Genetic Manipulation for Improved Nutritional Quality in Rice

The recent genetic modification techniques for improve soil conservation, nutrient uptake and utilization

Advances in genetic modification (GM) techniques have generated huge interest in improving nutrient utilization, maximizing nutrient uptake, and conserving soil in the pursuit of sustainable agriculture. Unfortunately, little is still known about the recent advancements in the application of GM tactics to enhance each of these areas. This review explores the latest GM strategies intended to support soil conservation, maximize nutrient uptake, and improve nutrient utilization in farming, highlighting the critical roles that soil health and nutrient management play in sustainable farming. GM strategies such as improving the efficiency of nutrient uptake through enhanced root systems and increased nutrient transport mechanisms are well discussed. This study suggests that addressing potential obstacles, such as ethical and regulatory concerns, is a necessity for long-term sustainability applications of GM technologies to raise agricultural yields.

Improving Rice Grain Quality Through Ecotype Breeding for Enhancing Food and Nutritional Security in Asia-Pacific Region

Rice grain is widely consumed as a staple food, providing essential nutrition for households, particularly marginalized families. It plays a crucial role in ensuring food security, promoting human nutrition, supporting good health, and contributing to global food and nutritional security. Addressing the diverse quality demands of emerging diverse and climate-risked population dietary needs requires the development of a single variety of rice grain that can meet the various dietary and nutritional requirements. However, there is a lack of concrete definition for rice grain quality, making it challenging to cater to the different demands. The lack of sufficient genetic study and development in improving rice grain quality has resulted in widespread malnutrition, hidden hunger, and micronutrient deficiencies affecting a significant portion of the global population. Therefore, it is crucial to identify genetically evolved varieties with marked qualities that can help address these issues. Various factors account for the declining quality of rice grain and requires further study to improve their quality for healthier diets. We characterized rice grain quality using Lancastrians descriptor and a multitude of intrinsic and extrinsic quality traits. Next, we examined various components of rice grain quality favored in the Asia-Pacific region. This includes preferences by different communities, rice industry stakeholders, and value chain actors. We also explored the biological aspects of rice grain quality in the region, as well as specific genetic improvements that have been made in these traits. Additionally, we evaluated the factors that can influence rice grain quality and discussed the future directions for ensuring food and nutritional security and meeting consumer demands for grain quality. We explored the diverse consumer bases and their varied preferences in Asian-Pacific countries including India, China, Nepal, Bhutan, Vietnam, Sri Lanka, Pakistan, Thailand, Cambodia, Philippines, Bangladesh, Indonesia, Korea, Myanmar and Japan. The quality preferences encompassed a range of factors, including rice head recovery, grain shape, uniform size before cooking, gelatinization, chalkiness, texture, amylose content, aroma, red-coloration of grain, soft and shine when cooked, unbroken when cooked, gelatinization, less water required for cooking, gelatinization temperature (less cooking time), aged rice, firm and dry when cooked (gel consistency), extreme white, soft when chewed, easy-to-cook rice (parboiled rice), vitamins, and minerals. These preferences were evaluated across high, low, and medium categories. A comprehensive analysis is provided on the enhancement of grain quality traits, including brown rice recovery, recovery rate of milled rice, head rice recovery, as well as morphological traits such as grain length, grain width, grain length-width ratio, and grain chalkiness. We also explored the characteristics of amylose, gel consistency, gelatinization temperature, viscosity, as well as the nutritional qualities of rice grains such as starch, protein, lipids, vitamins, minerals, phytochemicals, and bio-fortification potential. The various factors that impact the quality of rice grains, including pre-harvest, post-harvest, and genotype considerations were explored. Additionally, we discussed the future direction and genetic strategies to effectively tackle these challenges. These qualitative characteristics represent the fundamental focus of regional and national breeding strategies employed by different countries to meet consumer preference. Given the significance of rice as a staple food in Asia-Pacific countries, it is primarily consumed domestically, with only a small portion being exported internationally. All the important attributes must be clearly defined within specific parameters. It is crucial for geneticists and breeders to develop a rice variety that can meet the diverse demands of consumers worldwide by incorporating multiple desirable traits. Thus, the goal of addressing global food and nutritional security, and human healthy can be achieved.

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.

