Biofortification of rice with the essential amino acid lysine: molecular characterization, nutritional evaluation, and field performance

Grain lysine enrichment and improved stress tolerance in rice through protein engineering

Amino acids are a major source of nourishment for people living in regions where rice is a staple food. However, rice grain is deficient in essential amino acids including lysine. The activity of the enzyme dihydrodipicolinate synthase (DHDPS) is crucial for lysine production in higher plants, but it is tightly regulated through feedback inhibition by its end product, lysine, leading to limited activity in the grain and resulting in low lysine accumulation. We identified lysine binding sites in the DHDPS enzyme and introduced key mutations to make DHDPS lysine feedback insensitive. Using in vivo analysis and functional complementation assays, we confirmed that protein engineering of the DHDPS renders it insensitive to lysine. Expression of mutated DHDPS resulted in 29% higher lysine and 15% higher protein accumulation in rice grains than in the wild type. Importantly, the lysine content in transgenic grains was maintained in cooked rice. The transgenic plants also exhibited enhanced stress tolerance along with higher antioxidant levels, improved photosynthesis, and higher grain yield compared to wild-type plants. We have shown that protein engineering of DHDPS in rice can lead to accumulation of lysine in grains and impart abiotic stress tolerance. This approach could improve health in regions with nutrient deficiencies and environmental stressors that challenge food production and human health.

Navigating the challenges of engineering composite specialized metabolite pathways in plants

Plants are a valuable source of diverse specialized metabolites with numerous applications. However, these compounds are often produced in limited quantities, particularly under unfavorable ecological conditions. To achieve sufficient levels of target metabolites, alternative strategies such as pathway engineering in heterologous systems like microbes (e.g., bacteria and fungi) or cell-free systems can be employed. Another approach is plant engineering, which aims to either enhance the native production in the original plant or reconstruct the target pathway in a model plant system. Although increasing metabolite production in the native plant is a promising strategy, these source plants are often exotic and pose significant challenges for genetic manipulation. Effective pathway engineering requires comprehensive prior knowledge of the genes and enzymes involved, as well as the precursor, intermediate, branching, and final metabolites. Thus, a thorough elucidation of the biosynthetic pathway is closely linked to successful metabolic engineering in host or model systems. In this review, we highlight recent advances in strategies for biosynthetic pathway elucidation and metabolic engineering. We focus on efforts to engineer complex, multi-step pathways that require the expression of at least eight genes for transient and three genes for stable transformation. Reports on the engineering of complex pathways in stably transformed plants remain relatively scarce. We discuss the major hurdles in pathway elucidation and strategies for overcoming them, followed by an overview of achievements, challenges, and solutions in pathway reconstitution through metabolic engineering. Recent advances including computer-based predictions offer valuable platforms for the sustainable production of specialized metabolites in plants.

Quality maintenance and metabolite changes of grape berry treated by high voltage alternating electric field during near-freezing temperature storage

High Voltage Alternating Electric Field (HVAEF), as an emerging postharvest preservation technology, is environmentally friendly and has garnered significant attention from scholars. This study investigated the effects of HVAEF on the postharvest quality and metabolite changes in 'Shine Muscat' grapes stored at near-freezing temperatures. The results demonstrated that HVAEF halved the weight loss and decay rate, inhibited browning by preserving polyphenol content, and reduced polyphenol oxidase and peroxidase activities, thereby extending the storage time by more than 20 days. Metabolomic analysis of the grape berries from the upper, middle, and bottom parts of the bunch revealed that the upper berries contained higher sugar levels and were more significantly influenced by HVAEF treatment. Additionally, HVAEF notably reduced the accumulation of amino acids, such as valine, leucine, and lysine, compared to the control. This study provides new insights into the enhancement of quality in fresh fruits and vegetables through HVAEF technology.

Differences in cooking taste and physicochemical properties between compound nutritional rice and common rice

In this study, it was compared the physicochemical properties and cooking taste quality between four different types of compound nutritional rice (rice flour with the addition of other coarse grains, legumes, potatoes, and other powders, extruded as artificial rice grains) and common rice. We found that the protein and apparent amylose contents of compound nutritional rice were higher than that of common rice, up to 9.775% and 19.45% respectively. The γ-aminobutyric acid (GABA) and resistant starch contents were much lower than in common rice, and the dietary fiber content did not differ from that in common rice. The results of Fourier transform infrared spectroscopy (FTIR) and X-ray diffraction (XRD) analysis revealed that the starch properties and structure of the compound nutritional rice changed due to high temperature and high pressure processing. In particular, the crystalline structures of starch became V-shaped. In addition, the results of artificial tasting and tasting meter showed that the taste of compound nutritional rice was generally inferior to that of common rice. In summary, compound nutritional rice had problems such as nutritional imbalance and poor taste. There was still a lot of room for improving the taste quality of compound nutritional rice. Therefore, the future development of compound nutritional rice should focus on both nutritional balance and taste improvement. The results of this paper also provided a certain theoretical basis for this.

Polybrominated diphenyl ethers (PBDEs) decreased the protein quality of rice grains by disturbing amino acid metabolism

Polybrominated diphenyl ethers (PBDEs) in soils posed potential risks to crop growth and food safety due to their prevalence and persistence. PBDEs were capable of being absorbed and accumulated into crops, impacting their growth, whereas the interference on metabolic components and nutritional composition deserves further elucidation. This study integrated a combined non-targeted and targeted metabolomics method to explore the influences of 2,2',4,4'-tetrabromodiphenyl ether (BDE-47), 2,2',4,4',5-pentabromodiphenyl ether (BDE-99) and decabromodiphenyl ether (BDE-209) on the metabolic responses of rice (Oryza sativa). Metabolic pathways, which were associated with sugars, organic acids, and amino acids, were significantly disturbed under PBDE stresses. Particularly, 75% of the marked altered pathways belonged to amino acid metabolism, with alanine/aspartate/glutamate metabolism being commonly enhanced. The degradation of aspartic acid promoted the formation of downstream amino acids, among which the levels of lysine, methionine, isoleucine, and asparagine were increased by 1.31-3.15 folds compared to the control. Thus, the antioxidant capacity in rice plants was enhanced, particularly through the significant promotion of ascorbic acid-glutathione (AsA-GSH) cycle in rice leaves. The amino acids were promoted to resist reactive oxygen species (ROS) efficiently, thus were deficient for nutrient storage. When exposed to 4 μmol/kg PBDEs, the contents of amino acids and proteins in grains decreased by 9.1-32.1% and 8.6-34.8%, respectively. In particular, glutelin level was decreased by 5.6-41.2%, resulting in a decline in nutritional quality. This study demonstrated that PBDEs deteriorated the protein nutrition in rice grains by affecting amino acid metabolism, providing a new perspective for evaluating the ecological risks of PBDEs and securing agricultural products.

