Investigating glycemic potential of rice by unraveling compositional variations in mature grain and starch mobilization patterns during seed germination

Comprehensive lipidomic insights of differentially accumulating lipids in large pigmented rice sprout collection and the changes in the starch composition upon germination

Germination represents a vital bioprocess characterized by numerous biochemical transformations that significantly influence the nutritional characteristics of rice. The mobilization of starch and lipids during germination plays a pivotal role in altering the dietary profile of rice, thus potentially addressing the nutritional requirements of populations heavily reliant on rice as a staple food. To explore this potential, a comprehensive analysis encompassing lipidomics and starch composition was conducted on a diverse collection of pigmented rice sprouts. High-resolution mass spectrometry unveiled substantial shifts in the lipidome of pigmented rice sprouts, showcasing a notable enrichment in carotenoids and unsaturated triglycerides, with potential human health benefits. Notably, purple rice sprouts exhibited heightened levels of alpha- and beta-carotene. Analysis of starch composition revealed slight changes in amylose and amylopectin content; however, a consistent increase in digestible carbohydrates was observed across all rice varieties. Germination also led to a reduction in resistant starch content, with purple rice sprouts demonstrating a pronounced two-fold decrease (p < 0.05). These changes were corroborated by a 1.33% decrease in gelatinization enthalpy and a 0.40% reduction in the melting of the amylose-lipid complex. Furthermore, pasting property analysis indicated a substantial 42% decrease in the complexation index post-germination. We posit that the insights garnered from this study hold significant promise for the development of novel products enriched with health-promoting lipids and characterized by unique flour properties.

Proline Priming Enhances Seed Vigour and Biochemical Attributes of Rice (Oryza sativa L.) during Germination

Seed vigour is a desirable trait especially for direct seeded rice (DSR) cultivation. Seeds with high vigour could improve seed germination, support seedlings in competing with weeds for water and nutrients, and improving seedling establishment throughout the early stages of crop growth. The success of DSR system which account for more 25% of world cultivation areas is highly dependent on the seed vigour and seedling establishment. Seed priming is a promising technique to improve seed vigour. Proline is an amino acid that has been well studied for its roles in plants under different environmental stress conditions. Nevertheless, the effect of proline as a seed priming agent in improving seed vigour in rice remain elusive. In this research, the effect of 24 h of proline priming at various concentrations (0 mM, 1 mM, 2 mM, 10 mM and 20 mM) on rice seed vigour, amylase activity, and total soluble sugar (TSS) content of a Malaysia indica rice variety, MR269 was investigated. Results showed that seeds primed with lower concentration of proline (0 mM, 1 mM and 2 mM) had better germination responses while priming at high concentrations (10 mM and 20 mM) reduced seed germination. Among the concentration tested, priming with 1 mM proline enhanced seed vigour with significantly higher germination percentage (GP), germination rate index (GRI) and seedling vigour index (SVI). In addition, proline primed seeds also exhibited increased amylase activity and TSS content as compared to unprimed seeds. However, priming seed with 20 mM proline was detrimental to the seed vigour and seedling growth whereby lower GP, GRI and SVI and higher mean germination time (MGT) were observed. In short, this study shows that proline could be a potential seed priming agent to improve seed vigour in rice.

Triple gene mutations boost amylose and resistant starch content in rice: insights from sbe2b/sbe1/OE-Wxa mutants

Previous studies have modified rice's resistant starch (RS) content by mutating single and double genes. These mutations include knocking out or reducing the expression of sbe1 or sbe2b genes, as well as overexpressing Wxa . However, the impact of triple mutant sbe2b/sbe1/OE-Wxa on RS contents remained unknown. Here, we constructed a double mutant with sbe2b/RNAi-sbe1, based on IR36ae with sbe2b, and a triple mutant with sbe2b/RNAi-sbe1/OE-Wxa , based on the double mutant. The results showed that the amylose and RS contents gradually increased with an increase in the number of mutated genes. The triple mutant exhibited the highest amylose and RS contents, with 41.92% and 4.63%, respectively, which were 2- and 5-fold higher than those of the wild type, which had 22.19% and 0.86%, respectively. All three mutants altered chain length and starch composition compared to the wild type. However, there was minimal difference observed among the mutants. The Wxa gene contributed to the improvement of 1000-grain weight and seed-setting rate, in addition to the highest amylose and RS contents. Thus, our study offers valuable insight for breeding rice cultivars with a higher RS content and yields.

