homozygous osaap11 mutants without transgenic insertion. Subsequently, we conducted comprehensive investigations on the agronomic traits, rice grain quality traits, and transcriptomic analysis of these mutants. The results demonstrate that loss of OsAAP11 function led to a reduced amino acid content and total protein content in grains without affecting the agronomic traits of the plants; meanwhile, it significantly increased the peak viscosity, holding viscosity, and final viscosity values during the cooking process, thereby enhancing the eating and cooking quality. This study not only provides valuable genetic resources and fundamental materials for improving rice grain quality but also provides novel technical support for the rapid enhancement of rice grain quality.

Knockout of amino acid transporter gene OsLHT1 accelerates leaf senescence and enhances resistance to rice blast fungus

Plant amino acid transporters (AATs) regulate not only long-distance transport and reallocation of nitrogen (N) from source to sink organs, but also amount of amino acids in leaves hijacked by invaded pathogens. However, the function of AATs in plant defense responses to pathogen infection remains unknown. In this study, we found that rice amino acid transporter gene OsLHT1 was expressed in leaves and up-regulated by maturing, N starvation and inoculation of blast fungus Magnaporthe oryzae. Knockout of OsLHT1 resulted in development stage- and N supply-dependent premature senescence of leaves at vegetative growth stage. In comparison to wild type, Oslht1 mutant lines showed sustained rusty red spots on fully mature leaf blades irrespective of N supply levels. Notably, no relationship between the severity of leaf rusty red spots and concentration of total N or amino acids was found in Oslht1 mutants at different developmental stages. Disruption of OsLHT1 altered transport and metabolism of amino acids and biosynthesis of flavones and flavonoids, enhanced expression of jasmonic acid- and salicylic acid-related defense genes and production of jasmonic acid and salicylic acid, accumulation of reactive oxygen species. OsLHT1 inactivation dramatically prevented the leaf invasion of M. oryzae, the hemi-biotrophic ascomycete fungus. Overall, these results establish a module connecting the activity of amino acid transporter with leaf metabolism and defense to rice blast fungus.

Genome-Wide Urea Response in Rice Genotypes Contrasting for Nitrogen Use Efficiency

Rice is an ideal crop for improvement of nitrogen use efficiency (NUE), especially with urea, its predominant fertilizer. There is a paucity of studies on rice genotypes contrasting for NUE. We compared low urea-responsive transcriptomes of contrasting rice genotypes, namely Nidhi (low NUE) and Panvel1 (high NUE). Transcriptomes of whole plants grown with media containing normal (15 mM) and low urea (1.5 mM) revealed 1497 and 2819 differentially expressed genes (DEGs) in Nidhi and Panvel1, respectively, of which 271 were common. Though 1226 DEGs were genotype-specific in Nidhi and 2548 in Panvel1, there was far higher commonality in underlying processes. High NUE is associated with the urea-responsive regulation of other nutrient transporters, miRNAs, transcription factors (TFs) and better photosynthesis, water use efficiency and post-translational modifications. Many of their genes co-localized to NUE-QTLs on chromosomes 1, 3 and 9. A field evaluation under different doses of urea revealed better agronomic performance including grain yield, transport/uptake efficiencies and NUE of Panvel1. Comparison of our urea-based transcriptomes with our previous nitrate-based transcriptomes revealed many common processes despite large differences in their expression profiles. Our model proposes that differential involvement of transporters and TFs, among others, contributes to better urea uptake, translocation, utilization, flower development and yield for high NUE.

Molecular bases of rice grain size and quality for optimized productivity

The accomplishment of further optimization of crop productivity in grain yield and quality is a great challenge. Grain size is one of the crucial determinants of rice yield and quality; all of these traits are typical quantitative traits controlled by multiple genes. Research advances have revealed several molecular and developmental pathways that govern these traits of agronomical importance. This review provides a comprehensive summary of these pathways, including those mediated by G-protein, the ubiquitin-proteasome system, mitogen-activated protein kinase, phytohormone, transcriptional regulators, and storage product biosynthesis and accumulation. We also generalize the excellent precedents for rice variety improvement of grain size and quality, which utilize newly developed gene editing and conventional gene pyramiding capabilities. In addition, we discuss the rational and accurate breeding strategies, with the aim of better applying molecular design to breed high-yield and superior-quality varieties.