Biofortification as a solution for addressing nutrient deficiencies and malnutrition

Malnutrition, defined as both undernutrition and overnutrition, is a major global health concern affecting millions of people. One possible way to address nutrient deficiency and combat malnutrition is through biofortification. A comprehensive review of the literature was conducted to explore the current state of biofortification research, including techniques, applications, effectiveness and challenges. Biofortification is a promising strategy for enhancing the nutritional condition of at-risk populations. Biofortified varieties of basic crops, including rice, wheat, maize and beans, with elevated amounts of vital micronutrients, such as iron, zinc, vitamin A and vitamin C, have been successfully developed using conventional and advanced technologies. Additionally, the ability to specifically modify crop genomes to improve their nutritional profiles has been made possible by recent developments in genetic engineering, such as CRISPR-Cas9 technology. The health conditions of people have been shown to improve and nutrient deficiencies were reduced when biofortified crops were grown. Particularly in environments with limited resources, biofortification showed considerable promise as a long-term and economical solution to nutrient shortages and malnutrition. To fully exploit the potential of biofortified crops to enhance public health and global nutrition, issues such as consumer acceptance, regulatory permitting and production and distribution scaling up need to be resolved. Collaboration among governments, researchers, non-governmental organizations and the private sector is essential to overcome these challenges and promote the widespread adoption of biofortification as a key part of global food security and nutrition strategies.

New Insights into the Genetic Basis of Lysine Accumulation in Rice Revealed by Multi-Model GWAS

Lysine is an essential amino acid that cannot be synthesized in humans. Rice is a global staple food for humans but has a rather low lysine content. Identification of the quantitative trait nucleotides (QTNs) and genes underlying lysine content is crucial to increase lysine accumulation. In this study, five grain and three leaf lysine content datasets and 4,630,367 single nucleotide polymorphisms (SNPs) of 387 rice accessions were used to perform a genome-wide association study (GWAS) by ten statistical models. A total of 248 and 71 common QTNs associated with grain/leaf lysine content were identified. The accuracy of genomic selection/prediction RR-BLUP models was up to 0.85, and the significant correlation between the number of favorable alleles per accession and lysine content was up to 0.71, which validated the reliability and additive effects of these QTNs. Several key genes were uncovered for fine-tuning lysine accumulation. Additionally, 20 and 30 QTN-by-environment interactions (QEIs) were detected in grains/leaves. The QEI-sf0111954416 candidate gene LOC_Os01g21380 putatively accounted for gene-by-environment interaction was identified in grains. These findings suggested the application of multi-model GWAS facilitates a better understanding of lysine accumulation in rice. The identified QTNs and genes hold the potential for lysine-rich rice with a normal phenotype.

Lysine-rich rice partially enhanced the growth and development of skeletal system with better skeletal microarchitecture in young rats

Rice is the primary staple food for half of the world's population but is low in lysine content. Previously, we developed transgenic rice with enhanced free lysine content in rice seeds (lysine-rich rice), which was shown safe for consumption and improved the growth in rats. However, the effects of lysine-rich rice on skeletal growth and development remained unknown. In this study, we hypothesized that lysine-rich rice improved skeletal growth and development in weaning rats. Male weaning Sprague-Dawley rats received lysine-rich rice (HFL) diet, wild-type rice (WT) diet, or wild-type rice with various contents of lysine supplementation diet for 70 days. Bone microarchitectures were examined by microcomputed tomography, bone strength was investigated by mechanical test, and dynamics of bone growth were examined by histomorphometric analysis. In addition, we explored the molecular mechanism of lysine and skeletal growth through biochemical testing of growth hormone, bone turnover marker, and amino acid content of rat serum analysis, as well as in a cell culture system. Results indicated that the HFL diet improved rats' bone growth, strength, and microarchitecture compared with the WT diet group. In addition, the HFL diet increased the serum essential amino acids, growth hormone (insulin-like growth factor-1), and bone formation marker concentrations. The cell culture model showed that lysine deficiency reduced insulin-like growth factor-1 and Osterix expression, Akt/mammalian target of rapamycin signaling, and matrix mineralization, and inhibited osteoblast differentiation associated with bone growth. Our findings showed that lysine-rich rice improved skeletal growth and development in weaning rats. A further increase of rice lysine content is highly desirable to fully optimize bone growth and development.

Identification of Candidate Genes that Affect the Contents of 17 Amino Acids in the Rice Grain Using a Genome-Wide Haplotype Association Study

BACKGROUND

The amino acid content (AAC) of the rice grain is one of the most important determinants of nutritional quality in rice. Understanding the genetic basis of grain AAC and mining favorable alleles of target genes for AAC are important for developing new cultivars with improved nutritional quality.

RESULTS

Using a diverse panel of 164 accessions genotyped by 32 M SNPs derived from 3 K Rice Genome Project, we extracted 1,123,603 high quality SNPs in 44,248 genes and used them to construct haplotypes. We measured the contents of the 17 amino acids that included seven essential amino acids and 10 dispensable amino acids. Through a genome-wide haplotype association study, 261 gene-trait associations containing 174 genes for the 17 components of AAC were detected, and 34 of these genes were associated with at least two components. Furthermore, the associated SNPs in genes were also identified by a traditional genome-wide association study to identify the key natural variations in the specific genes.

CONCLUSIONS

The genome-wide haplotype association study allowed us to detected candidate genes directly and to identify key natural genetic variation as well. In the present study, twelve genes have been cloned, and 34 genes were associated with at least two components, suggesting that the genome-wide haplotype association study approach used in the current study is an efficient way to identify candidate genes for target traits. The identified candidate genes, favorable haplotypes, and key natural variations affecting AAC provide valuable resources for further functional characterization and genetic improvement of rice nutritional quality.