The mediation mechanism of calcium ions on black bean type 3 resistant starch: Metabolomics, structure characteristics and digestibility

The type 3 resistant starch (RS3) is beneficial for blood glucose management. A high quality RS3 was provided and its formation mechanism after calcium ion (Ca2+) treatment was investigated in this study. The metabolomics, structure and digestion properties were evaluated. Metabolomics was performed by untargeted UHPLC-Q-TOF/MS, and a total of 11 significantly different metabolites was found. The NMR, ATR-FTIR, and XRD results showed that the degree of double helix decreased from 5.34 to 1.07, crystallinity decreased from 33.58 % to 19.88 %, and the amorphous region increased from 69.76 % to 78.33 %. Large particle polymers were observed by SEM on the granule surface of starch with Ca2+ treatment. Digestion test showed that Ca2+ increased the RS3 from 9.70 % to 22.26 %. The result indicated that Ca2+ induced the formation of chelates between Ca2+ and -OH, promoted the RS3 content and regulated carbohydrate metabolism. The study provided theoretical basis for producing low-glycemic black bean foods.

Health-promoting germinated rice and value-added foods: a comprehensive and systematic review of germination effects on brown rice

Over the last 30 years, thousands of articles have appeared examining the effects of soaking and germinating brown rice (BR). Variable germination conditions and methods have been employed to measure different health-beneficial parameters in a diverse germplasm of BR. Research results may therefore appear inconsistent with occasional anomalies, and it may be difficult to reach consensus concerning expected trends. Herein, we amassed a comprehensive review on germinated brown rice (GBR), attempting to codify 133 peer-reviewed articles regarding the effects on 164 chemical parameters related to health and nutrition in BR and in value-added food products. The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-2020) approach was used to direct the flow of the literature search. A pair-wise comparison t-test was performed to deliver an overall approach indicating when a given compound has been found to significantly increase or decrease through germination, which was grouped into GABA and polyamines, γ-Oryzanol and phytosterols, phenolic compounds, vitamins, proteins and amino acids, starchy carbohydrates, free sugars, lipids, minerals and phytic acid. This resource will stimulate interest in germinating rice and optimistically help increase both production and consumption of highly nutritious, health-beneficial rice with pigmented bran.

Orbitrap Mass Spectrometry-Based Profiling of Secondary Metabolites in Two Unexplored Eminium Species and Bioactivity Potential

The study aimed at the metabolite profiling and evaluation of antioxidant and enzyme inhibitory properties of methanol extracts from flowers, leaves, and tubers of unexplored Eminium intortum (Banks & Sol.) Kuntze and E. spiculatum (Blume) Schott (Araceae). A total of 83 metabolites, including 19 phenolic acids, 46 flavonoids, 11 amino, and 7 fatty acids were identified by UHPLC-HRMS in the studied extracts for the first time. E. intortum flower and leaf extracts had the highest total phenolic and flavonoid contents (50.82 ± 0.71 mg GAE/g and 65.08 ± 0.38 RE/g, respectively). Significant radical scavenging activity (32.20 ± 1.26 and 54.34 ± 0.53 mg TE/g for DPPH and ABTS) and reducing power (88.27 ± 1.49 and 33.13 ± 0.68 mg TE/g for CUPRAC and FRAP) were observed in leaf extracts. E. intortum flowers showed the maximum anticholinesterase activity (2.72 ± 0.03 mg GALAE/g). E. spiculatum leaves and tubers exhibited the highest inhibition towards α-glucosidase (0.99 ± 0.02 ACAE/g) and tirosinase (50.73 ± 2.29 mg KAE/g), respectively. A multivariate analysis revealed that O-hydroxycinnamoylglycosyl-C-flavonoid glycosides mostly accounted for the discrimination of both species. Thus, E. intortum and E. spiculatum can be considered as potential candidates for designing functional ingredients in the pharmaceutical and nutraceutical industries.