The LHT Gene Family in Rice: Molecular Characterization, Transport Functions and Expression Analysis

Amino acid transporters (AATs) are integral membrane proteins and play important roles in plant growth and development as well as environmental responses. In contrast to the amino acid permease (AAP) subfamily, functional studies of the lysine and histidine transporter (LHT) subfamily have not been made in rice. In the current study, six LHT genes were found in the rice genome. To further investigate the functions of these genes, analyses were performed regarding gene and protein structures, chromosomal locations, evolutionary relationships, cis-acting elements of promoters, gene expression, and yeast complementation. We found that the six OsLHT genes are distributed on 4 out of the 12 chromosomes and that the six OsLHT genes were grouped into two clusters based on the phylogenetic analysis. Protein structure analyses showed that each OsLHT protein has 11 helical transmembrane domains. Yeast complementation assays showed that these OsLHT genes have conserved transport substrates within each cluster. The four members from cluster 1 showed broad amino acid selectivity, while OsLHT5 and OsLHT6 may transport other substrates besides amino acids. Additionally, quantitative real-time PCR analysis of the six OsLHT genes revealed that they have different expression patterns at different developmental stages and in different tissues. It also revealed that some OsLHT genes were responsive to PEG, NaCl and cold treatments, indicating their critical roles in abiotic stress response. Our results will be useful for further characterizing the crucial biological functions of rice LHT genes.

Natural variations of OsAUX5, a target gene of OsWRKY78, control the neutral essential amino acid content in rice grains

Grain essential amino acid (EAA) levels contribute to rice nutritional quality. However, the molecular mechanisms underlying EAA accumulation and natural variation in rice grains remain unclear. Here we report the identification of a previously unrecognized auxin influx carrier subfamily gene, OsAUX5, which encodes an amino acid transporter that functions in uptake of multiple amino acids. We identified an elite haplotype of Pro::OsAUX5^Hap2 that enhances grain EAA accumulation without an apparent negative effect on agronomic traits. Natural variations of OsAUX5 occur in the cis elements of its promoter, which are differentially activated because of the different binding affinity between OsWRKY78 and the W-box, contributing to grain EAA variation among rice varieties. The two distinct haplotypes were shown to have originated from different Oryza rufipogon progenitors, which contributed to the divergence between japonica and indica. Introduction of the indica-type Pro::OsAUX5^Hap2 genotype into japonica could significantly increase EAA levels, indicating that indica-type Pro::OsAUX5^Hap2 can be utilized to increase grain EAAs of japonica varieties. Collectively, our study uncovers an WRKY78-OsAUX5-based regulatory mechanism controlling grain EAA accumulation and provides a potential target for breeding EAA-rich rice.

Breeding for Higher Yields of Wheat and Rice through Modifying Nitrogen Metabolism

Wheat and rice produce nutritious grains that provide 32% of the protein in the human diet globally. Here, we examine how genetic modifications to improve assimilation of the inorganic nitrogen forms ammonium and nitrate into protein influence grain yield of these crops. Successful breeding for modified nitrogen metabolism has focused on genes that coordinate nitrogen and carbon metabolism, including those that regulate tillering, heading date, and ammonium assimilation. Gaps in our current understanding include (1) species differences among candidate genes in nitrogen metabolism pathways, (2) the extent to which relative abundance of these nitrogen forms across natural soil environments shape crop responses, and (3) natural variation and genetic architecture of nitrogen-mediated yield improvement. Despite extensive research on the genetics of nitrogen metabolism since the rise of synthetic fertilizers, only a few projects targeting nitrogen pathways have resulted in development of cultivars with higher yields. To continue improving grain yield and quality, breeding strategies need to focus concurrently on both carbon and nitrogen assimilation and consider manipulating genes with smaller effects or that underlie regulatory networks as well as genes directly associated with nitrogen metabolism.

