Relationship of Rice Grain Amylose, Gelatinization Temperature and Pasting Properties for Breeding Better Eating and Cooking Quality of Rice Varieties

Effects of degree of milling on bran layer structure, physicochemical properties and cooking quality of brown rice

Effects of varying degree of milling (DOM) (0-22%) on the bran layer structure, physicochemical properties, and cooking quality of brown rice were explored. As the DOM increased, bran degree, protein, lipid, dietary fiber, amylose, mineral elements, and color parameters (a* and b* values) of milled rice decreased while starch and L* value increased. Microscopic fluorescence images showed that the pericarp, combined seed coat-nucellus layer, and aleurone layer were removed in rice processed at DOM of 6.6%, 9.2%, and 15.4%, respectively. The pasting properties, thermal properties, and palatability of rice increased as the DOM increased. Principal component and correlation analysis indicated that excessive milling lead to a decline in nutritional value of rice with limited impact on enhancing palatability. Notably, when parts of aleurone cell wall were retained, rice samples exhibited high cooking and sensory properties. It serves as a potential guide to the production of moderately milled rice.

OsG6PGH1 affects various grain quality traits and participates in the salt stress response of rice

Cytoplasmic 6-phosphogluconate dehydrogenase (G6PGH) is a key enzyme in the pentose phosphate pathway that is involved in regulating various biological processes such as material metabolism, and growth and development in plants. However, it was unclear if OsG6PGH1 affected rice grain quality traits. We perform yeast one-hybrid experiments and reveal that OsG6PGH1 may interact with OsAAP6. Subsequently, yeast in vivo point-to-point experiments and local surface plasmon resonance experiments verified that OsG6PGH1 can bind to OsAAP6. OsG6PGH1 in rice is a constitutive expressed gene that may be localized in the cytoplasm. OsAAP6 and protein-synthesis metabolism-related genes are significantly upregulated in OsG6PGH1 overexpressing transgenic positive endosperm, corresponding to a significant increase in the number of protein bodies II, promoting accumulation of related storage proteins, a significant increase in grain protein content (GPC), and improved rice nutritional quality. OsG6PGH1 positively regulates amylose content, negatively regulates chalkiness rate and taste value, significantly affects grain quality traits such as appearance, cooking, and eating qualities of rice, and is involved in regulating the expression of salt stress related genes, thereby enhancing the salt-stress tolerance of rice. Therefore, OsG6PGH1 represents an important genetic resource to assist in the design of high-quality and multi-resistant rice varieties.

Starch Properties and Morphology of Eight Floury Endosperm Mutants in Rice

Besides increasing grain yield, improving rice (Oryza sativa L.) quality has been paid more and more attention recently. Cooking and eating quality (CEQ) is an important indicator of rice quality. Since CEQs are quantitative traits and challenging for measurement, efforts have mainly focused on two major genes, Wx and SSIIa. Chalkiness and floury endosperm significantly affect the eating quality of rice, leading to noticeable changes in CEQ. Due to the easily observable phenotype of floury endosperm, cloning single gene mutations that cause floury endosperm and evaluating changes in CEQs indirectly facilitate the exploration of the minor genes controlling CEQ. In this study, eight mutants with different degrees of floury endosperm, generated through ethylmethane sulfonate (EMS) mutagenesis, were analyzed. These mutants exhibited wide variation in starch morphology and CEQs. Particularly, the z2 mutant showed spherical starch granules significantly increased rapid visco analyzer (RVA) indexes and urea swelling, while the z4 mutant displayed extremely sharp starch granules and significantly decreased RVA indexes and urea swelling compared to the wild type. Additionally, these mutants still maintained correlations with certain RVA profiles, suggesting that the genes PUL, which affect these indexes, may not undergo mutation. Cloning these mutated genes in the future, especially in z2 and z4, will enhance the genetic network of rice eating quality and hold significant importance for molecular marker-assisted breeding to improve rice quality.

Genome-wide association study of cooking-caused grain expansion in rice (Oryza sativa L.)

Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.