Genetically Modified Rice Is Associated with Hunger, Health, and Climate Resilience

While nearly one in nine people in the world deals with hunger, one in eight has obesity, and all face the threat of climate change. The production of rice, an important cereal crop and staple food for most of the world's population, faces challenges due to climate change, the increasing global population, and the simultaneous prevalence of hunger and obesity worldwide. These issues could be addressed at least in part by genetically modified rice. Genetic engineering has greatly developed over the century. Genetically modified rice has been approved by the ISAAA's GM approval database as safe for human consumption. The aim behind the development of this rice is to improve the crop yield, nutritional value, and food safety of rice grains. This review article provides a summary of the research data on genetically modified rice and its potential role in improving the double burden of malnutrition, primarily through increasing nutritional quality as well as grain size and yield. It also reviews the potential health benefits of certain bioactive components generated in genetically modified rice. Furthermore, this article discusses potential solutions to these challenges, including the use of genetically modified crops and the identification of quantitative trait loci involved in grain weight and nutritional quality. Specifically, a quantitative trait locus called grain weight on chromosome 6 has been identified, which was amplified by the Kasa allele, resulting in a substantial increase in grain weight and brown grain. An overexpressing a specific gene in rice, Oryza sativa plasma membrane H+-ATPase1, was observed to improve the absorption and assimilation of ammonium in the roots, as well as enhance stomatal opening and photosynthesis rate in the leaves under light exposure. Cloning research has also enabled the identification of several underlying quantitative trait loci involved in grain weight and nutritional quality. Finally, this article discusses the increasing threats of climate change such as methane-nitrous oxide emissions and global warming, and how they may be significantly improved by genetically modified rice through modifying a water-management technique. Taken together, this comprehensive review will be of particular importance to the field of bioactive components of cereal grains and food industries trying to produce high-quality functional cereal foods through genetic engineering.

Combined Hybridization and Evaluation of High-Lysine Rice: Nutritional and Physicochemical Qualities and Field Performance

Rice, as a major food crop, provides necessary energy and nutrition for humans and livestock. However, its nutritional value is affected by lysine. Using point mutation, we previously obtained AK2 (aspartokinase) and DHDPS1 (dihydrodipicolinate synthase) genes insensitive to lysine feedback inhibition and constructed transgenic lines AK2-52 and DHDPS1-22, which show increased lysine synthesis, as well as Ri-12, which shows decreased lysine degradation by inhibiting rice lysine ketoglutarate reductase/saccharopine dehydrogenase (LKR/SDH) activity. In this study, further transgenic lines were hybridized and evaluated. The lysine content of mature seeds from pyramid lines PRD and PRA increased 32.5- and 29.8-fold, respectively, compared with the wild-type, while the three-gene pyramiding line PRDA had a moderate lysine content. The total lysine, total free lysine, and total protein contents of PRD and PRA also increased and had no obvious impact on the physical and chemical quality, seed appearance, and main agronomic traits. Meanwhile, comparative analysis with polygenic polymeric lines GR containing bacterial AK (lysC) and DHDPS (dapA) genes revealed differences in the way bacterial and endogenous rice AK and DHDPS regulate lysine biosynthesis. These results provide a reference for further evaluation and commercialization of high-lysine transgenic rice.

Advances in Crop Breeding Through Precision Genome Editing

The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.

Amino Acids in Rice Grains and Their Regulation by Polyamines and Phytohormones

Rice is one of the most important food crops in the world, and amino acids in rice grains are major nutrition sources for the people in countries where rice is the staple food. Phytohormones and plant growth regulators play vital roles in regulating the biosynthesis of amino acids in plants. This paper reviewed the content and compositions of amino acids and their distribution in different parts of ripe rice grains, and the biosynthesis and metabolism of amino acids and their regulation by polyamines (PAs) and phytohormones in filling grains, with a focus on the roles of higher PAs (spermidine and spermine), ethylene, and brassinosteroids (BRs) in this regulation. Recent studies have shown that higher PAs and BRs (24-epibrassinolide and 28-homobrassinolide) play positive roles in mediating the biosynthesis of amino acids in rice grains, mainly by enhancing the activities of the enzymes involved in amino acid biosynthesis and sucrose-to-starch conversion and maintaining redox homeostasis. In contrast, ethylene may impede amino acid biosynthesis by inhibiting the activities of the enzymes involved in amino acid biosynthesis and elevating reactive oxygen species. Further research is needed to unravel the temporal and spatial distribution characteristics of the content and compositions of amino acids in the filling grain and their relationship with the content and compositions of amino acids in different parts of a ripe grain, to elucidate the cross-talk between or among phytohormones in mediating the anabolism of amino acids, and to establish the regulation techniques for promoting the biosynthesis of amino acids in rice grains.

Extreme Low-Temperature Stress Affects Nutritional Quality of Amino Acids in Rice

Global climate change has increased the frequency of extreme climate events, and their effects on the nutritional quality, especially on amino acids in rice, have not been quantified. The data from a 3-year low temperature stress (LTS) experiment including two rice varieties (Huaidao 5 and Nanjing 46), seven minimum/maximum temperature levels (one optimal 21/27°C and six LTS levels from 17/23 to 6/12°C), and three LTS durations (3, 6, and 9 days) after flowering, revealed significant interactive effects of LTS at different stages, durations, and temperature levels on the content and accumulation of amino acids. LTS increased rice total amino acid content, while decreasing its accumulation, with higher sensitivities to LTS at the flowering stage than at the grain filling stage. In most treatments, the lysine (the first limiting amino acid) and phenylalanine content were increased under LTS at early and peak flowering stages but decreased at the grain filling stage in both varieties, and only leucine content was increased at all three stages after flowering, while the content of other essential amino acids differed among the two varieties. With an increase of 1°C·d per day in the accumulated cold degree days, the relative content of the essential amino acids was increased by 0.01-0.41%, depending on the rice variety and growth stage. Our results suggest that LTS can improve nutritional quality of amino acids of rice grains in terms of amino acids content, especially at flowering stage. These results provide critical insights for assessing the potential impact of extreme climates on the nutrient quality of rice under future climate change.

CRISPR-Based Genome Editing: Advancements and Opportunities for Rice Improvement

To increase the potentiality of crop production for future food security, new technologies for plant breeding are required, including genome editing technology—being one of the most promising. Genome editing with the CRISPR/Cas system has attracted researchers in the last decade as a safer and easier tool for genome editing in a variety of living organisms including rice. Genome editing has transformed agriculture by reducing biotic and abiotic stresses and increasing yield. Recently, genome editing technologies have been developed quickly in order to avoid the challenges that genetically modified crops face. Developing transgenic-free edited plants without introducing foreign DNA has received regulatory approval in a number of countries. Several ongoing efforts from various countries are rapidly expanding to adopt the innovations. This review covers the mechanisms of CRISPR/Cas9, comparisons of CRISPR/Cas9 with other gene-editing technologies—including newly emerged Cas variants—and focuses on CRISPR/Cas9-targeted genes for rice crop improvement. We have further highlighted CRISPR/Cas9 vector construction model design and different bioinformatics tools for target site selection.

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.