Transcriptome and Metabolome Analyses Reveals the Pathway and Metabolites of Grain Quality Under Phytochrome B in Rice (Oryza sativa L.)

BACKGROUND

Grain size and chalkiness is a critical agronomic trait affecting rice yield and quality. The application of transcriptomics to rice has widened the understanding of complex molecular responsive mechanisms, differential gene expression, and regulatory pathways under varying conditions. Similarly, metabolomics has also contributed drastically for rice trait improvements. As master regulators of plant growth and development, phys influence seed germination, vegetative growth, photoperiodic flowering, shade avoidance responses. OsPHYB can regulate a variety of plant growth and development processes, but little is known about the roles of rice gene OsPHYB in modulating grain development.

RESULTS

In this study, rice phytochrome B (OsPHYB) was edited using CRISPR/Cas9 technology. We found that OsPHYB knockout increased rice grain size and chalkiness, and increased the contents of amylose, free fatty acids and soluble sugar, while the gel consistency and contents of proteins were reduced in mutant grains. Furthermore, OsPHYB is involved in the regulation of grain size and chalk formation by controlling cell division and complex starch grain morphology. Transcriptomic analysis revealed that loss of OsPHYB function affects multiple metabolic pathways, especially enhancement of glycolysis, fatty acid, oxidative phosphorylation, and antioxidant pathways, as well as differential expression of starch and phytohormone pathways. An analysis of grain metabolites showed an increase in the free fatty acids and lysophosphatidylcholine, whereas the amounts of sugars, alcohols, amino acids and derivatives, organic acids, phenolic acids, alkaloids, nucleotides and derivatives, and flavonoids decreased, which were significantly associated with grain size and chalk formation.

CONCLUSIONS

Our study reveals that, OsPHYB plays an important regulatory role in the growth and development of rice grains, especially grain size and chalkiness. Furthermore, OsPHYB regulates grain size and chalkiness formation by affecting gene metabolism interaction network. Thus, this study not only revealed that OsPHYB plays a vital role in regulating grain size and chalkiness of rice but reveal new functions and highlighted the importance and value of OsPHYB in rice grain development and provide a new strategy for yield and quality improvement in rice breeding.

Genome-wide association studies provide genetic insights into natural variation of seed-size-related traits in mungbean

Although mungbean (Vigna radiata (L.) R. Wilczek) is an important legume crop, its seed yield is relatively low. To address this issue, here 196 accessions with 3,607,508 SNP markers were used to identify quantitative trait nucleotides (QTNs), QTN-by-environment interactions (QEIs), and their candidate genes for seed length (SL), seed width, and 100-seed weight (HSW) in two environments. As a result, 98 QTNs and 20 QEIs were identified using 3VmrMLM, while 95, >10,000, and 15 QTNs were identified using EMMAX, GEMMA, and CMLM, respectively. Among 809 genes around these QTNs, 12 were homologous to known seed-development genes in rice and Arabidopsis thaliana, in which 10, 2, 1, and 0 genes were found, respectively, by the above four methods to be associated with the three traits, such as VrEmp24/25 for SL and VrKIX8 for HSW. Eight of the 12 genes were significantly differentially expressed between two large-seed and two small-seed accessions, and VrKIX8, VrPAT14, VrEmp24/25, VrIAR1, VrBEE3, VrSUC4, and Vrflo2 were further verified by RT-qPCR. Among 65 genes around these QEIs, VrFATB, VrGSO1, VrLACS2, and VrPAT14 were homologous to known seed-development genes in A. thaliana, although new experiments are necessary to explore these novel GEI-trait associations. In addition, 54 genes were identified in comparative genomics analysis to be associated with seed development pathway, in which VrKIX8, VrABA2, VrABI5, VrSHB1, and VrIKU2 were also identified in genome-wide association studies. This result provided a reliable approach for identifying seed-size-related genes in mungbean and a solid foundation for further molecular biology research on seed-size-related genes.