More than the main structural genes: Regulation of resistant starch formation in rice endosperm and its potential application

In the past decade, research on resistant starch has evoked interest due to the prevention and inhibition of chronic human diseases, such as diabetes, cancer, and obesity. Increasing the amylose content (AC) and resistant starch (RS) has been pivotal in improving the nutritional benefit of rice. However, the exact mechanism of RS formation is complex due to interconnected genetic factors regulating amylose-amylopectin variation. In this review, we discussed the regulatory factors influencing the RS formation centered on the transcription, post-transcriptional, and post-translational processes. Furthermore, we described the developments in RS and AC levels in rice compared with other high RS cereals. Briefly, we enumerated potential applications of high RS mutants in health, medical, and other industries. We contest that the information captured herein can be deployed for marker-assisted breeding and precision breeding techniques through genome editing to improve rice varieties with enhanced RS content.

The waxy mutation in sorghum and other cereal grains reshapes the gut microbiome by reducing levels of multiple beneficial species

Waxy starches from cereal grains contain >90% amylopectin due to naturally occurring mutations that block amylose biosynthesis. Waxy starches have unique organoleptic characteristics (e.g. sticky rice) as well as desirable physicochemical properties for food processing. Using isogenic pairs of wild type sorghum lines and their waxy derivatives, we studied the effects of waxy starches in the whole grain context on the human gut microbiome. In vitro fermentations with human stool microbiomes show that beneficial taxonomic and metabolic signatures driven by grain from wild type parental lines are lost in fermentations of grain from the waxy derivatives and the beneficial signatures can be restored by addition of resistant starch. These undesirable effects are conserved in fermentations of waxy maize, wheat, rice and millet. We also demonstrate that humanized gnotobiotic mice fed low fiber diets supplemented with 20% grain from isogenic pairs of waxy vs. wild type parental sorghum have significant differences in microbiome composition and show increased weight gain. We conclude that the benefits of waxy starches on food functionality can have unintended tradeoff effects on the gut microbiome and host physiology that could be particularly relevant in human populations consuming large amounts of waxy grains.

Metabolic Variations in Brown Rice Fertilised with Different Levels of Nitrogen

Nitrogen is a necessary element for plant growth; therefore, it is important to study the influence of N fertilisers on crop metabolites. In this study, we investigate the variability of endogenous metabolites in brown rice fertilised with different amounts of nitrogen. We identified 489 metabolites in brown rice. Compared to non-nitrogen fertilised groups, there were 59 differentially activated metabolic pathways in the nitrogen-fertilised groups. Additionally, there were significantly differential secondary metabolites, especially flavonoids, between groups treated with moderate (210 kg N/hm2) and excessive amounts of nitrogen (420 kg N/hm2). Nitrogen fertilisation upregulated linoleic acid metabolism and most steroids, steroid derivatives, and flavonoid compounds, which have antioxidant activity. The DPPH, ABTS, and hydroxyl radical scavenging rates were higher in fertilised groups than in the non-fertilised group. These findings provide a theoretical basis to enhance the health benefits of brown rice by improving fertilisation.