Matrix Metalloproteinase-9 Testing of Golden Rice Cookies With Piper Crocatum Active Extract for Preventing Foot Ulcers in Patients With Diabetes: Protocol for a Randomized Controlled Trial

BACKGROUND

Diabetic foot ulcers (DFUs) present a formidable challenge to both patients and health care systems. DFUs significantly reduce the quality of life for patients, prolong hospital stays, and are the cause of approximately 70,000 lower limb amputations across the globe annually. Prevention of DFUs primarily involves the optimization of blood sugar levels and the effective management of complications, particularly peripheral neuropathy. Golden Rice has been proven to lower blood sugar levels due to its beta-carotene content, and Piper crocatum (P. crocatum) has been found to be effective in reducing the risk factors of DFUs through biomolecular regulation because of its polyphenol content.

OBJECTIVE

The principal objective of this study is to identify the efficacy of P. crocatum-enriched cookies, with Golden Rice as their primary ingredient, in preventing DFUs. The evaluation will center on their impact on the expression of matrix metalloproteinase-9 (MMP-9), a pivotal factor in the development of DFUs.

METHODS

This study is an experimental clinical research that follows the randomized controlled trial method and uses a single-blind design. The participants in the study are outpatients from primary health centers in Makassar, Indonesia, who have been diagnosed with diabetes mellitus. The sample for the study will be randomly selected and subsequently categorized into 2 groups: the intervention group and the control group. The intervention group consumes P. crocatum-enriched Golden Rice cookies, while the control group receives cookies without these additives. The participants from both groups will consume their respective cookies (packaged identically) twice a day for 14 days. The cookies will be prepared according to a modified recipe with an emphasis on low glucose content, resulting in 51 calories per cookie, comprising 1% carbohydrates, 6% fat, 4% cholesterol, and 4% fiber, excluding gluten, sugar, and salt. They will be baked at 158°C for 20 minutes. The process involves the addition of 20% Golden Rice and 10% P. crocatum ethanol extract, both prepared via maceration with 96% ethanol. The dependent variable in this study is the expression of gelatinases matrix metalloproteinase, to be assessed at 2 distinct time points-preintervention (pretest) and postintervention (posttest)-with the evaluation conducted through the western blotting method.

RESULTS

The recruitment and testing phase started in January 2024. The study is scheduled to be completed by the end of March 2024. Data analysis will commence in April 2024, and the publication of the results is anticipated in the same year (2024). The study will report on the changes in primary data, encompassing gelatinases matrix metalloproteinase, as well as secondary data, including the ankle-brachial index, neuropathy score, and random blood glucose level.

CONCLUSIONS

The findings of this trial are expected to significantly impact the selection of strategies by health care practitioners to enhance diabetes self-management, particularly in the domain of therapeutic snacking, for patients diagnosed with diabetes mellitus.

TRIAL REGISTRATION

Thai Clinical Trials Registry TCTR20230502001; https://www.thaiclinicaltrials.org/show/TCTR20230502001.

INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID)

PRR1-10.2196/49940.

Dual functional roles of nutritional additives in nutritional fortification and safety of thermally processed food: Potential, limitations, and perspectives

The Maillard reaction (MR) has been established to be a paramount contributor to the characteristic sensory property of thermally processed food products. Meanwhile, MR also gives rise to myriads of harmful byproducts (HMPs) (e.g., advanced glycation end products (AGEs) and acrylamide). Nutritional additives have attracted increasing attention in recent years owing to their potential to simultaneously improve nutritional quality and attenuate HMP formation. In this manuscript, a brief overview of various nutritional additives (vitamins, minerals, fatty acids, amino acids, dietary fibers, and miscellaneous micronutrients) in heat-processed food is provided, followed by a summary of the formation mechanisms of AGEs and acrylamide highlighting the potential crosstalk between them. The main body of the manuscript is on the capability of nutritional additives to modulate AGE and acrylamide formation besides their traditional roles as nutritional enhancers. Finally, limitations/concerns associated with their use to attenuate dietary exposure to HMPs and future perspectives are discussed. Literature data support that through careful control of the addition levels, certain nutritional additives possess promising potential for simultaneous improvement of nutritional value and reduction of AGE and acrylamide content via multiple action mechanisms. Nonetheless, there are some major concerns that may limit their wide applications for achieving such dual functions, including influence on sensory properties of food products, potential overestimation of nutrition enhancement, and introduction of hazardous alternative reaction products or derivatives. These could be overcome through comprehensive assay of dose-response relationships and systematic evaluation of the diverse combinations from the same and/or different categories of nutritional additives to establish synergistic mixtures.