An amino acid transporter-like protein (OsATL15) facilitates the systematic distribution of thiamethoxam in rice for controlling the brown planthopper

Characterization and genetic engineering of plant transporters involved in the pesticide uptake and translocation facilitate pesticide relocation to the tissue where the pests feed, thus improving the bioavailability of the agrichemicals. We aimed to identify thiamethoxam (THX) transporters in rice and modify their expression for better brown planthopper (BPH) control with less pesticide application. A yeast library expressing 1385 rice transporters was screened, leading to the identification of an amino acid transporter-like (ATL) gene, namely OsATL15, which facilitates THX uptake in both yeast cells and rice seedlings. In contrast to a decrease in THX content in osatl15 knockout mutants, ectopic expression of OsATL15 under the control of the CaMV 35S promoter or a vascular-bundle-specific promoter gdcsPpro significantly increased THX accumulation in rice plants, thus further enhancing the THX efficacy against BPH. OsATL15 was localized in rice cell membrane and abundant in the root transverse sections, vascular bundles of leaf blade, and stem longitudinal sections, but not in hull and brown rice at filling stages. Our study shows that OsATL15 plays an essential role in THX uptake and its systemic distribution in rice. OsATL15 could be valuable in achieving precise pest control by biotechnology approaches.

Comprehensive analysis of the LHT gene family in tobacco and functional characterization of NtLHT22 involvement in amino acids homeostasis

Amino acids are vital nitrogen (N) sources for plant growth, development, and yield. The uptake and translocation of amino acids are mediated by amino acid transporters (AATs). The AATs family including lysine-histidine transporters (LHTs), amino acid permeases (AAPs), and proline transporters (ProTs) subfamilies have been identified in various plants. However, little is known about these genes in tobacco. In this study, we identified 23 LHT genes, the important members of AATs, in the tobacco genome. The gene structure, phylogenetic tree, transmembrane helices, chromosomal distribution, cis-regulatory elements, and expression profiles of NtLHT genes were systematically analyzed. Phylogenetic analysis divided the 23 NtLHT genes into two conserved subgroups. Expression profiles confirmed that the NtLHT genes were differentially expressed in various tissues, indicating their potential roles in tobacco growth and development. Cis-elements analysis of promoters and expression patterns after stress treatments suggested that NtLHT genes probable participate in abiotic stress responses of tobacco. In addition, Knock out and overexpression of NtLHT22 changed the amino acids homeostasis in the transgenic plants, the contents of amino acids were significantly decreased in NtLHT22 overexpression plants than wild-type. The results from this study provide important information for further studies on the molecular functions of the NtLHT genes.

Amino acid transporter gene TaATLa1 from Triticum aestivum L. improves growth under nitrogen sufficiency and is down regulated under nitrogen deficiency

TaATLa1 was identified to respond to nitrogen deprivation through transcriptome analysis of wheat seedlings. TaATLa1 specifically transports Gln, Glu, and Asp, and affects the biomass of Arabidopsis and wheat. Nitrogen is an essential macronutrient and plays a crucial role in wheat production. Amino acids, the major form of organic nitrogen, are remobilized by amino acid transporters (AATs) in plants. AATs are commonly described as central components of essential developmental processes and yield formation via taking up and transporting amino acids in plants. However, few studies have reported the detailed biochemical properties and biological functions of these AATs in wheat. In this study, key genes encoding AATs were screened from transcriptome analysis of wheat seedlings treated with normal nitrogen (NN) and nitrogen deprivation (ND). Among them, 21 AATs were down-regulated and eight AATs were up-regulated under ND treatment. Among the homoeologs, TaATLa1.1-3A, TaATLa1.1-3B, and TaATLa1.1-3D (TaATLa1.1-3A, -3B, and -3D), belonging to amino acid transporter-like a (ATLa) subfamily, were significantly down-regulated in response to ND in wheat, and accordingly were selected for functional analyses. The results demonstrated that TaATLa1.1-3A, -3B, and -3D effectively transported glutamine (Gln), glutamate (Glu), and aspartate (Asp) in yeast. Overexpression of TaAILa1.1-3A, -3B, and -3D in Arabidopsis thaliana L. significantly increased amino acid content in leaves, storage protein content in seeds and the plant biomass under NN. Knockdown of TaATLa1.1-3A, -3B, and -3D in wheat seedlings resulted in a significant block of amino acid remobilization and growth inhibition. Taken together, TaATLa1.1-3A, -3B, and -3D contribute substantially to Arabidopsis and wheat growth. We propose that TaATLa1.1-3A, -3B, and -3D may participate in the source-sink translocation of amino acid, and they may have profound implications for wheat yield improvement.