Applications of Genomic Tools in Plant Breeding: Crop Biofortification

Crop breeding has mainly been focused on increasing productivity, either directly or by decreasing the losses caused by biotic and abiotic stresses (that is, incorporating resistance to diseases and enhancing tolerance to adverse conditions, respectively). Quite the opposite, little attention has been paid to improve the nutritional value of crops. It has not been until recently that crop biofortification has become an objective within breeding programs, through either conventional methods or genetic engineering. There are many steps along this long path, from the initial evaluation of germplasm for the content of nutrients and health-promoting compounds to the development of biofortified varieties, with the available and future genomic tools assisting scientists and breeders in reaching their objectives as well as speeding up the process. This review offers a compendium of the genomic technologies used to explore and create biodiversity, to associate the traits of interest to the genome, and to transfer the genomic regions responsible for the desirable characteristics into potential new varieties. Finally, a glimpse of future perspectives and challenges in this emerging area is offered by taking the present scenario and the slow progress of the regulatory framework as the starting point.

Current Status and Potential of Biofortification to Enhance Crop Nutritional Quality: An Overview

Around 2 billion people are suffering from chronic malnutrition or “hidden hunger”, which is the result of many diseases and disorders, including cognitive degeneration, stunting growth, and mortality. Thus, biofortification of staple food crops enriched with micronutrients is a more sustainable option for providing nutritional supplements and managing malnutrition in a society. Since 2001, when the concept of biofortification came to light, different research activities have been carried out, like the development of target populations, breeding or genetic engineering, and the release of biofortified cultivars, in addition to conducting nutritional efficacy trials and delivery plan development. Although, being a cost-effective intervention, it still faces many challenges, like easy accessibility of biofortified cultivars, stakeholders’ acceptance, and the availability of biofortified germplasm in the public domain, which varies from region to region. Hence, this review is focused on the recent potential, efforts made to crop biofortification, impacts analysis on human health, cost-effectiveness, and future perspectives to further strengthen biofortification programs. Through regular interventions of sustainable techniques and methodologies, biofortification holds huge potential to solve the malnutrition problem through regular interventions of nutrient-enriched staple food options for billions of people globally.

Lysine biofortification of crops to promote sustained human health in the 21st century

Crop biofortification is pivotal in preventing malnutrition, with lysine considered the main limiting essential amino acid (EAA) required to maintain human health. Lysine deficiency is predominant in developing countries where cereal crops are the staple food, highlighting the need for efforts aimed at enriching the staple diet through lysine biofortification. Successful modification of aspartate kinase (AK) and dihydrodipicolinate synthase (DHDPS) feedback inhibition has been used to enrich lysine in transgenic rice plants without yield penalty, while increases in the lysine content of quality protein maize have been achieved via marker-assisted selection. Here, we reviewed the lysine metabolic pathway and proposed the use of metabolic engineering targets as the preferred option for fortification of lysine in crops. Use of gene editing technologies to translate the findings and engineer lysine catabolism is thus a pioneering step forward.

How do rice seedlings of landrace Pokkali survive in saline fields after transplantation? Physiology, biochemistry, and photosynthesis

Rice, one of the most important staple food crops in the world, is highly sensitive to soil salinity at the seedling stage. The ultimate yield of this crop is a function of the number of seedlings surviving after transplantation in saline water. Oryza sativa cv. IR64 is a high-yielding salinity-sensitive variety, while Pokkali is a landrace traditionally cultivated by the local farmers in the coastal regions in India. However, the machinery responsible for the seedling-stage tolerance in Pokkali is not understood. To bridge this gap, we subjected young seedlings of these contrasting genotypes to salinity and performed detailed investigations about their growth parameters, ion homeostasis, biochemical composition, and photosynthetic parameters after every 24 h of salinity for three days. Taken together, all the physiological and biochemical indicators, such as proline accumulation, K⁺/Na⁺ ratio, lipid peroxidation, and electrolyte leakage, clearly revealed significant differences between IR64 and Pokkali under salinity, establishing their contrasting nature at this stage. In response to salinity, the F_v/F_m ratio (maximum quantum efficiency of Photosystem II as inferred from Chl a fluorescence) and the energy conserved for the electron transport after the reduction of Q_A (the primary electron acceptor of PSII), to Q_A^-, and reduction of the end electron acceptor molecules towards the PSI (Photosystem I) electron acceptor side was higher in Pokkali than IR64 plants. These observations reflect a direct contribution of photosynthesis towards seedling-stage salinity tolerance in rice. These findings will help to breed high-yielding crops for salinity prone agricultural lands.

Comparative Study of Physicochemical Properties and Starch Granule Structure in Seven Ginkgo Kernel Flours

Ginkgo biloba L. is an important economic tree species in China, and its kernels have been used as a popular food in Asian countries. Herein, the morphology, basic chemical components, starch granule structures, and physicochemical properties of kernel flours from seven ginkgo cultivars were investigated, and their relationships were analyzed. The kernels were oval or spherical in shape, with variable sizes. The starch granules exhibited both regular and irregular Maltese cross patterns. Amylose was mainly distributed in amorphous growth rings. A spatial variation in the 865/942 cm-1 ratio was observed within individual starch granules. Variations in total starch content, apparent amylose content (AAC), crude protein content (CPC), total amino acid content (TAAC), starch fine structure, and thermal and pasting properties were observed among the seven kernel flours. Pearson correlation coefficients and principle component analyses showed that the thermal properties were affected by kernel CPC, TAAC, AAC, and starch fine structure, while the pasting properties were affected by AAC and starch fine structure. Furthermore, experiments showed that the seed protein structure and α-amylase activity affected the pasting properties of ginkgo kernel flours.

Bayesian Network Analysis of Lysine Biosynthesis Pathway in Rice

Lysine is the first limiting essential amino acid in rice because it is present in the lowest quantity compared to all the other amino acids. Amino acids are the building block of proteins and play an essential role in maintaining the human body’s healthy functioning. Rice is a staple food for more than half of the global population; thus, increasing the lysine content in rice will help improve global health. In this paper, we studied the lysine biosynthesis pathway in rice (Oryza sativa) to identify the regulators of the lysine reporter gene LYSA (LOC_Os02g24354). Genetically intervening at the regulators has the potential to increase the overall lysine content in rice. We modeled the lysine biosynthesis pathway in rice seedlings under normal and saline (NaCl) stress conditions using Bayesian networks. We estimated the model parameters using experimental data and identified the gene DAPF(LOC_Os12g37960) as a positive regulator of the lysine reporter gene LYSA under both normal and saline stress conditions. Based on this analysis, we conclude that the gene DAPF is a potent candidate for genetic intervention. Upregulating DAPF using methods such as CRISPR-Cas9 gene editing strategy has the potential to upregulate the lysine reporter gene LYSA and increase the overall lysine content in rice.