Impacts of Inherent Components and Nitrogen Fertilizer on Eating and Cooking Quality of Rice: A Review

With the continuous improvement of living standards, the preferences of consumers are shifting to rice varieties with high eating and cooking quality (ECQ). Milled rice is mainly composed of starch, protein, and oil, which constitute the physicochemical basis of rice taste quality. This review summarizes the relationship between rice ECQ and its intrinsic ingredients, and also briefly introduces the effects of nitrogen fertilizer management on rice ECQ. Rice varieties with higher AC usually have more long branches of amylopectin, which leach less when cooking, leading to higher hardness, lower stickinesss, and less panelist preference. High PC impedes starch pasting, and it may be hard for heat and moisture to enter the rice interior, ultimately resulting in worse rice eating quality. Rice with higher lipid content had a brighter luster and better eating quality, and starch lipids in rice have a greater impact on rice eating quality than non-starch lipids. The application of nitrogen fertilizer can enhance rice yield, but it also decreases the ECQ of rice. CRNF has been widely used in cereal crops such as maize, wheat, and rice as a novel, environmentally friendly, and effective fertilizer, and could increase rice quality to a certain extent compared with conventional urea. This review shows a benefit to finding more reasonable nitrogen fertilizer management that can be used to regulate the physical and chemical indicators of rice grains in production and to improve the taste quality of rice without affecting yield.

Dietary Fibre Impacts the Texture of Cooked Whole Grain Rice

Consumers' general preference for white rice over whole grain rice stems from the hardness and low palatability of cooked whole grain rice; however, strong links have been found between consuming a large amount of white rice, leading a sedentary lifestyle, and acquiring type 2 diabetes. This led us to formulate a new breeding goal to improve the softness and palatability of whole grain rice while promoting its nutritional value. In this study, the association between dietary fibre profiles (using an enzymatic method combined with high-performance liquid chromatography) and textural properties of whole grain rice (using a texture analyser) was observed. The results showed that a variation in the ratio of soluble dietary fibre (SDF) and insoluble dietary fibre (IDF) influenced the textural characteristics of cooked whole grain rice; found a strong association between SDF to IDF ratio and hardness (r = -0.74, p < 0.01) or gumminess (r = -0.69, p < 0.01) of cooked whole grain rice, and demonstrated that the SDF to IDF ratio was also moderately correlated with cohesiveness (r = -0.45, p < 0.05), chewiness (r = -0.55, p < 0.01), and adhesiveness (r = 0.45, p < 0.05) of cooked whole grain rice. It is suggested that the SDF to IDF ratio can be used as a biomarker for breeding soft and highly palatable whole grain rice of cultivated tropical indica rice to achieve consumer well-being. Lastly, a simple modified method from the alkaline disintegration test was developed for high-throughput screening of dietary fibre profiles in the whole grain indica rice samples.

Molecular bases of rice grain size and quality for optimized productivity

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

The 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.

Changes in the chemical, physical, and sensory properties of rice according to its germination rate

This study aimed to decipher the association among the physicochemical properties, sensory quality, and germination rate of rice samples stored at different storage conditions and for different durations (stored at 10, 20, and 30 °C for 8 months). The germination rate of the samples varied from 0.3 to 98.7%. A reduced germination rate increased the lipid oxidation, hardness, and most pasting properties of rice, whereas seed viability, moisture content, and adhesiveness were reduced. Amylose and protein contents were not influenced by the changes in germination rate. However, with a decrease in germination rate, the surface endosperm cells were aggregated, whereas the sizes of inner endosperm cells in cooked rice were reduced. Several metabolites involved in rice sensory quality were also altered, and a related pathway was proposed. Collectively, these results suggest that germination rate could serve as a potential indicator to track the changes in rice quality.

Rapid Assessment of Rice Quality Traits Using Low-Cost Digital Technologies

Aroma and other physicochemical parameters are important attributes influencing consumer perception and acceptance of rice. However, current methods using multiple instruments and laboratory analysis make these assessments costly and time-consuming. Therefore, this study aimed to assess rice quality traits of 17 commercial rice types using a low-cost electronic nose and portable near-infrared spectrometer coupled with machine learning (ML). Specifically, artificial neural networks (ANN) were used to classify the type of rice and predict rice quality traits (aromas, color, texture, and pH of cooked rice) as targets. The ML models developed showed that the chemometrics obtained from both sensor technologies successfully classified the rice (Model 1: 98.7%; Model 2: 98.6%) and predicted the peak area of aromas obtained by gas chromatography-mass spectroscopy found in raw (Model 3: R = 0.95; Model 6: R = 0.95) and cooked rice (Model 4: R = 0.98; Model 7: R = 0.96). Furthermore, a high R = 0.98 was obtained for Model 5 to estimate the color, texture, and pH of cooked rice. The proposed method is rapid, low-cost, reliable, and may help the rice industry increase high-quality rice production and accelerate the adoption of digital technologies and artificial intelligence to support the rice value chain.