Genetic and molecular factors in determining grain number per panicle of rice

It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.

Rice Straw Utilisation for Bioenergy Production: A Brief Overview

Unsustainable rice straw management causes environmental impacts; hence, utilisation of rice straw for bioenergy is a promising strategy for sustainable rice straw management. Although rice straw has a high potential for bioenergy generation, the whole production cycle and application may cause environmental damage that is not fully understood. Hence, environmental performance studies are required to determine the most effective rice straw utilisation options. A comprehensive approach, such as life-cycle assessment (LCA), can give comprehensive information on the possible environmental effects of rice straw utilisation for bioenergy. Therefore, this study briefly overviews the LCA of rice straw utilisation for bioenergy production. It is found that utilisation of rice straw for bioenergy could reduce global warming potential compared to energy production from fossil fuels. However, it is suggested that other impact categories in LCA be evaluated in the bioenergy production from rice straw research to determine the overall sustainability of the production.

Transcriptome analysis reveals multiple effects of nitrogen accumulation and metabolism in the roots, shoots, and leaves of potato (Solanum tuberosum L.)

BACKGROUND

Nitrogen (N) is a major element and fundamental constituent of grain yield. N fertilizer plays an essential role in the roots, shoots, and leaves of crop plants. Here, we obtained two N-sensitive potato cultivars.

RESULTS

The plants were cultivated in the pots using N-deficient and N-sufficient conditions. Crop height, leaf chlorophyll content, dry matter, and N-accumulation significantly decreased under N-deficient conditions. Furthermore, we performed a comprehensive analysis of the phenotype and transcriptome, GO terms, and KEGG pathways. We used WGCNA of co-expressed genes, and 116 differentially expressed hub genes involved in photosynthesis, nitrogen metabolism, and secondary metabolites to generate 23 modules. Among those modules, six NRT gene families, four pigment genes, two auxin-related genes, and two energy-related genes were selected for qRT-PCR validation.

CONCLUSIONS

Overall, our study demonstrates the co-expressed genes and potential pathways associated with N transport and accumulation in potato cultivars' roots, shoots, and leaves under N-deficient conditions. Therefore, this study provides new ideas to conduct further research on improving nitrogen use efficiency in potatoes.

Yield-associated putative gene regulatory networks in Oryza sativa L. subsp. indica and their association with high-yielding genotypes

BACKGROUND

With the increase in population and economies of developing countries in Asia and Africa, the research towards securing future food demands is an imminent need. Among japonica and indica genotypes, indica rice varieties are largely cultivated across the globe. However, our present understanding of yield-contributing gene information stems mainly from japonica and studies on the yield potential of indica genotypes are limited.

METHODS AND RESULTS

In the present study, yield contributing orthologous genes previously characterized from japonica varieties were identified in the indica genome and analysed with binGO tool for GO biological processes categorization. Transcription factor binding site enrichment analysis in the promoters of yield-related genes of indica was performed with MEME-AME tool that revealed putative common TF regulators are enriched in flower development, two-component signalling and water deprivation biological processes. Gene regulatory networks revealed important TF-target interactions that might govern yield-related traits. Some of the identified candidate genes were validated by qRT-PCR analysis for their expression and association with yield-related traits among 16 widely cultivated popular indica genotypes. Further, SNP-metabolite-trait association analysis was performed using high-yielding indica variety Rasi. This resulted in the identification of putative SNP variations in TF regulators and targeted yield genes significantly linked with metabolite accumulation.