Lysine biofortification in rice by modulating feedback inhibition of aspartate kinase and dihydrodipicolinate synthase

Lysine is the main limiting essential amino acid (EAA) in the rice seeds, which is a major energy and nutrition source for humans and livestock. In higher plants, the rate-limiting steps in lysine biosynthesis pathway are catalysed by two key enzymes, aspartate kinase (AK) and dihydrodipicolinate synthase (DHDPS), and both are extremely sensitive to feedback inhibition by lysine. In this study, two rice AK mutants (AK1 and AK2) and five DHDPS mutants (DHDPS1-DHDPS5), all single amino acid substitution, were constructed. Their protein sequences passed an allergic sequence-based homology alignment. Mutant proteins were recombinantly expressed in Escherichia coli, and all were insensitive to the lysine analog S-(2-aminoethyl)-l-cysteine (AEC) at concentrations up to 12 mm. The AK and DHDPS mutants were transformed into rice, and free lysine was elevated in mature seeds of transgenic plants, especially those expressing AK2 or DHDPS1, 6.6-fold and 21.7-fold higher than the wild-type (WT) rice, respectively. We then engineered 35A2D1L plants by simultaneously expressing modified AK2 and DHDPS1, and inhibiting rice LKR/SDH (lysine ketoglutaric acid reductase/saccharopine dehydropine dehydrogenase). Free lysine levels in two 35A2D1L transgenic lines were 58.5-fold and 39.2-fold higher than in WT and transgenic rice containing native AK and DHDPS, respectively. Total free amino acid and total protein content were also elevated in 35A2D1L transgenic rice. Additionally, agronomic performance analysis indicated that transgenic lines exhibited normal plant growth, development and seed appearance comparable to WT plants. Thus, AK and DHDPS mutants may be used to improve the nutritional quality of rice and other cereal grains.

Mineral Biofortification of Vegetables as a Tool to Improve Human Diet

Vegetables represent pillars of good nutrition since they provide important phytochemicals such as fiber, vitamins, antioxidants, as well as minerals. Biofortification proposes a promising strategy to increase the content of specific compounds. As minerals have important functionalities in the human metabolism, the possibility of enriching fresh consumed products, such as many vegetables, adopting specific agronomic approaches, has been considered. This review discusses the most recent findings on agronomic biofortification of vegetables, aimed at increasing in the edible portions the content of important minerals, such as calcium (Ca), magnesium (Mg), iodine (I), zinc (Zn), selenium (Se), iron (Fe), copper (Cu), and silicon (Si). The focus was on selenium and iodine biofortification thus far, while for the other mineral elements, aspects related to vegetable typology, genotypes, chemical form, and application protocols are far from being well defined. Even if agronomic fortification is considered an easy to apply technique, the approach is complex considering several interactions occurring at crop level, as well as the bioavailability of different minerals for the consumer. Considering the latter, only few studies examined in a broad approach both the definition of biofortification protocols and the quantification of bioavailable fraction of the element.

Roles of DNA Methylation in Cold Priming in Tartary Buckwheat

Plants experience a wide array of environmental stimuli, some of which are frequent occurrences of cold weather, which have priming effects on agricultural production and agronomic traits. DNA methylation may act as an epigenetic regulator for the cold response of Tartary buckwheat (Fagopyrum tataricum). Combined with long-term field observation and laboratory experiments, comparative phenome, methylome, and transcriptome analyses were performed to investigate the potential epigenetic contributions for the cold priming of Tartary buckwheat variety Dingku1. Tartary buckwheat cv. Dingku1 exhibited low-temperature resistance. Single-base resolution maps of the DNA methylome were generated, and a global loss of DNA methylation was observed during cold responding in Dingku1. These sites with differential methylation levels were predominant in the intergenic regions. Several hundred genes had different DNA methylation patterns and expressions in different cold treatments (cold memory and cold shock), such as CuAO, RPB1, and DHE1. The application of a DNA methylation inhibitor caused a change of the free lysine content, suggesting that DNA methylation can affect metabolite accumulation for Tartary buckwheat cold responses. The results of the present study suggest important roles of DNA methylation in regulating cold response and forming agronomic traits in Tartary buckwheat.

Nutrition and antioxidant profiling in the unpolished and polished grains of eleven indigenous aromatic rice cultivars

The present study emphasized on the yet-unexplored exhaustive analyses of nutritional and antioxidant parameters in the unpolished and polished grains of eleven indigenous aromatic rice varieties. Tulaipanji appeared to be a highly demanding variety by virtue of having sufficient levels of micronutrients like Fe, Zn and Cu (linked with higher expression of fer2, ZIP and NAS3), inorganic phosphorus, hexose sugars, total amino acids and lysine (correlated with higher expression of glutelin and RLRH1), tocopherol (due to higher HGGT expression), total phenolic content, flavonoids, anthocyanins (concomitant with higher expression of PPO, PAL and ANS), LOX activity and LOX1 gene expression, and overall higher total antioxidant capacity, particularly in the polished grains. The importance of IET-21261, with regard to higher content of phytic acid and total phosphorus (with high IPK1 expression), β-carotene (with high PSY expression) and tocopherol (with high HGGT expression), and of Kalonunia, with respect to cysteine and γ-oryzanol in the polished grains, was also significant. Lower α-amylase enzyme activity and α-amylase expression led to considerable starch accumulation, with lower sucrose content, in the unpolished grains of Radhunipagal and polished grains of Pusa Basmati-1. Paramanya registered the highest content of thiamine and TH1 expression, together with minimum methylglyoxal level (low TPI expression). Paramanya and Radhunipagal maintained a higher pool of majority of the nutritional and antioxidant components in their unpolished grains. The polished grains of all the genotypes showed strikingly lower nutritional constituents, as compared to unpolished grains. The knowledge gained from this study will largely provide a road map to the farmers and rice consumers for making proper choice of the aromatic genotypes for large-scale cultivation and dietary consumption to derive maximum nutritional benefits.

Genetic Manipulation for Improved Nutritional Quality in Rice

Food with higher nutritional value is always desired for human health. Rice is the prime staple food in more than thirty developing countries, providing at least 20% of dietary protein, 3% of dietary fat and other essential nutrients. Several factors influence the nutrient content of rice which includes agricultural practices, post-harvest processing, cultivar type as well as manipulations followed by selection through breeding and genetic means. In addition to mutation breeding, genetic engineering approach also contributed significantly for the generation of nutrition added varieties of rice in the last decade or so. In the present review, we summarize the research update on improving the nutritional characteristics of rice by using genetic engineering and mutation breeding approach. We also compare the conventional breeding techniques of rice with modern molecular breeding techniques toward the generation of nutritionally improved rice variety as compared to other cereals in areas of micronutrients and availability of essential nutrients such as folate and iron. In addition to biofortification, our focus will be on the efforts to generate low phytate in seeds, increase in essential fatty acids or addition of vitamins (as in golden rice) all leading to the achievements in rice nutrition science. The superiority of biotechnology over conventional breeding being already established, it is essential to ascertain that there are no serious negative agronomic consequences for consumers with any difference in grain size or color or texture, when a nutritionally improved variety of rice is generated through genetic engineering technology.