Raman Multi-Omic Snapshots of Koshihikari Rice Kernels Reveal Important Molecular Diversities with Potential Benefits in Healthcare

This study exploits quantitative algorithms of Raman spectroscopy to assess, at the molecular scale, the nutritional quality of individual kernels of the Japanese short-grain rice cultivar Koshihikari in terms of amylose-to-amylopectin ratio, fractions of phenylalanine and tryptophan aromatic amino acid residues, protein-to-carbohydrate ratio, and fractions of protein secondary structures. Statistical assessments on a large number of rice kernels reveal wide distributions of the above nutritional parameters over nominally homogeneous kernel batches. This demonstrates that genetic classifications cannot catch omic fluctuations, which are strongly influenced by a number of extrinsic factors, including the location of individual grass plants within the same rice field and the level of kernel maturation. The possibility of collecting nearly real-time Raman "multi-omic snapshots" of individual rice kernels allows for the automatic (low-cost) differentiation of groups of kernels with restricted nutritional characteristics that could be used in the formulation of functional foods for specific diseases and in positively modulating the intestinal microbiota for protection against bacterial infection and cancer prevention.

Explicating genetic architecture governing nutritional quality in pigmented rice

Rice is one of the most important staple plant foods that provide a major source of calories and nutrients for tackling the global hunger index especially in developing countries. In terms of nutritional profile, pigmented rice grains are favoured for their nutritional and health benefits. The pigmented rice varieties are rich sources of flavonoids, anthocyanin and proanthocyanidin that can be readily incorporated into diets to help address various lifestyle diseases. However, the cultivation of pigmented rice is limited due to low productivity and unfavourable cooking qualities. With the advances in genome sequencing, molecular breeding, gene expression analysis and multi-omics approaches, various attempts have been made to explore the genetic architecture of rice grain pigmentation. In this review, we have compiled the current state of knowledge of the genetic architecture and nutritional value of pigmentation in rice based upon the available experimental evidence. Future research areas that can help to deepen our understanding and help in harnessing the economic and health benefits of pigmented rice are also explored.

Enhancing micronutrient absorption through simultaneous fortification and phytic acid degradation

Phytic acid (PA), an endogenous antinutrient in cereals and legumes, hinders mineral absorption by forming less bioavailable, stable PA-mineral complexes. For individual micronutrients, the PA-to-mineral molar ratio below the critical level ensures better bioavailability and is achieved by adding minerals or removing PA from cereals and pulses. Although several PA reduction and fortification strategies are available, the inability to completely eradicate or degrade PA using available techniques always subdues fortification's impact by hindering fortified micronutrient absorption. The bioavailability of micronutrients could be increased through simultaneous PA degradation and fortification. Following primary PA reduction of the raw material, the fortification step should also incorporate additional essential control stages to further PA inactivation, improving micronutrient absorption. In this review, the chemistry of PA interaction with metal ions, associated controlling parameters, and its impact on PA reduction during fortification is also evaluated, and further suggestions were made for the fortification's success.

The changing landscape of agriculture: role of precision breeding in developing smart crops

Food plants play a crucial role in human survival, providing them essential nutrients. However, traditional breeding methods have not been able to keep up with the demands of the growing population. The improvement of food plants aims to increase yield, quality, and resistance to biotic and abiotic stresses. With CRISPR/Cas9, researchers can identify and edit key genes conferring desirable qualities in agricultural plants, including increased yield, enhanced product quality attributes, and increased tolerance to biotic and abiotic challenges. These modifications have enabled the creation of "smart crops" that exhibit rapid climatic adaptation, resistance to extreme weather conditions and high yield and quality. The use of CRISPR/Cas9 combined with viral vectors or growth regulators has made it possible to produce more efficient modified plants with certain conventional breeding methods. However, ethical and regulatory aspects of this technology must be carefully considered. Proper regulation and application of genome editing technology can bring immense benefits to agriculture and food security. This article provides an overview of genetically modified genes and conventional as well as emerging tools, including CRISPR/Cas9, that have been utilized to enhance the quality of plants/fruits and their products. The review also discusses the challenges and prospects associated with these techniques.