CONCLUSIONS

The study suggests some of the high yielding indica genotypes such as Ravi003, Rasi and Kavya could be used as potential donors in breeding programs based on yield gene expression analysis and SNP-metabolites associations.

Genes and Their Molecular Functions Determining Seed Structure, Components, and Quality of Rice

With the improvement of people's living standards and rice trade worldwide, the demand for high-quality rice is increasing. Therefore, breeding high quality rice is critical to meet the market demand. However, progress in improving rice grain quality lags far behind that of rice yield. This might be because of the complexity of rice grain quality research, and the lack of consensus definition and evaluation standards for high quality rice. In general, the main components of rice grain quality are milling quality (MQ), appearance quality (AQ), eating and cooking quality (ECQ), and nutritional quality (NQ). Importantly, all these quality traits are determined directly or indirectly by the structure and composition of the rice seeds. Structurally, rice seeds mainly comprise the spikelet hull, seed coat, aleurone layer, embryo, and endosperm. Among them, the size of spikelet hull is the key determinant of rice grain size, which usually affects rice AQ, MQ, and ECQ. The endosperm, mainly composed of starch and protein, is the major edible part of the rice seed. Therefore, the content, constitution, and physicochemical properties of starch and protein are crucial for multiple rice grain quality traits. Moreover, the other substances, such as lipids, minerals, vitamins, and phytochemicals, included in different parts of the rice seed, also contribute significantly to rice grain quality, especially the NQ. Rice seed growth and development are precisely controlled by many genes; therefore, cloning and dissecting these quality-related genes will enhance our knowledge of rice grain quality and will assist with the breeding of high quality rice. This review focuses on summarizing the recent progress on cloning key genes and their functions in regulating rice seed structure and composition, and their corresponding contributions to rice grain quality. This information will facilitate and advance future high quality rice breeding programs.

Plant nitrogen nutrition: The roles of arbuscular mycorrhizal fungi

Nitrogen (N) is the most abundant mineral nutrient required by plants, and crop productivity depends heavily on N fertilization in many soils. Production and application of N fertilizers consume huge amounts of energy and substantially increase the costs of agricultural production. Excess N compounds released from agricultural systems are also detrimental to the environment. Thus, increasing plant N uptake efficiency is essential for the development of sustainable agriculture. Arbuscular mycorrhizal (AM) fungi are beneficial symbionts of most terrestrial plants that facilitate plant nutrient uptake and increase host resistance to diverse environmental stresses. AM association is an endosymbiotic process that relies on the differentiation of both host plant roots and AM fungi to create novel contact interfaces within the cells of plant roots. AM plants have two pathways for nutrient uptake: either direct uptake via the root hairs and root epidermis, or indirectly through AM fungal hyphae into root cortical cells. Over the last few years, great progress has been made in deciphering the molecular mechanisms underlying the AM-mediated modulation of nutrient uptake processes, and a growing number of fungal and plant genes responsible for the uptake of nutrients from soil or transfer across the fungi-root interface have been identified. Here, we mainly summarize the recent advances in N uptake, assimilation, and translocation in AM symbiosis, and also discuss how N interplays with C and P in modulating AM development, as well as the synergies between AM fungi and soil microbial communities in N uptake.