Effects of Variety, Early Harvest and Germination on Pasting Properties and Cooked Grain Texture of Brown Rice

Brown rice is superior to white rice in nutritional value and in prevention of chronic diseases. However, it is not the preference of consumers and the relative consumption of brown rice is limited due to a number of factors including chewiness and perceived hard texture after cooking. While both early harvested brown rice and germinated brown rice have been shown to contain superior nutritional components, there is limited knowledge on textural properties of these types of brown rice relative to standard brown rice, and how varieties may affect such properties. Thus, the present study examined the effect of variety, early harvest and germination on those properties of 8 rice varieties with contrasting amylose content and known texture in terms of milled rice. Early harvest and germination decreased pasting viscosities and cooked grain hardness. However, their effect on the characteristics of flour and whole grains differed, in which germination had greater effect on pasting properties, while early harvest on texture of cooked grains. Softer texture of brown rice, about 32% lower could be achieved by germination, and 46% by harvesting early. There was a good relationship between pasting characteristics particularly setback and hardness among different varieties in brown rice, germinated brown rice and also in early harvest brown rice. This is the first time the comparison of texture between the 3 brown rice types has been reported. The results also provide new options for selection of desired characteristics for food processing and brown rice consumption. This article is protected by copyright. All rights reserved.

Effects of Biochar Amendment and Nitrogen Fertilizer on RVA Profile and Rice Grain Quality Attributes

Improving rice production in modern agriculture relies heavily on the overuse of chemical fertilizer, which adversely affects grain quality. Biochar (BC) application is well known for enhancing rice yield under reduced nitrogen (N) application. Therefore, we conducted a two-year field experiment in 2019 and 2020 to evaluate RVA profile characteristics, grain milling, and appearance qualities under four BC rates (0, 10, 20, 30 t ha⁻¹) in combination with two N levels (135 and 180 kg ha⁻¹). The results showed that BC at 30 t ha⁻¹ along with 135 kg N ha⁻¹ improved rapid visco-analyzer (RVA) profile attributes, including peak viscosity (4081.3), trough viscosity (3168.0), break down (913.3), final viscosity (5135.7), and set back (1967.7). Grain yield, grain rain length, milled rice rate, percent grains with chalkiness, amylose, and starch content were improved by 27%, 23%, 37%, 24%, 14%, and 8%, respectively, in the plots treated with the combination of 30 t BC ha⁻¹ and 180 kg N ha⁻¹. A positive coefficient of correlation was observed in RVA profile, milling, and apparent quality of rice with soil properties. These results suggested that BC at 20 to 30 t ha⁻¹ in combination with 135 kg N ha⁻¹ is a promising option for enhancing grain yield, RVA profile, appearance, and milling quality.

Dry cultivation with ratoon system impacts rice quality using rice flour physicochemical traits, fatty and amino acids contents

A field experiment was conducted to explore the impact on rice quality using high-quality (HH) or drought-resistant (HY) cultivars under flooding irrigation (F) or dry cultivation (D) in ratooning rice system by evaluating the metabolism or physicochemical traits of starch, fatty acids, and amino acids affecting grain quality. Compared to FHY and DHY in the main or ratoon season, DHH in ratoon season (DHHR) exhibited a higher appearance and processing quality but lower cooking quality. DHHR mainly synthesized long branch chain amylopectin to construct the crystalline regions with increased crystallinity, crystallites size, interplanar spacing, dislocation density, Asp and Thr in brown and head rice. Also, it accumulated more of C16:0, C18:0, C18:1, C18:2, and C18:3 but reduced glutelin in head rice. An increase in functional groups and diversity was seen in brown and head rice, respectively. Overall, these traits improved the processing, appearance, and pasting quality of DHHR.