Regulatory roles of noncoding RNAs in callus induction and plant cell dedifferentiation

Plant regulatory noncoding RNAs (ncRNAs) have emerged as key modulators of gene expression during callus induction. Their further study may promote the design of innovative plant tissue culture protocols. The use of plants by humans has recently taken on a new and expanding insight due to the advent of genetic engineering technologies. In this context, callus cultures have shown remarkable potential for synthesizing valuable biomolecules, crop improvement, plant micropropagation, and biodiversity preservation. A crucial stage in callus production is the conversion of somatic cells into totipotent cells; compelling evidence indicates that stress factors, transcriptional regulators, and plant hormones can trigger this biological event. Besides, posttranscriptional regulators of gene expression might be essential participants in callus induction. However, research related to the analysis of noncoding RNAs (ncRNAs) that modulate callogenesis and plant cell dedifferentiation in vitro is still at an early stage. During the last decade, some relevant studies have enlightened the fact that different classes of ncRNAs, such as microRNAs (miRNAs), small interfering RNAs (siRNAs), and long noncoding RNAs (lncRNAs) are implicated in plant cell dedifferentiation through regulating the expression levels of diverse gene targets. Hence, understanding the molecular relevance of these ncRNAs in the aforesaid biological processes might represent a promising source of new biotechnological approaches for callus culture and plant improvement. In this current work, we review the experimental evidence regarding the prospective roles of ncRNAs in callus induction and plant cell dedifferentiation to promote this field of study.

Impacts of Climate Change on Rice Grain: A Literature Review on What Is Happening, and How Should We Proceed?

More than half of the people on Earth get their calories, proteins, and minerals from rice grains. Staple increases in the quantity and quality of rice grains are key to ending hunger and malnutrition. Rice production, however, is vulnerable to climate change, and the climate on Earth is becoming more fluctuating with the atmospheric change induced by human activities. As a result, the impacts of climate change on rice grain (ICCRG) have sparked widespread concern. In order to reveal the development and the trend in the study on the ICCRG, a bibliometric analysis was conducted. The results showed that both the model simulations and the field experiment-based observations, as reflected by APSIM (the Agricultural Production Systems sIMulator) and free-air carbon dioxide (CO₂) enrichment, are of concern to researchers worldwide, especially in China, India, the United States, and Japan. Different types of warming include short-term, nighttime, soil and water, and canopy, and their interactions with other climate factors, such as CO₂, or agronomic factors, such as nitrogen level, are also of concern to researchers. Spatiotemporal variations in changing weather and regional adaptations from developed and developing countries are challenging the evaluation of ICCRG from an economic perspective. In order to improve the efficacy of breeding adaptable cultivars and developing agronomic management, interdisciplinary studies integrating molecular biology, plant physiology, agronomy, food chemistry, ecology, and socioeconomics are needed.

Improving yield and quality of rice under acid rain stress by regulating nitrogen assimilation with exogenous Ca2

Acid rain threatens crop yield and nutritional quality, and Ca²⁺ can regulate plant responses to abiotic stresses. To improve the yield and nutritional quality of crops under acid rain stress, we applied exogenous Ca²⁺ to regulate nitrogen assimilation in rice seedlings under simulated acid rain stress (pH 4.5 or 3.0), taking yield and nutritional quality of rice as evaluation criteria. We found that Ca²⁺ (5 mM) maintained the total nitrogen content of rice at the seedling and booting stages to alleviate the inhibitory effect of simulated acid rain on rice yield. Meanwhile, Ca²⁺ improved the activity of glutamate synthase to eliminate the disruption of glutamine synthetase/glutamate synthase balance under simulated acid rain. It decreased the efficiency of nitrogen assimilation, thereby reducing the inhibition of essential amino acid content in rice. The mitigation effect on simulated acid rain at pH 4.5 was better than that of simulated acid rain at pH 3.0. Overall, Ca²⁺ may reduce the negative effect of acid rain on the yield and nutritional quality of crops.