An iron (II) dependent oxygenase performs the last missing step of plant lysine catabolism

Despite intensive study, plant lysine catabolism beyond the 2-oxoadipate (2OA) intermediate remains unvalidated. Recently we described a missing step in the D-lysine catabolism of Pseudomonas putida in which 2OA is converted to D-2-hydroxyglutarate (2HG) via hydroxyglutarate synthase (HglS), a DUF1338 family protein. Here we solve the structure of HglS to 1.1 Å resolution in substrate-free form and in complex with 2OA. We propose a successive decarboxylation and intramolecular hydroxylation mechanism forming 2HG in a Fe(II)- and O₂-dependent manner. Specificity is mediated by a single arginine, highly conserved across most DUF1338 proteins. An Arabidopsis thaliana HglS homolog coexpresses with known lysine catabolism enzymes, and mutants show phenotypes consistent with disrupted lysine catabolism. Structural and biochemical analysis of Oryza sativa homolog FLO7 reveals identical activity to HglS despite low sequence identity. Our results suggest DUF1338-containing enzymes catalyze the same biochemical reaction, exerting the same physiological function across bacteria and eukaryotes.

Hydroxyglutarate synthase (HglS) converts 2-oxoadipate to D-2- hydroxyglutarate during lysine catabolism in bacteria. Here the authors use structural and biochemical approaches to show that HglS acts via successive decarboxylation and intramolecular hydroxylation and that homologous enzymes catalyze the final step of lysine catabolism in plants.

Improving nutritional quality of rice for human health

This review surveys rice nutritional value, mainly focusing on breeding achievements via adoption of both genetic engineering and non-transgenic strategies to improve key nutrients associated with human health. Rice (Oryza sativa) is an essential component of the diets and livelihoods of over 3.5 billion people. Polished rice is mostly consumed as staple food, fulfilling daily energy demands and part of the protein requirement. Brown rice is comparatively more nutritious, containing more lipids, minerals, vitamins, dietary fiber, micronutrients, and bioactive compounds. In this article, we review the nutritional facts about rice including the level of γ-aminobutyric acid, resistant starch, lysine, iron, zinc, β-carotene, folate, anthocyanin, various carotenoids, and flavonoids, focusing on their synthesis and metabolism and the advances in their biofortification via adoption of both conventional and genetic engineering strategies. We conclude that besides representing a staple food, rice has the potential to become a source of various essential nutrients or bioactive compounds through appropriate genetic improvements to benefit human health and prevent certain chronic diseases. Finally, we discuss the available, non-genetically engineering strategies for the nutritional improvement of rice, including their main strengths and constraints.

The Modular Control of Cereal Endosperm Development

Expansion of the human population demands a significant increase in cereal production. The main component of cereal grains is endosperm, a body of starchy endosperm (SE) cells surrounded by aleurone (AL) cells with transfer cells (TC) at the base and embryo surrounding (ESR) cells adjacent to the embryo. The data reviewed here emphasize the modular nature of endosperm by first suggesting that sucrose promotes development of the fertilized triploid endosperm cell. Next, that the basal syncytial endosperm responds to glucose by turning on TC development. The default endosperm cell fate is SE and ESR differentiation is likely activated by signaling from the embryo. Cells on the exterior surface of the endosperm are specified as AL cells.

Connections Between Amino Acid Metabolisms in Plants: Lysine as an Example

Extensive efforts have been made to fortify essential amino acids and boost nutrition in plants, but unintended effects on growth and physiology are also observed. Understanding how different amino acid metabolisms are connected with other biological pathways is therefore important. In addition to protein synthesis, amino acid metabolism is also tightly linked to energy and carbohydrate metabolism, the carbon-nitrogen budget, hormone and secondary metabolism, stress responses, and so on. Here, we update the currently available information on the connections between amino acid metabolisms, which tend to be overlooked in higher plants. Particular emphasis was placed on the connections between lysine metabolism and other pathways, such as tryptophan metabolism, the tricarboxylic acid cycle, abiotic and biotic stress responses, starch metabolism, and the unfolded protein response. Interestingly, regulation of lysine metabolism was found to differ between plant species, as is the case between dicots and monocots. Determining the metabolic connection between amino acid metabolisms will help improve our understanding of the metabolic flux, supporting studies on crop nutrition.

Lysine, Lysine-Rich, Serine, and Serine-Rich Proteins: Link Between Metabolism, Development, and Abiotic Stress Tolerance and the Role of ncRNAs in Their Regulation

Lysine (Lys) is indispensable nutritionally, and its levels in plants are modulated by both transcriptional and post-transcriptional control during plant ontogeny. Animal glutamate receptor homologs have been detected in plants, which may participate in several plant processes through the Lys catabolic products. Interestingly, a connection between Lys and serotonin metabolism has been established recently in rice. 2-Aminoadipate, a catabolic product of Lys appears to play a critical role between serotonin accumulation and the color of rice endosperm/grain. It has also been shown that expression of some lysine-methylated proteins and genes encoding lysine-methyltransferases (KMTs) are regulated by cadmium even as it is known that Lys biosynthesis and its degradation are modulated by novel mechanisms. Three complex pathways co-exist in plants for serine (Ser) biosynthesis, and the relative preponderance of each pathway in relation to plant development or abiotic stress tolerance are being unfolded slowly. But the phosphorylated pathway of L-Ser biosynthesis (PPSB) appears to play critical roles and is essential in plant metabolism and development. Ser, which participates indirectly in purine and pyrimidine biosynthesis and plays a pivotal role in plant metabolism and signaling. Also, L-Ser has been implicated in plant responses to both biotic and abiotic stresses. A large body of information implicates Lys-rich and serine/arginine-rich (SR) proteins in a very wide array of abiotic stresses. Interestingly, a link exists between Lys-rich K-segment and stress tolerance levels. It is of interest to note that abiotic stresses largely influence the expression patterns of SR proteins and also the alternative splicing (AS) patterns. We have checked if any lncRNAs form a cohort of differentially expressed genes from the publicly available PPSB, sequence read archives of NCBI GenBank. Finally, we discuss the link between Lys and Ser synthesis, catabolism, Lys-proteins, and SR proteins during plant development and their myriad roles in response to abiotic stresses.

Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.