Comparative RNA-Seq analysis unravels molecular mechanisms regulating therapeutic properties in the grains of traditional rice Kavuni

Developing rice varieties with enhanced levels of functional bioactives is an important intervention for achieving food and nutritional security in Asia where rice is the staple food and Type II diabetes incidences are higher. The present study was aimed at dissecting out the molecular events underlying the accumulation of bio active compounds in pigmented traditional rice Kavuni. Comparative transcriptome profiling in the developing grains of Kavuni and a white rice variety ASD 16 generated 37.7 and 29.8 million reads respectively. Statistical analysis identified a total of 9177 exhibiting significant differential expression (DEGs) between the grains of Kavuni and ASD 16. Pathway mapping of DEGs revealed the preferential up-regulation of genes involved in the biosynthesis of amylose and dietary fibres in Kavuni accounting for its low glycemic index (GI). Transcripts involved in the biosynthesis of carotenoids, flavonoids, anthocyanins, phenolic acids and phenylpropanoids were also found to be up-regulated in the grains of Kavuni. This study identified up-regulation of key transcripts involved in the accumulation of phenolic acids having potential for inhibiting major hydrolytic enzymes α-amylase and α-glucosidase and thus accounting for the slow digestibility leading to low GI. Overall, this study has identified molecular targets for the genetic manipulation of anti-diabetic and anti-oxidant traits in rice.

The Impact of Rice Lipid on In Vitro Rice Starch Digestibility

The negative role of lipids in rice starch digestion is well-known; however, the effect of individual native lipids on starch digestibility has not been studied. In this study, native rice lipids, such as triacylglycerols (TAGs), diacylglycerols (DAGs), phosphatidylcholines (PCs) and lysophospholipids (LPLs), were analyzed using liquid chromatography−mass spectrometry (LC-MS) and correlated with in vitro rice starch digestibility. Most of the tested lipids exhibited a negative correlation with the in vitro starch digestibility with the correlations being more pronounced for LPLs. Removal of lipids from rice flour increased the in vitro starch digestibility. Conversely, a lipid extract addition to rice flour reduced the starch digestibility. Addition of 1% pure lysophosphatidylcholine (LPC)16:0, TAG54:6, DAG36:4 or PC36:2 individually to rice flour reduced starch digestibility by different extents in the order of LPC16:0 > TAG54:6 > PC36:2 > DAG36:4. LPC16:0 was the most abundant lipid among all the assessed lipids in the white rice (milled rice), and addition of 1% LPC 16:0 to rice flour reduced glucose release following three hours of in vitro starch digestion by 7.4%. There may be a scope to breed rice with a lipid composition to reach a desired starch digestibility or simply through addition of certain lipids before cooking the rice.

Transcriptomics View over the Germination Landscape in Biofortified Rice

Hidden hunger, or micronutrient deficiency, is a worldwide problem. Several approaches are employed to alleviate its effects (e.g., promoting diet diversity, use of dietary supplements, chemical fortification of processed food), and among these, biofortification is considered as one of the most cost-effective and highly sustainable. Rice is one of the best targets for biofortification since it is a staple food for almost half of the world’s population as a high-energy source but with low nutritional value. Multiple biofortified rice lines have been produced during the past decades, while few studies also reported modifications in germination behavior (in terms of enhanced or decreased germination percentage or speed). It is important to underline that rapid, uniform germination, and seedling establishment are essential prerequisites for crop productivity. Combining the two traits, biofortified, highly-nutritious seeds with improved germination behavior can be envisaged as a highly-desired target for rice breeding. To this purpose, information gathered from transcriptomics studies can reveal useful insights to unveil the molecular players governing both traits. The present review aims to provide an overview of transcriptomics studies applied at the crossroad between biofortification and seed germination, pointing out potential candidates for trait pyramiding.

OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty

To address the future food security in Asia, we need to improve the genetic gain of grain yield while ensuring the consumer acceptance. This study aimed to identify novel genes influencing the number of upper secondary rachis branches (USRB) to elevate superior grains without compromising grain quality by studying the genetic variance of 310 diverse O. sativa var. indica panel using single- and multi-locus genome-wide association studies (GWAS), gene set analyses and gene regulatory network analysis. GWAS of USRB identified 230 significant (q-value < 0.05) SNPs from chromosomes 1 and 2. GWAS targets narrowed down using gene set analyses identified large effect association on an important locus LOC_Os02g50790/LOC_Os02g50799 encoding a nuclear-pore anchor protein (OsTPR). The superior haplotype derived from non-synonymous SNPs identified in OsTPR was specifically associated with increase in USRB with superior grains being low chalk. Through haplotype mining, we further demonstrated the synergy of offering added yield advantage due to superior allele of OsTPR in elite materials with low glycaemic index (GI) property. We further validated the importance of OsTPR using recombinant inbred lines (RILs) population by introgressing a superior allele of OsTPR into elite materials resulted in raise in productivity in high amylose background. This confirmed a critical role for OsTPR in influencing yield while maintaining grain and nutritional quality.

The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition

Brown rice (Oryza sativa) possesses various nutritionally dense bioactive phytochemicals exhibiting a wide range of antioxidant, anti-cancer, and anti-diabetic properties known to promote various human health benefits. However, despite the wide claims made about the importance of brown rice for human nutrition the underlying metabolic diversity has not been systematically explored. Non-targeted metabolite profiling of developing and mature seeds of a diverse genetic panel of 320 rice cultivars allowed quantification of 117 metabolites. The metabolite genome-wide association study (mGWAS) detected genetic variants influencing diverse metabolic targets in developing and mature seeds. We further interlinked genetic variants on chromosome 7 (6.06-6.43 Mb region) with complex epistatic genetic interactions impacting multi-dimensional nutritional targets, including complex carbohydrate starch quality, the glycemic index, antioxidant catechin, and rice grain color. Through this nutrigenomics approach rare gene bank accessions possessing genetic variants in bHLH and IPT5 genes were identified through haplotype enrichment. These variants were associated with a low glycemic index, higher catechin levels, elevated total flavonoid contents, and heightened antioxidant activity in the whole grain with elevated anti-cancer properties being confirmed in cancer cell lines. This multi-disciplinary nutrigenomics approach thus allowed us to discover the genetic basis of human health-conferring diversity in the metabolome of brown rice.

Isolation, modification, and characterization of rice starch with emphasis on functional properties and industrial application: a review

Starch is one of the organic compounds after cellulose found most abundantly in nature. Starch significantly varies in their different properties like physical, chemical, thermal, morphological and functional. Therefore, starch is modified to increase the beneficial characteristics and remove the shortcomings issues of native starches. The modification methods can change the extremely flexible polymer of starch with their modified physical and chemical properties. These altered structural attributes are of great technological values which have a wide industrial potential in food and non-food. Among them, the production of novel starches is mainly one that evolves with new value-added and functional properties is on high industrial demands. This paper provides an overview of the rice starch components and their effect on the technological and physicochemical properties of obtained starch. Besides, the tuned techno-functional properties of the modified starches through chemical modification means are highlighted.HighlightsNative and modified starches varies largely in physicochemical and functional traits.Modified physical and chemical properties of starch can change the extremely flexible polymer of starch.Techno-functional properties of the modified starches through chemical modification means are highlighted.Dual modification improves the starch functionality and increases the industrial applications.Production of novel starches is on high industrial demands because it mainly evolves with new value added and functional properties.

Impact of ultrasonic treatment on rice starch and grain functional properties: A review

As a green, nonthermal, and innovative technology, ultrasonication generates acoustic cavitation in an aqueous medium, developing physical forces that affect the starch chemistry and rice grain characteristics. This review describes the current information on the effect of ultrasonication on the morphological, textural, and physicochemical properties of rice starch and grain. In a biphasic system, ultrasonication introduced fissures and cracks, which facilitated higher uptake of water and altered the rice starch characteristics impacting textural properties. In wholegrain rice, ultrasonic treatment stimulated the production of health-related metabolites, facilitated the higher uptake of micronutrient fortificants, and enhanced the palatability by softening the rice texture. This review provides insights into the future direction on the utilization of ultrasonication for the applications towards the improvement of rice functional properties.