Genetic and phenotypic characterization of rice grain quality traits to define research strategies for improving rice milling, appearance, and cooking qualities in Latin America and the Caribbean

Rice (Oryza sativa L.)grain quality is a set of complex interrelated traits that include grain milling, appearance, cooking, and edible properties. As consumer preferences in Latin America and the Caribbean evolve, determining what traits best capture regional grain quality preferences is fundamental for breeding and cultivar release. In this study, a genome-wide association study (GWAS), marker-assisted selection (MAS), and genomic selection (GS) were evaluated to help guide the development of new breeding strategies for rice grain quality improvement. For this purpose, 284 rice lines representing over 20 yr of breeding in Latin America and the Caribbean were genotyped and phenotyped for 10 different traits including grain milling, appearance, cooking, and edible quality traits. Genetic correlations among the 10 traits ranged from -0.83 to 0.85. A GWAS identified 19 significant marker/trait combinations associated with eight grain quality traits. Four functional markers, three located in the Waxy and one in the starch synthase IIa genes, were significantly associated with six grain-quality traits. These markers individually explained 51-75% of the phenotypic variance depending on the trait, clearly indicating their potential utility for MAS. Cross-validation studies to evaluate predictive abilities of four different GS models for each of the 10 quality traits were conducted and predictive abilities ranged from 0.3 to 0.72. Overall, the machine learning model random forest had the highest predictive abilities and was especially effective for traits where large effect quantitative trait loci were identified. This study provides the foundation for deploying effective molecular breeding strategies for grain quality in Latin American rice breeding programs.

Unique Glutelin Expression Patterns and Seed Endosperm Structure Facilitate Glutelin Accumulation in Polyploid Rice Seed

BACKGROUND

Rice is not only an essential food but also a source of high quality protein. Polyploidy is an evolutionary trajectory in plants, and enhancing glutelin by polyploidization is an attractive strategy for improving the nutritional value of rice seeds and presents a great potential for enhancing the commercial value of rice. Elucidating the mechanisms underlying glutelin synthesis and accumulation in tetraploid rice is of great significance.

RESULTS

To enhance the nutritional value of rice, we developed tetraploid rice and evaluated the contents of various nutrient elements in mature seeds. The results revealed a significant increase in protein contents, including the total seed storage proteins, glutelins, and amino acids in tetraploid rice when compared with those in diploid rice. Tandem mass tag-based quantitative proteomic analyses of seeds revealed that glutelins regulated by several glutelin genes in 9311-4x were significantly up-regulated (≥1.5-fold), which was further verified by immunoblot analyses. In addition, temporal expression patterns of various glutelin subunits in different rice lines were investigated. The results revealed significant differences in the expression patterns between diploid and tetraploid rice seeds. Cytohistological analyses results revealed that the thickness of aleurone cell layers increased significantly by 32% in tetraploid rice, the structures of protein storage vacuoles (PSVs) in sub-aleurone cells were more diverse and abundant than those of diploid rice. Temporal expression and proteomic analyses results revealed that protein disulfide isomerase-like 1-1 expression levels were higher in tetraploid rice than in diploid rice, and that the gene responded to oxidative folding with increased levels of proglutelin and appropriate distribution of seed glutelins in tetraploid rice.

CONCLUSION

The results of the present study revealed that polyploidization increased glutelin content by influencing glutelin biosynthesis, transport, and deposition, while variations in glutelin accumulation between tetraploid and diploid rice were largely manifested in the initial time, duration, and relative levels of various glutelin gene expressions during seed filling stages. These findings provide novel insights into improving the protein quality and nutritional value of rice seeds by polyploid breeding.

CRISPR Genome Editing Technology: A Powerful Tool Applied to Developing Agribusiness

The natural increase of the world's population implies boosting agricultural demand. In the current non-optimistic global scenario, where adverse climate changes come associated with substantial population growth, the main challenge in agribusiness is food security. Recently, the CRISPR/Cas system has emerged as a friendly gene editing biotechnological tool, enabling a precise manipulation of genomes and enhancement of desirable traits in several organisms. This review highlights the CRISPR/Cas system as a paramount tool for the improvement of agribusiness products and brings up-to-date findings showing its potential applications in improving agricultural-related traits in major plant crops and farm animals, all representing economic-relevant commodities responsible for feeding the world. Several applied pieces of research have successfully demonstrated the CRISPR/Cas ability in boosting interesting traits in agribusiness products, including animal productivity and welfare, crop yield growth, and seed quality, reflecting positive impacts in both socioeconomics and human health aspects. Hence, the CRISPR/Cas system has revolutionized bioscience and biotechnology, and its concrete application in agribusiness goods is on the horizon.