A tale of two metals: Biofortification of rice grains with iron and zinc

Iron (Fe) and zinc (Zn) are essential micronutrients needed by virtually all living organisms, including plants and humans, for proper growth and development. Due to its capacity to easily exchange electrons, Fe is important for electron transport in mitochondria and chloroplasts. Fe is also necessary for chlorophyll synthesis. Zn is a cofactor for several proteins, including Zn-finger transcription factors and redox metabolism enzymes such as copper/Zn superoxide dismutases. In humans, Fe participates in oxygen transport, electron transport, and cell division whereas Zn is involved in nucleic acid metabolism, apoptosis, immunity, and reproduction. Rice (Oryza sativa L.) is one of the major staple food crops, feeding over half of the world's population. However, Fe and Zn concentrations are low in rice grains, especially in the endosperm, which is consumed as white rice. Populations relying heavily on rice and other cereals are prone to Fe and Zn deficiency. One of the most cost-effective solutions to this problem is biofortification, which increases the nutritional value of crops, mainly in their edible organs, without yield reductions. In recent years, several approaches were applied to enhance the accumulation of Fe and Zn in rice seeds, especially in the endosperm. Here, we summarize these attempts involving transgenics and mutant lines, which resulted in Fe and/or Zn biofortification in rice grains. We review rice plant manipulations using ferritin genes, metal transporters, changes in the nicotianamine/phytosiderophore pathway (including biosynthetic genes and transporters), regulators of Fe deficiency responses, and other mutants/overexpressing lines used in gene characterization that resulted in Fe/Zn concentration changes in seeds. This review also discusses research gaps and proposes possible future directions that could be important to increase the concentration and bioavailability of Fe and Zn in rice seeds without the accumulation of deleterious elements. We also emphasize the need for a better understanding of metal homeostasis in rice, the importance of evaluating yield components of plants containing transgenes/mutations under field conditions, and the potential of identifying genes that can be manipulated by gene editing and other nontransgenic approaches.

Using synthetic biology to improve photosynthesis for sustainable food production

Photosynthesis is responsible for the primary productivity and maintenance of life on Earth, boosting biological activity and contributing to the maintenance of the environment. In the past, traditional crop improvement was considered sufficient to meet food demands, but the growing demand for food coupled with climate change has modified this scenario over the past decades. However, advances in this area have not focused on photosynthesis per se but rather on fixed carbon partitioning. In short, other approaches must be used to meet an increasing agricultural demand. Thus, several paths may be followed, from modifications in leaf shape and canopy architecture, improving metabolic pathways related to CO₂ fixation, the inclusion of metabolic mechanisms from other species, and improvements in energy uptake by plants. Given the recognized importance of photosynthesis, as the basis of the primary productivity on Earth, we here present an overview of the latest advances in attempts to improve plant photosynthetic performance. We focused on points considered key to the enhancement of photosynthesis, including leaf shape development, RuBisCO reengineering, Calvin-Benson cycle optimization, light use efficiency, the introduction of the C₄ cycle in C₃ plants and the inclusion of other CO₂ concentrating mechanisms (CCMs). We further provide compelling evidence that there is still room for further improvements. Finally, we conclude this review by presenting future perspectives and possible new directions on this subject.

Impact of ultrasonication applications on color profile of foods

Food color is a feature that provides preliminary information about their preference or consumption. There are dominant pigments that determine the color of each food; the most important pigments are anthocyanins (red-purple color), chlorophylls (green color), carotenoids (yellow-orange color), and betalains (red color). These pigments can be easily affected by temperature, light, oxygen, or pH, thereby altering their properties. Therefore, while processing, it is necessary to prevent the deterioration of these pigments to the maximum possible extent. Ultrasonication, which is one of the emerging non-thermal methods, has multidimensional applications in the food industry. The present review collates information on various aspects of ultrasonication technology, its mechanism of action, influencing factors, and the competence of different ultrasonication applications (drying, irradiation, extraction, pasteurization, cooking, tempering, etc.) in preserving the color of food. It was concluded that ultrasonication treatments provide low-temperature processing at a short time, which positively influences the color properties. However, selecting optimum ultrasonic processing conditions (frequency, power, time, etc.) is crucial for each food to obtain the best color. The key challenges and limitations of the technique and possible future applications are also covered in the paper, serving as a touchstone for further research in this area.