Impact of processing techniques on the glycemic index of rice

Rice is an important starchy staple food and generally, rice varieties are known to have a higher glycemic index (GI). Over the years, the significance of GI on human health is being better understood and is known to be associated with several lifestyle disorders. Apart from the intrinsic characteristics of rice, different food processing techniques are known to have implications on the GI of rice. This work details the effect of domestic and industrial-level processing techniques on the GI of rice by providing an understanding of the resulting physicochemical changes. An attempt has been made to relate the process-dependent digestion behavior, which in turn reflects on the GI. The role of food constituents is elaborated and the various in vitro and in vivo approaches that have been used to determine the GI of foods are summarized. Considering the broader perspective, the effect of cooking methods and additives is explained. Given the significance of the cereal grain, this work concludes with the challenges and key thrust areas for future research.

Promoting Human Nutrition and Health through Plant Metabolomics: Current Status and Challenges

Simple Summary

This review summarizes the status, applications, and challenges of plant metabolomics in the context of crop breeding, food quality and safety, and human nutrition and health. It also highlights the importance of plant metabolomics in elucidating biochemical and genetic bases of traits associated with nutritive and healthy beneficial foods and other plant products to secure food supply, to ensure food quality, to protect humans from malnutrition and other diseases. Meanwhile, this review calls for comprehensive collaborations to accelerate relevant researches and applications in the context of human nutrition and health.

Abstract

Plant metabolomics plays important roles in both basic and applied studies regarding all aspects of plant development and stress responses. With the improvement of living standards, people need high quality and safe food supplies. Thus, understanding the pathways involved in the biosynthesis of nutritionally and healthily associated metabolites in plants and the responses to plant-derived biohazards in humans is of equal importance to meet people’s needs. For each, metabolomics has a vital role to play, which is discussed in detail in this review. In addition, the core elements of plant metabolomics are highlighted, researches on metabolomics-based crop improvement for nutrition and safety are summarized, metabolomics studies on plant natural products including traditional Chinese medicine (TCM) for health promotion are briefly presented. Challenges are discussed and future perspectives of metabolomics as one of the most important tools to promote human nutrition and health are proposed.

In Vitro Glycemic Response of Indigenous Pigmented Rice Cultivars from South India and Influence of Different Carbohydrate Components

Staple diet patterns such as white rice consumption play an important part in the occurrence of chronic lifestyle-related disease like diabetes. This study intended to identify pigmented rice cultivars from India as an alternative to white rice. Nine carbohydrate components were quantified in six red and two black pigmented rice varieties. In vitro starch digestibility was also analyzed and the predicted glycemic index (pGI) was estimated. The relationship between the carbohydrate components and the pGI of the rice varieties was analyzed. The rice varieties, Kattuyanam and Chennangi exhibited high levels of insoluble dietary fibre, total dietary fibre and amylose. High soluble dietary fibre contents were observed in Poonghar and Aruvadam kuruvai. The levels of resistant starch and slowly digestible starch were found to be the highest in Karupakavuni. The results indicated Kattuyanam, Chennangi, Karungkuruvai, and Poonghar to be low pGI rice varieties (< 55). The three varieties, Kesari, Karupakavuni, and Aruvadam kuruvai were categorized under the medium pGI category (56-69). Mapillai samba had a high pGI of 70 which could be due to processing (partially milled and parboiled), but had significantly lower pGI than the white rice, Sona masuri (GI – 76). The dietary fibre components, resistant starch, slowly digestible starch, and the amylose content were negatively correlated with the pGI. Among these components, the insoluble dietary fibre, total dietary fibre, and resistant starch with significantly high (p ≤0.01) correlation were found to be the major determining factors of pGI in the studied pigmented rice cultivars. The inclusion of the identified pigmented rice varieties with low to medium glycemic response in the diet could become a key role in the dietary management of diabetes, especially among the rice-eating population.