Rice Grain Quality Benchmarking Through Profiling of Volatiles and Metabolites in Grains Using Gas Chromatography Mass Spectrometry

Gas chromatograph coupled with mass spectrometer is widely used to profile volatiles and metabolites from the homogenized rice flour obtained from mature grains. Rice grains consist of central endosperm which stores majorly starch and, in addition, accumulate various storage proteins as storage reserves. The outer nutritious aleurone layer stores lipids, sugar alcohols, volatiles, antioxidants, vitamins, and various micronutrients. Once paddy sample is dehulled, milled, and ground cryogenically, the brown rice flour is subjected to extraction of primary metabolites and volatiles using an appropriate extraction method. In metabolite profiling of the liquid extract obtained from the rice sample, mixture is initially subjected to methoxyamination then silylation before being subjected to untargeted metabolite profiling. Peaks obtained are processed for noise reduction and specific signal selection. Volatile compounds are initially extracted using a solid phase adsorbent prior to analysis. All these compounds, metabolites, and volatiles are detected in the mass selective detector by fragmentation at 70 eV ionization energy and the resultant mass spectrum compared with a built-in library of compounds. Data mined from the gas chromatography mass spectrometry analysis are then subjected to post-processing statistical analysis.

New insights into the metabolism of aspartate-family amino acids in plant seeds

Aspartate-family amino acids. Aspartate (Asp)-family pathway, via several metabolic branches, leads to four key essential amino acids: Lys, Met, Thr, and Ile. Among these, Lys and Met have received the most attention, as they are the most limiting amino acid in cereals and legumes crops, respectively. The metabolic pathways of these four essential amino acids and their interactions with regulatory networks have been well characterized. Using this knowledge, extensive efforts have been devoted to augmenting the levels of these amino acids in various plant organs, especially seeds, which serve as the main source of human food and livestock feed. Seeds store a number of storage proteins, which are utilized as nutrient and energy resources. Storage proteins are composed of amino acids, to guarantee the continuation of plant progeny. Thus, understanding the seed metabolism, especially with respect to the accumulation of aspartate-derived amino acids Lys and Met, is a crucial factor for sustainable agriculture. In this review, we summarized the Asp-family pathway, with some new examples of accumulated Asp-family amino acids, particularly Lys and Met, in plant seeds. We also discuss the recent advances in understanding the roles of Asp-family amino acids during seed development.

Characterization of recombinant dihydrodipicolinate synthase from the bread wheat Triticum aestivum

Recombinant wheat DHDPS was produced for the first time in milligram quantities and shown to be an enzymatically active tetramer in solution using analytical ultracentrifugation and small angle X-ray scattering. Wheat is an important cereal crop with an extensive role in global food supply. Given our rapidly growing population, strategies to increase the nutritional value and production of bread wheat are of major significance in agricultural science to satisfy our dietary requirements. Lysine is one of the most limiting essential amino acids in wheat, thus, a thorough understanding of lysine biosynthesis is of upmost importance to improve its nutritional value. Dihydrodipicolinate synthase (DHDPS; EC 4.3.3.7) catalyzes the first committed step in the lysine biosynthesis pathway of plants. Here, we report for the first time the expression and purification of recombinant DHDPS from the bread wheat Triticum aestivum (Ta-DHDPS). The optimized protocol yielded 36 mg of > 98% pure recombinant Ta-DHDPS per liter of culture. Enzyme kinetic studies demonstrate that the recombinant Ta-DHDPS has a K_M (pyruvate) of 0.45 mM, K_M (l-aspartate-4-semialdehyde) of 0.07 mM, k_cat of 56 s^-1, and is inhibited by lysine (IC ₅₀ ^LYS of 0.033 mM), which agree well with previous studies using labor-intensive purification from wheat suspension cultures. We subsequently employed circular dichroism spectroscopy, analytical ultracentrifugation and small angle X-ray scattering to show that the recombinant enzyme is folded with 60% α/β structure and exists as a 7.5 S tetrameric species with a R_g of 33 Å and D_max of 118 Å. This study is the first to report the biophysical properties of the recombinant Ta-DHDPS in aqueous solution and offers an excellent platform for future studies aimed at improving nutritional value and primary production of bread wheat.

GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality

Identification of grain shape determining genes can facilitate breeding of rice cultivars with optimal grain shape and appearance quality. Here, we identify GS9 (Grain Shape Gene on Chromosome 9) gene by map-based cloning. The gs9 null mutant has slender grains, while overexpression GS9 results in round grains. GS9 encodes a protein without known conserved functional domain. It regulates grain shape by altering cell division. The interaction of GS9 and ovate family proteins OsOFP14 and OsOFP8 is modulated by OsGSK2 kinase, a key regulator of the brassinosteroids signaling pathway. Genetic interaction analysis reveals that GS9 functions independently from other previously identified grain size genes. Introducing the gs9 allele into elite rice cultivars significantly improves grain shape and appearance quality. It suggests potential application of gs9, alone or in combination with other grain size determining genes, in breeding of rice varieties with optimized grain shape.

An integrated multi-layered analysis of the metabolic networks of different tissues uncovers key genetic components of primary metabolism in maize

Primary metabolism plays a pivotal role in normal plant growth, development and reproduction. As maize is a major crop worldwide, the primary metabolites produced by maize plants are of immense importance from both calorific and nutritional perspectives. Here a genome-wide association study (GWAS) of 61 primary metabolites using a maize association panel containing 513 inbred lines identified 153 significant loci associated with the level of these metabolites in four independent tissues. The genome-wide expression level of 760 genes was also linked with metabolite levels within the same tissue. On average, the genetic variants at each locus or transcriptional variance of each gene identified here were estimated to have a minor effect (4.4-7.8%) on primary metabolic variation. Thirty-six loci or genes were prioritized as being worthy of future investigation, either with regard to functional characterization or for their utility for genetic improvement. This target list includes the well-known opaque 2 (O2) and lkr/sdh genes as well as many less well-characterized genes. During our investigation of these 36 loci, we analyzed the genetic components and variations underlying the trehalose, aspartate and aromatic amino acid pathways, thereby functionally characterizing four genes involved in primary metabolism in maize.

A Connection between Lysine and Serotonin Metabolism in Rice Endosperm

Cereal endosperms produce a vast array of metabolites, including the essential amino acid lysine (Lys). Enhanced accumulation of Lys has been achieved via metabolic engineering in cereals, but the potential connection between metabolic engineering and Lys fortification is unclear. In mature seeds of engineered High Free Lysine (HFL) rice (Oryza sativa), the endosperm takes on a characteristic dark-brown appearance. In this study, we use an integrated metabolomic and transcriptomic approach combined with functional validation to elucidate the key metabolites responsible for the dark-brown phenotype. Importantly, we found that serotonin biosynthesis was elevated dramatically and closely linked with dark-brown endosperm color in HFL rice. A functional connection between serotonin and endosperm color was confirmed via overexpression of TDC3, a key enzyme of serotonin biosynthesis. Furthermore, we show that both the jasmonate signaling pathway and TDC expression were strongly induced in the late stage of endosperm development of HFL rice, coinciding with serotonin accumulation and dark-brown pigmentation. We propose a model for the metabolic connection between Lys and serotonin metabolism in which elevated 2-aminoadipate from Lys catabolism may play a key role in the connection between the jasmonate signaling pathway, serotonin accumulation, and the brown phenotype in rice endosperm. Our data provide a deeper understanding of amino acid metabolism in rice. In addition, the finding that both Lys and serotonin accumulate in HFL rice grains should promote efforts to create a nutritionally favorable crop.