Developing new lines of Japonica rice for higher quality and yield under arid conditions

Rice is the world's largest food crop, and its production needs to be doubled by 2050 to cope with population growth and associated demand. In addition to the value of improving yields, quality is also important for breeders and consumers, but it pays less attention in arid regions. During two successive summer growing seasons, the experimental material focused on 34 genotypes developed from different crosses on Fn generation after fixation as well as six of the most recent commercial cultivars used for comparisons. The results showed that a high yield of grain followed by high milling and grain quality characteristics were observed among the 34 genotypes used in this analysis. Highly important and positive correlations between the percentage of hulling and the percentage of milling (0.424) and the yield ability could be accomplished by choosing the number of panicles per plant and the weight of the panicles. Selection criteria for good quality should be met by the percentage of head rice and many mineral elements, particularly zinc and iron. As a consequence, the genotypes M.J 5460S/SK105-1, M.J 5460S/GZ7768-1, M.J 5460S/G177-1, M.J 5460S/SK105-3 and M.J 5460S/SK106-4 had desirable high yield and quality characteristics and could be used as promising accessions to the rice breeding program in arid regions. In addition to commercial genotypes, improved Japonica rice genotypes could be produced in arid conditions for higher yield and quality, leading to an increase in total production, supporting food security and nutrition.

A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency

In rice (Oryza sativa), amylose content (AC) is the major factor that determines eating and cooking quality (ECQ). The diversity in AC is largely attributed to natural allelic variation at the Waxy (Wx) locus. Here we identified a rare Wx allele, Wx^mw , which combines a favorable AC, improved ECQ and grain transparency. Based on a phylogenetic analysis of Wx genomic sequences from 370 rice accessions, we speculated that Wx^mw may have derived from recombination between two important natural Wx alleles, Wxⁱⁿ and Wx^b . We validated the effects of Wx^mw on rice grain quality using both transgenic lines and near-isogenic lines (NILs). When introgressed into the japonica Nipponbare (NIP) background, Wx^mw resulted in a moderate AC that was intermediate between that of NILs carrying the Wx^b allele and NILs with the Wx^mp allele. Notably, mature grains of NILs fixed for Wx^mw had an improved transparent endosperm relative to soft rice. Further, we introduced Wx^mw into a high-yielding japonica cultivar via molecular marker-assisted selection: the introgressed lines exhibited clear improvements in ECQ and endosperm transparency. Our results suggest that Wx^mw is a promising allele to improve grain quality, especially ECQ and grain transparency of high-yielding japonica cultivars, in rice breeding programs.

Breeding of High Cooking and Eating Quality in Rice by Marker-Assisted Backcrossing (MABc) Using KASP Markers

The primary goals of rice breeding programs are grain quality and yield potential improvement. With the high demand for rice varieties of premium cooking and eating quality, we developed low-amylose content breeding lines crossed with Samgwang and Milkyqueen through the marker-assisted backcross (MABc) breeding program. Trait markers of the SSIIIa gene referring to low-amylose content were identified through an SNP mapping activity, and the markers were applied to select favorable lines for a foreground selection. To rapidly recover the genetic background of Samgwang (recurrent parent genome, RPG), 386 genome-wide markers were used to select BC₁F₁ and BC₂F₁ individuals. Seven BC₂F₁ lines with targeted traits were selected, and the genetic background recovery range varied within 97.4–99.1% of RPG. The amylose content of the selected BC₂F₂ grains ranged from 12.4–16.8%. We demonstrated the MABc using a trait and genome-wide markers, allowing us to efficiently select lines of a target trait and reduce the breeding cycle effectively. In addition, the BC₂F₂ lines confirmed by molecular markers in this study can be utilized as parental lines for subsequent breeding programs of high-quality rice for cooking and eating.

Deploying viscosity and starch polymer properties to predict cooking and eating quality models: A novel breeding tool to predict texture

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Multivariate analysis was used to develop twelve cooking and eating quality classes.

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Two-layered random forest model was used to predict rice classification.

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High classification accuracy of cooking and eating quality ideotypes were obtained.

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Mismatches from IRRI-released and consumer-preferred lines was capture by the model.