Balancing the double-edged sword effect of increased resistant starch content and its impact on rice texture: its genetics and molecular physiological mechanisms

Resistant starch (RS) is the portion of starch that escapes gastrointestinal digestion and acts as a substrate for fermentation of probiotic bacteria in the gut. Aside from enhancing gut health, RS contributes to a lower glycemic index. A genome-wide association study coupled with targeted gene association studies was conducted utilizing a diverse panel of 281 resequenced Indica rice lines comprising of ~2.2 million single nucleotide polymorphisms. Low-to-intermediate RS phenotypic variations were identified in the rice diversity panel, resulting in novel associations of RS to several genes associated with amylopectin biosynthesis and degradation. Selected rice lines encoding superior alleles of SSIIa with medium RS and inferior alleles with low RS groups were subjected to detailed transcriptomic, metabolomic, non-starch dietary fibre (DF), starch structural and textural attributes. The gene regulatory networks highlighted the importance of a protein phosphatase alongside multiple genes of starch metabolism. Metabolomics analyses resulted in the identification of several metabolite hubs (carboxylic acid, sugars and polyamines) in the medium RS group. Among DF, mannose and galactose from the water-insoluble fraction were found to be highly associated with low and medium RS lines, respectively. Starch structural analyses revealed that a moderate increase in RS is also linked to an elevation of amylose 1 and amylose 2 fractions. Although rice lines with medium RS content negatively affected textural and viscosity properties in comparison to low RS, the textural property of medium RS lines was in the same acceptable range as IR64, a rice mega variety popular in Asia.

The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain

Improving the nutritional quality of rice grains through modulation of bioactive compounds and micronutrients represents an efficient means of addressing nutritional security in societies which depend heavily on rice as a staple food. White rice makes a major contribution to the calorific intake of Asian and African populations, but its nutritional quality is poor compared to that of pigmented (black, purple, red orange, or brown) variants. The compounds responsible for these color variations are the flavonoids anthocyanin and proanthocyanidin, which are known to have nutritional value. The rapid progress made in the technologies underlying genome sequencing, the analysis of gene expression and the acquisition of global 'omics data, genetics of grain pigmentation has created novel opportunities for applying molecular breeding to improve the nutritional value and productivity of pigmented rice. This review provides an update on the nutritional value and health benefits of pigmented rice grain, taking advantage of both indigenous and modern knowledge, while also describing the current approaches taken to deciphering the genetic basis of pigmentation.

Transcriptome Analysis and Identification of Genes Associated with Starch Metabolism in Castanea henryi Seed (Fagaceae)

Starch is the most important form of carbohydrate storage and is the major energy reserve in some seeds, especially Castanea henryi. Seed germination is the beginning of the plant's life cycle, and starch metabolism is important for seed germination. As a complex metabolic pathway, the regulation of starch metabolism in C. henryi is still poorly understood. To explore the mechanism of starch metabolism during the germination of C. henryi, we conducted a comparative gene expression analysis at the transcriptional level using RNA-seq across four different germination stages, and analyzed the changes in the starch and soluble sugar contents. The results showed that the starch content increased in 0-10 days and decreased in 10-35 days, while the soluble sugar content continuously decreased in 0-30 days and increased in 30-35 days. We identified 49 candidate genes that may be associated with starch and sucrose metabolism. Three ADP-glucose pyrophosphorylase (AGPase) genes, two nucleotide pyrophosphatase/phosphodiesterases (NPPS) genes and three starch synthases (SS) genes may be related to starch accumulation. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate the expression levels of these genes. Our study combined transcriptome data with physiological and biochemical data, revealing potential candidate genes that affect starch metabolism during seed germination, and provides important data about starch metabolism and seed germination in seed plants.