FE-SEM/EDX Based Zinc Mobilization Analysis of Burkholderia cepacia and Pantoea rodasii and Their Functional Annotation in Crop Productivity, Soil Quality, and Zinc Biofortification of Paddy

The experimental study was contrived to characterize two zinc-solubilizing bacteria (ZSB), namely BMRR126 and BMAR64, and their role in zinc (Zn) biofortification of rice. These bacteria solubilized Zn profoundly, determined qualitatively by halo-zone formation on a solid medium and quantitatively in a liquid broth by AAS and SEM-EDX. The lowering of pH and contact angle assessment of the liquid broth unveiled the establishment of the acidic conditions in a medium suitable for Zn solubilization. The characterization of both isolates on the basis of 16S rRNA gene analysis was identified as Burkholderia cepacia and Pantoea rodasii, respectively. These strains were also found to have some plant probiotic traits namely phosphate solubilization, production of siderophore, indole acetic acid (IAA), exopolysaccharide (EPS), and ammonia. The field experiments were performed at two diverse locations and under all treatments; the simultaneous use of BMRR126 and BMAR64 with zinc oxide (ZnO) resulted in the highest growth and productivity of the paddy crop. The utmost Zn achievement in the grain was estimated in a treatment (T9) (25.07 mg/kg) containing a consortium of BMRR126 and BMAR64 along with ZnO for the Terai region. The treatment containing single ZSB bioinoculant BMRR126 (T7) showed an elevated Zn amount in the rice grain (33.25 mg/kg) for the Katchar region. The soil parameters (pH, EC, organic carbon, NPK, available Zn, and dehydrogenase activity) were also positively influenced under all bacterial treatments compared to the uninoculated control. Our study clearly accentuates the need for Zn solubilizing bacteria (ZSB) to provide the benefits of Zn-biofortification in different regions.

Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice

Nutritional quality improvement of rice is the key to ensure global food security. Consequently, enormous efforts have been made to develop genomics and transcriptomics resources for rice. The available omics resources along with the molecular understanding of trait development can be utilized for efficient exploration of genetic resources for breeding programs. In the present study, 80 genes known to regulate the nutritional and cooking quality of rice were extensively studied to understand the haplotypic variability and gene expression dynamics. The haplotypic variability of selected genes were defined using whole-genome re-sequencing data of ~4700 diverse genotypes. The analytical workflow identified 133 deleterious single-nucleotide polymorphisms, which are predicted to affect the gene function. Furthermore, 788 haplotype groups were defined for 80 genes, and the distribution and evolution of these haplotype groups in rice were described. The nucleotide diversity for the selected genes was significantly reduced in cultivated rice as compared with that in wild rice. The utility of the approach was successfully demonstrated by revealing the haplotypic association of chalk5 gene with the varying degree of grain chalkiness. The gene expression atlas was developed for these genes by analyzing RNA-Seq transcriptome profiling data from 102 independent sequence libraries. Subsequently, weighted gene co-expression meta-analyses of 11,726 publicly available RNAseq libraries identified 19 genes as the hub of interactions. The comprehensive analyses of genetic polymorphisms, allelic distribution, and gene expression profiling of key quality traits will help in exploring the most desired haplotype for grain quality improvement. Similarly, the information provided here will be helpful to understand the molecular mechanism involved in the development of nutritional and cooking quality traits in rice.

Plant Molecular Farming, a Tool for Functional Food Production

The demand of functional food is increasing for improving human health. Plant molecular farming (PMF) employs plants as bioreactors for the production of pharmaceuticals. Now PMF has been used to produce antibodies, vaccines, and medicinal proteins, but it has not been well-studied for production of nutraceuticals and functional food. In this perspective, we extend the concept of PMF, present an updated overview of PMF for functional food development, including the progress, problem, and strategy, and then speculate how to use the PMF strategy to produce functional foods, especially with four major staple food crops (rice, wheat, maize, and soybean). Finally, we discuss the opportunities and challenges of PMF on functional food production in the future.

A Comparative Metabolomic Analysis Reveals the Nutritional and Therapeutic Potential of Grains of the Traditional Rice Variety Mappillai Samba

Rice (Oryza sativa L.) is the staple food of the majority of the population, particularly in Asia and Africa. Enriching rice with nutritional and therapeutic contents can improve its benefits for patients with lifestyle disorders. This study aimed to profile the phytochemical contents of the therapeutically known traditional rice Mappillai Samba against white rice CBMAS 14065 using non-targeted gas chromatography-mass spectrometry (GC-MS/MS). An analysis of the data using a mass spectrometry-data independent analysis (MS-DIAL) and MetaboAnalyst identified 113 metabolites belonging to 21 different classes of metabolites. A partial least square-discriminant analysis (PLS-DA) revealed 43 variable importance in projection (VIP) metabolites. This study identified therapeutically important metabolites, including phenylpropanoids, phytosterols, flavonoids, and polyamines, in the grains of Mappillai Samba. Three significant metabolic pathways, viz., phenylpropanoid biosynthesis, ubiquinone and other terpenoid-quinone biosynthesis, and steroid biosynthesis, were responsible for the grain metabolome variation between CBMAS 14065 and Mappillai Samba. Overall, the results of this study unravelled the biochemical complexity of Mappillai Samba, paving the way for the genetic mapping of the therapeutic compound accumulation in rice and the development of similar therapeutic rice varieties through molecular breeding.