Tissue specific expression of UMAMIT amino acid transporters in wheat

Wheat grain protein content and composition are important for its end-use quality. Protein synthesis during the grain filling phase is supported by the amino acids remobilized from the vegetative tissue, the process in which both amino acid importers and exporters are expected to be involved. Previous studies identified amino acid importers that might function in the amino acid remobilization in wheat. However, the amino acid exporters involved in this process have been unexplored so far. In this study, we have curated the Usually Multiple Amino acids Move In and out Transporter (UMAMIT) family of transporters in wheat. As expected, the majority of UMAMITs were found as triads in the A, B, and D genomes of wheat. Expression analysis using publicly available data sets identified groups of TaUMAMITs expressed in root, leaf, spike, stem and grain tissues, many of which were temporarily regulated. Strong expression of TaUMAMITs was detected in the late senescing leaves and transfer cells in grains, both of which are the expected site of apoplastic amino acid transport during grain filling. Biochemical characterization of selected TaUMAMITs revealed that TaUMAMIT17 shows a strong amino acid export activity and might play a role in amino acid transfer to the grains.

Major Genomic Regions for Wheat Grain Weight as Revealed by QTL Linkage Mapping and Meta-Analysis

Grain weight is a key determinant for grain yield potential in wheat, which is highly governed by a type of quantitative genetic basis. The identification of major quantitative trait locus (QTL) and functional genes are urgently required for molecular improvements in wheat grain yield. In this study, major genomic regions and putative candidate genes for thousand grain weight (TGW) were revealed by integrative approaches with QTL linkage mapping, meta-analysis and transcriptome evaluation. Forty-five TGW QTLs were detected using a set of recombinant inbred lines, explaining 1.76-12.87% of the phenotypic variation. Of these, ten stable QTLs were identified across more than four environments. Meta-QTL (MQTL) analysis were performed on 394 initial TGW QTLs available from previous studies and the present study, where 274 loci were finally refined into 67 MQTLs. The average confidence interval of these MQTLs was 3.73-fold less than that of initial QTLs. A total of 134 putative candidate genes were mined within MQTL regions by combined analysis of transcriptomic and omics data. Some key putative candidate genes similar to those reported early for grain development and grain weight formation were further discussed. This finding will provide a better understanding of the genetic determinants of TGW and will be useful for marker-assisted selection of high yield in wheat breeding.

Genetic Engineering and Genome Editing for Improving Nitrogen Use Efficiency in Plants

Low nitrogen availability is one of the main limiting factors for plant growth and development, and high doses of N fertilizers are necessary to achieve high yields in agriculture. However, most N is not used by plants and pollutes the environment. This situation can be improved by enhancing the nitrogen use efficiency (NUE) in plants. NUE is a complex trait driven by multiple interactions between genetic and environmental factors, and its improvement requires a fundamental understanding of the key steps in plant N metabolism—uptake, assimilation, and remobilization. This review summarizes two decades of research into bioengineering modification of N metabolism to increase the biomass accumulation and yield in crops. The expression of structural and regulatory genes was most often altered using overexpression strategies, although RNAi and genome editing techniques were also used. Particular attention was paid to woody plants, which have great economic importance, play a crucial role in the ecosystems and have fundamental differences from herbaceous species. The review also considers the issue of unintended effects of transgenic plants with modified N metabolism, e.g., early flowering—a research topic which is currently receiving little attention. The future prospects of improving NUE in crops, essential for the development of sustainable agriculture, using various approaches and in the context of global climate change, are discussed.

Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen

Global use of nitrogen (N) fertilizers has increased sevenfold from 1960 to 1995 but much of the N applied is lost to the environment. Modifying the temporal and spatial distribution of organic N within the plant can lead to improved grain yield and/or grain protein content for the same or reduced N fertilizer inputs. Biotechnological approaches to modify whole plant distribution of amino acids and ureides has proven successful in several crop species. Manipulating selective autophagy pathways in crops has also improved N remobilization efficiency to sink tissues whilst the contribution of ribophagy, RNA and purine catabolism to N recycling in crops is still too early to foretell. Improved recycling and remobilization of N must exploit N-stress responsive transcriptional regulators, N-sensing or phloem-localized promotors and genetic variation for N-responsive traits.