A High-Throughput In Vitro Assay for Screening Rice Starch Digestibility

The development of rice that can produce slow and steady postprandial glucose in the bloodstream is a response to alarmingly high global rates of obesity and related chronic diseases. However, rice grain quality programs from all over the world currently do not have access to a high-throughput method to distinguish rice breeding materials that are digested slowly. The objective of this study was to develop a high-throughput in vitro assay to screen the digestibility of cooked white rice grains and to investigate its ability to differentiate rice genotypes with a low starch digestibility rate. The digestibility rate and extent of three commercial rice genotypes with diverse GI values (Doongara, Reiziq and Waxy) were successfully differentiated using the protocol. Further investigations with eight rice genotypes indicated the percentage of starch hydrolysed at a single time point of the assay (SH-60) successfully differentiated genotypes with a low digestibility rate (the SH-60 of Doongara and YRL127 was 50% and 59%, respectively) from genotypes with an intermediate or high digestibility rate (SH-60 values were between 64% and 93%). Application of this methodology in rice breeding programs may assist in the screening and development of new varieties with a desirable postprandial glycaemic response.

Integrating a genome-wide association study with a large-scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

Reliably generating rice varieties with low glycaemic index (GI) is an important nutritional intervention given the high rates of Type II diabetes incidences in Asia where rice is staple diet. We integrated a genome-wide association study (GWAS) with a transcriptome-wide association study (TWAS) to determine the genetic basis of the GI in rice. GWAS utilized 305 re-sequenced diverse indica panel comprising ~2.4 million single nucleotide polymorphisms (SNPs) enriched in genic regions. A novel association signal was detected at a synonymous SNP in exon 2 of LOC_Os05g03600 for intermediate-to-high GI phenotypic variation. Another major hotspot region was predicted for contributing intermediate-to-high GI variation, involves 26 genes on chromosome 6 (GI6.1). These set of genes included GBSSI, two hydrolase genes, genes involved in signalling and chromatin modification. The TWAS and methylome sequencing data revealed cis-acting functionally relevant genetic variants with differential methylation patterns in the hot spot GI6.1 region, narrowing the target to 13 genes. Conversely, the promoter region of GBSSI and its alternative splicing allele (G allele of Wxa ) explained the intermediate-to-high GI variation. A SNP (C˃T) at exon-10 was also highlighted in the preceding analyses to influence final viscosity (FV), which is independent of amylose content/GI. The low GI line with GC haplotype confirmed soft texture, while other two low GI lines with GT haplotype were characterized as hard and cohesive. The low GI lines were further confirmed through clinical in vivo studies. Gene regulatory network analysis highlighted the role of the non-starch polysaccharide pathway in lowering GI.

Molecular structure-property relations controlling mashing performance of amylases as a function of barley grain size

In brewing, amylases are key enzymes in hydrolyzing barley starch to sugars, which are utilized in fermentation to produce ethanol. Starch fermentation depends on sugars produced by amylases and starch molecular structure, both of which vary with barley grain size. Grain size is a major industrial specification for selecting barley for brewing. An in-depth study is given of how enzyme activity and starch structure vary with grain size, the impact of these factors on fermentable sugar production, and the underlying mechanisms. Micro-malting and mashing experiments were based on commercial methodologies. Starch molecular structural parameters were obtained using size-exclusion chromatography, and fitted using biosynthesis-based models. Correlation analysis using the resulting parameters showed larger grain sizes contained fewer long amylopectin chains, higher amylase activities and soluble protein level. Medium grain sizes released most sugars during mashing, because of higher starch utilization from the action of amylases, and shorter amylose chains. As starch is the substrate for amylase-driven fermentable sugars production, measuring its structure should be a prime indication for mashing performance, and should be used as an industry specification when selecting barley grains for brewing.