Biofortified Crops Generated by Breeding, Agronomy, and Transgenic Approaches Are Improving Lives of Millions of People around the World

Biofortification is an upcoming, promising, cost-effective, and sustainable technique of delivering micronutrients to a population that has limited access to diverse diets and other micronutrient interventions. Unfortunately, major food crops are poor sources of micronutrients required for normal human growth. The manuscript deals in all aspects of crop biofortification which includes-breeding, agronomy, and genetic modification. It tries to summarize all the biofortification research that has been conducted on different crops. Success stories of biofortification include lysine and tryptophan rich quality protein maize (World food prize 2000), Vitamin A rich orange sweet potato (World food prize 2016); generated by crop breeding, oleic acid, and stearidonic acid soybean enrichment; through genetic transformation and selenium, iodine, and zinc supplementation. The biofortified food crops, especially cereals, legumes, vegetables, and fruits, are providing sufficient levels of micronutrients to targeted populations. Although a greater emphasis is being laid on transgenic research, the success rate and acceptability of breeding is much higher. Besides the challenges biofortified crops hold a bright future to address the malnutrition challenge.

Characterization of Agronomy, Grain Physicochemical Quality, and Nutritional Property of High-Lysine 35R Transgenic Rice with Simultaneous Modification of Lysine Biosynthesis and Catabolism

Lysine is the first limiting essential amino acid in rice. We previously constructed a series of transgenic rice lines to enhance lysine biosynthesis (35S), down-regulate its catabolism (Ri), or simultaneously achieve both metabolic effects (35R). In this study, nine transgenic lines, three from each group, were selected for both field and animal feeding trials. The results showed that the transgene(s) caused no obvious effects on field performance and main agronomic traits. Mature seeds of transgenic line 35R-17 contained 48-60-fold more free lysine than in wild type and had slightly lower apparent amylose content and softer gel consistency. Moreover, a 35-day feeding experiment showed that the body weight gain, food efficiency, and protein efficiency ratio of rats fed the 35R-17 transgenic rice diet were improved when compared with those fed wild-type rice diet. These data will be useful for further evaluation and potential commercialization of 35R high-lysine transgenic rice.

Improved growth performance, food efficiency, and lysine availability in growing rats fed with lysine-biofortified rice

Rice is an excellent source of protein, and has an adequate balance of amino acids with the exception of the essential amino acid lysine. By using a combined enhancement of lysine synthesis and suppression of its catabolism, we had produced two transgenic rice lines HFL1 and HFL2 (High Free Lysine) containing high concentration of free lysine. In this study, a 70-day rat feeding study was conducted to assess the nutritional value of two transgenic lines as compared with either their wild type (WT) or the WT rice supplemented with different concentrations of L-lysine. The results revealed that animal performance, including body weight, food intake, and food efficiency, was greater in the HFL groups than in the WT group. Moreover, the HFL diets had increased protein apparent digestibility, protein efficiency ratio, and lysine availability than the WT diet. Based on the linear relationship between dietary L-lysine concentrations and animal performance, it indicated that the biological indexes of the HFL groups were similar or better than that of the WT20 group, which was supplemented with L-lysine concentrations similar to those present in the HFL diets. Therefore, lysine-biofortified rice contributed to improved growth performance, food efficiency, and lysine availability in growing rats.

Subchronic feeding study of high-free-lysine transgenic rice in Sprague-Dawley rats

Lysine is considered to be the first essential amino acid in rice. An elite High-Free-Lysine transgenic line HFL1 was previously produced by metabolic engineering to regulate lysine metabolism. In this study, a 90-day toxicology experiment was undertaken to investigate the potential health effect of feeding different doses of HFL1 rice to Sprague-Dawley rats. During the trial, body weight gain, food consumption and food efficiency were recorded, and no adverse effect was observed in rats fed transgenic (T) rice diets compared with non-transgenic (N) or control diets. At both midterm and final assessments, hematological parameters and serum chemistry were measured, and organ weights and histopathology were examined at the end of the trial. There was no diet-related difference in most hematological or serum chemistry parameters or organ weights between rats fed the T diets and those fed the N or control diets. Some parameters were found to differ between T groups and their corresponding N and/or control groups, but no adverse histological effect was observed. Taken together, the data from the current trial demonstrates that high lysine transgenic rice led to no adverse effect in Sprague-Dawley rats given a diet containing up to 70% HFL1 rice in 90 days.

Differential distribution of amino acids in plants

Plants are a rich source of amino acids and their individual abundance in plants is of great significance especially in terms of food. Therefore, it is of utmost necessity to create a database of the relative amino acid contents in plants as reported in literature. Since in most of the cases complete analysis of profiles of amino acids in plants was not reported, the units used and the methods applied and the plant parts used were different, amino acid contents were converted into relative units with respect to lysine for statistical analysis. The most abundant amino acids in plants are glutamic acid and aspartic acid. Pearson's correlation analysis among different amino acids showed that there were no negative correlations between the amino acids. Cluster analysis (CA) applied to relative amino acid contents of different families. Alismataceae, Cyperaceae, Capparaceae and Cactaceae families had close proximity with each other on the basis of their relative amino acid contents. First three components of principal component analysis (PCA) explained 79.5% of the total variance. Factor analysis (FA) explained four main underlying factors for amino acid analysis. Factor-1 accounted for 29.4% of the total variance and had maximum loadings on glycine, isoleucine, leucine, threonine and valine. Factor-2 explained 25.8% of the total variance and had maximum loadings on alanine, aspartic acid, serine and tyrosine. 14.2% of the total variance was explained by factor-3 and had maximum loadings on arginine and histidine. Factor-4 accounted 8.3% of the total variance and had maximum loading on the proline amino acid. The relative content of different amino acids presented in this paper is alanine (1.4), arginine (1.8), asparagine (0.7), aspartic acid (2.4), cysteine (0.5), glutamic acid (2.8), glutamine (0.6), glycine (1.0), histidine (0.5), isoleucine (0.9), leucine (1.7), lysine (1.0), methionine (0.4), phenylalanine (0.9), proline (1.1), serine (1.0), threonine (1.0), tryptophan (0.3), tyrosine (0.7) and valine (1.2).