Acceptance of new rice genotypes demanded by rice value chain depends on premium value of varieties that match consumer demands of regional preferences. High throughput prediction tools are not available to breeders to classify cooking and eating quality (CEQ) ideotypes and to capture texture of varieties. The pasting properties in combination with starch properties were used to develop two layered models in order to classify the rice varieties into twelve distinct CEQ ideotypes with unique sensory profiles. Classification models developed using random forest method depicted the overall accuracy of 96 %. These CEQ models were found to be robust to predict ideotypes in both Indica and Japonica diversity panels grown under dry and wet seasons and across the years. We conducted random forest modeling using 1.8 million high density SNPs and identified top 1000 SNP features which explained CEQ model classification with the accuracy of 0.81. Furthermore these CEQ models were found to be valuable to predict textural preferences of IRRI breeding lines released during 1960–2013 and mega varieties preferred in South and South East Asia.

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

Grain quality is an important breeding objective in rice, and the appearance of the grain also affects its commercial value in the market. The aim of this study was to decode the rice grain qualities and appearances, such as gelatinization temperature (GT), amylose content (AC), grain protein content (GPC), pericarp color (PC), length/width ratio (LWR), and grain volume (GV) at phenotypic and genetic levels, as well as the relationships among them. A genome-wide association study (GWAS) was used to identify the quantitative trait locus (QTLs) associated with the target traits using mixed linear model (MLM) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) methods. In general, AC was negatively correlated with GPC and GV, while it was positively correlated with LWR and PC. GPC was positively correlated with LWR. Using the rice diversity panel 1 (RDP1) population, we identified 11, 6, 2, 7, 11, and 6 QTLs associated with GT, AC, GPC, PC, LWR, and GV, respectively. Five germplasm lines, superior in grain qualities and appearances for basic breeding materials or improvement, were identified. Notably, an F-box gene OsFbox394 was located in the linkage disequilibrium (LD) block of qLWR7-2, which specifically expresses in endosperm and seed tissues, suggesting that this gene may regulate the seed development in rice grain. Besides, different haplotypes of OsHyPRP45 showed significant differences in AC, indicating that this gene may be related to AC in rice grain.

Empirical characterization of hydration behavior of Indian paddy varieties by physicochemical characterization and kinetic studies

Temperature is an important factor in the determination of hydration kinetics in paddy, and it varies with variety. To understand this hydration behavior, the current study analyses the hydration kinetics of 12 different paddy varieties of India that were exposed to different soaking temperatures. The protein content of the paddy samples was found to be in the range of 6.13 to 9.19%; whereas, starch content was between 67.79 and 84.88%. The physicochemical composition of paddy varieties as well as variation in time-temperature of hydration was found to be decisive in ascertaining the hydration behavior. An increased hydration rate was observed with increasing hydration temperature as well as with higher amylose content of paddy. Among the varieties studied, the ratio of amylose to amylopectin was between 0.37 and 0.77. For all samples, the gelatinization temperature was in the range of 65.60 to 83.10 °C, which in turn was negatively correlated with amylose content, and influenced the hydration behavior of paddy. The optimum time-temperature condition range for hydration for each paddy variety was between 50 and 60°C for 2 to 3.5 hr, depending upon the variety. The activation energy for the paddy samples in this investigation was found to be in the range of 8.70 to 23.10 kJ/mol. The kinetic modeling of hydration was conducted using Peleg's model, with a good fit. The data indicated that with increment in hydration temperature, the rate of hydration was enhanced in all varieties with a decrease in the Peleg's rate constant (K₁ ) and capacity constant (K₂ ). These constants indicate a direct temperature-dependence of water absorption in paddy. PRACTICAL APPLICATION: The hydration of paddy is an important procedure in paddy processing, and across the world, many industries are working on it. Irrespective of the variety, paddy processing globally has remained tricky. Knowledge about the hydration behavior of paddy would enable food processors to better understand the effect of process parameters and to model their experimental setup to obtain the desired physicochemical attributes, as well as process yield. Customers would benefit from adequately processed paddy with better digestibility for which industry would have to invest less in terms of time and resources, thereby making the hydrated paddy more affordable.