l-Aspartate: An Essential Metabolite for Plant Growth and Stress Acclimation

L-aspartate (Asp) serves as a central building block, in addition to being a constituent of proteins, for many metabolic processes in most organisms, such as biosynthesis of other amino acids, nucleotides, nicotinamide adenine dinucleotide (NAD), the tricarboxylic acid (TCA) cycle and glycolysis pathway intermediates, and hormones, which are vital for growth and defense. In animals and humans, lines of data have proved that Asp is indispensable for cell proliferation. However, in plants, despite the extensive study of the Asp family amino acid pathway, little attention has been paid to the function of Asp through the other numerous pathways. This review aims to elucidate the most important aspects of Asp in plants, from biosynthesis to catabolism and the role of Asp and its metabolic derivatives in response to changing environmental conditions. It considers the distribution of Asp in various cell compartments and the change of Asp level, and its significance in the whole plant under various stresses. Moreover, it provides evidence of the interconnection between Asp and phytohormones, which have prominent functions in plant growth, development, and defense. The updated information will help improve our understanding of the physiological role of Asp and Asp-borne metabolic fluxes, supporting the modular operation of these networks.

Targeting Nitrogen Metabolism and Transport Processes to Improve Plant Nitrogen Use Efficiency

In agricultural cropping systems, relatively large amounts of nitrogen (N) are applied for plant growth and development, and to achieve high yields. However, with increasing N application, plant N use efficiency generally decreases, which results in losses of N into the environment and subsequently detrimental consequences for both ecosystems and human health. A strategy for reducing N input and environmental losses while maintaining or increasing plant performance is the development of crops that effectively obtain, distribute, and utilize the available N. Generally, N is acquired from the soil in the inorganic forms of nitrate or ammonium and assimilated in roots or leaves as amino acids. The amino acids may be used within the source organs, but they are also the principal N compounds transported from source to sink in support of metabolism and growth. N uptake, synthesis of amino acids, and their partitioning within sources and toward sinks, as well as N utilization within sinks represent potential bottlenecks in the effective use of N for vegetative and reproductive growth. This review addresses recent discoveries in N metabolism and transport and their relevance for improving N use efficiency under high and low N conditions.

The Amino Acid Transporter OsAAP4 Contributes to Rice Tillering and Grain Yield by Regulating Neutral Amino Acid Allocation through Two Splicing Variants

BACKGROUND

Amino acids, which are transported by amino acid transporters, are the major forms of organic nitrogen utilized by higher plants. Among the 19 Amino Acid Permease transporters (AAPs) in rice, only a small number of these genes have been reported to influence rice growth and development. However, whether other OsAAPs are responsible for rice growth and development is unclear.

RESULTS

In this study, we demonstrate that OsAAP4 promoter sequences are divergent between Indica and Japonica, with higher expression in the former, which produces more tillers and higher grain yield than does Japonica. Overexpression of two different splicing variants of OsAAP4 in Japonica ZH11 significantly increased rice tillering and grain yield as result of enhancing the neutral amino acid concentrations of Val, Pro, Thr and Leu. OsAAP4 RNA interference (RNAi) and mutant lines displayed opposite trends compared with overexpresing (OE) lines. In addition, exogenous Val or Pro at 0.5 mM significantly promoted the bud outgrowth of lines overexpressing an OsAAP4a splicing variant compared with ZH11, and exogenous Val or Pro at 2.0 mM significantly enhanced the bud outgrowth of lines overexpressing splicing variant OsAAP4b compared with ZH11. Of note, the results of a protoplast amino acid-uptake assay showed that Val or Pro at different concentrations was specifically transported and accumulated in these overexpressing lines. Transcriptome analysis further demonstrated that OsAAP4 may affect nitrogen transport and metabolism, and auxin, cytokinin signaling in regulating rice tillering.

CONCLUSION

Our results suggested that OsAAP4 contributes to rice tiller and grain yield by regulating neutral amino acid allocation through two different splicing variants and that OsAAP4 might have potential applications in rice breeding.

Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants

C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.