GWAS to spot candidate genes associated with grain quality traits in diverse rice accessions of North East India

INTRODUCTION

North East (NE) India is the second centre for the origin of rice and is enriched with a diverse collection of traditional rice accessions. These genotypes possess unique traits of breeding interest and are rich in grain nutritional and cooking qualities. Therefore, quantitative trait loci (QTLs)/genes associated with the various quality traits may be identified through genome-wide association studies (GWAS) and used in crop improvement programmes.

METHODS AND RESULTS

A pool of 526 unique rice accessions from Assam, North East (NE) India were characterized by using 9 grain-quality traits and grouped into 16 clusters. Among these, the highest number of 156 (29.65%) genotypes belongs to diverse phenotypic classes; Sali, Lahi, and Chokuwa were grouped into cluster 6. The first three principal components showed 54.76% of morphological variability with Eigenvalue >1. Genome-wide association studies (GWAS) was performed in 103 rice accessions using 42,446 SNP markers. A total of 11 significant marker-trait associations were detected for 5 grain-quality traits, explaining 0.22-8.86% of phenotypic variation (PV). In-silico mining of QTLs detected 'candidate genes' associated with the quality traits.

CONCLUSIONS

The phenotypic diversity among the 526 rice accessions of NE India was studied using grain quality traits and grouped into 16 significantly different clusters. The QTLs, or candidate genes identified for various grain quality traits, may be used in breeding programmes for the development of improved rice varieties.

Raman Molecular Fingerprints of Rice Nutritional Quality and the Concept of Raman Barcode

The nutritional quality of rice is contingent on a wide spectrum of biochemical characteristics, which essentially depend on rice genome, but are also greatly affected by growing/environmental conditions and aging during storage. The genetic basis and related identification of genes have widely been studied and rationally linked to accumulation of micronutrients in grains. However, genetic classifications cannot catch quality fluctuations arising from interannual, environmental, and storage conditions. Here, we propose a quantitative spectroscopic approach to analyze rice nutritional quality based on Raman spectroscopy, and disclose analytical algorithms for the determination of: (i) amylopectin and amylose concentrations, (ii) aromatic amino acids, (iii) protein content and structure, and (iv) chemical residues. The proposed Raman algorithms directly link to the molecular composition of grains and allow fast/non-destructive determination of key nutritional parameters with minimal sample preparation. Building upon spectroscopic information at the molecular level, we newly propose to represent the nutritional quality of labeled rice products with a barcode specially tailored on the Raman spectrum. The Raman barcode, which can be stored in databases promptly consultable with barcode scanners, could be linked to diet applications (apps) to enable a rapid, factual, and unequivocal product identification based on direct molecular screening.

A fluorescence biosensor based on single-stranded DNA and carbon quantum dots for acrylamide detection

As a potential carcinogen produced in food thermal processing, acrylamide (AM) can cause irreversible harm to human health. For the detection of AM in food products, a simple fluorescent biosensor based on single-stranded DNA (ssDNA) and carbon quantum dots (CQDs) was developed. Reduced fluorescence intensity of CQDs at 445 nm (excitation at 350 nm) was induced by the attachment of ssDNA. In the presence of AM, ssDNA was preferentially bound to AM by hydrogen bonding and the degree of fluorescence reduction was smaller than that without AM. Under optimized conditions, results showed that the sensing approach for detecting AM had a low detection limit of 2.41 × 10^-8 M in the standard solution, and a linear relationship ranging from 5 × 10^-3 to 1 × 10^-7 M with the determination coefficient (R²) of 0.9895 was obtained. Furthermore, a good recovery percentage (91.36-98.11%) in bread crust showed the potential for practical applications of this proposed biosensor.

Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement

Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.