Genetic Analysis for Cooking and Eating Quality of Super Rice and Fine Mapping of a Novel Locus qGC10 for Gel Consistency

Rice (Oryza sativa L.) is an important cereal that provides food for more than half of the world's population. Besides grain yield, improving grain quality is also essential to rice breeders. Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) are considered to be three indicators for cooking and eating quality in rice. Using a genetic map of RILs derived from the super rice Liang-You-Pei-Jiu with high-density SNPs, we detected 3 QTLs for AC, 3 QTLs for GT, and 8 QTLs for GC on chromosomes 3, 4, 5, 6, 10, and 12. Wx locus, an important determinator for AC and GC, resided in one QTL cluster for AC and GC, qAC6 and qGC6 here. And a novel major QTL qGC10 on chromosome 10 was identified in both Lingshui and Hangzhou. With the BC₄F₂ population derived from a CSSL harboring the segment for qGC10 from 93-11 in PA64s background, it was fine mapped between two molecular markers within 181 kb region with 27 annotated genes. Quantitative real-time PCR results showed that eight genes were differentially expressed in endosperm of two parents. After DNA sequencing, only LOC_Os10g04900, which encodes a F-box domain containing protein, has 2 bp deletion in the exon of PA64s, resulting in a premature stop codon. Therefore, LOC_Os10g04900 is considered to be the most likely candidate gene for qGC10 associated with gel consistency. Identification of qGC10 provides a new genetic resource for improvement of rice quality.

Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

BACKGROUND

Carbon (C) and nitrogen (N) are two fundamental components of starch and protein, which are important determinants of grain yield and quality. The food preferences of consumers and the expected end-use of grains in different rice-growing regions require diverse varieties that differ in terms of the grain N content (GNC) and grain C content (GCC) of milled rice. Thus, it is important that quantitative trait loci (QTLs)/genes with large effects on the variation of GNC and GCC are identified in breeding programs.

RESULTS

To dissect the genetic basis of the variation of GNC and GCC in rice, the Dumas combustion method was used to analyze 751 diverse accessions regarding the GNC, GCC, and C/N ratio of the milled grains. The GCC and GNC differed significantly among the rice subgroups, especially between Xian/Indica (XI) and Geng/Japonica (GJ). Interestingly, in the GJ subgroup, the GNC was significantly lower in modern varieties (MV) than in landraces (LAN). In the XI subgroup, the GCC was significantly higher in MV than in LAN. One, six, and nine QTLs, with 55 suggestively associated single nucleotide polymorphisms, were detected for the GNC, GCC, and C/N ratio in three panels during a single-locus genome-wide association study (GWAS). Three of these QTLs were also identified in a multi-locus GWAS. We screened 113 candidate genes in the 16 QTLs in gene-based haplotype analyses. Among these candidate genes, LOC_Os01g06240 at qNC-1.1, LOC_Os05g33300 at qCC-5.1, LOC_Os01g04360 at qCN-1.1, and LOC_Os05g43880 at qCN-5.2 may partially explain the significant differences between the LAN and MV. These candidate genes should be cloned and may be useful for molecular breeding to rapidly improve the GNC, GCC, and C/N ratio of rice.

CONCLUSIONS

Our findings represent valuable information regarding the genetic basis of the GNC and GCC and may be relevant for enhancing the application of favorable haplotypes of candidate genes for the molecular breeding of new rice varieties with specific grain N and C contents.

Imposed Water Deficit after Anthesis for the Improvement of Macronutrients, Quality, Phytochemicals, and Antioxidants in Rice Grain

The control of protein and amylose content is the principal challenge in rice nutrient and quality improvement. In this study, water deficits in 2- and 3-day intervals were imposed on two Japonica cultivars K1 and K3, and an Indica K4 subtype after anthesis to harvest. It was observed that although rice yield was affected, the protein content was increased 6.53–6.63% to 9.93–10.16%. The amylose quantity was reduced significantly from 22.00–22.43% to 16.33–17.56%, while fatty acids in rice grain were not influenced. Total anthocyanins were greatly promoted by 53.1% as compared to the non-treated trials. The antioxidant capacity in rice grain increased up to 59.1% in 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging and 41.6% in reducing power assays. Findings of this research revealed that the 3-day interval of water deficit imposition was the most effective to improve rice macronutrients and quality, as well as beneficial phytochemicals and antioxidants in rice grain. The water control after anthesis to harvest in rice cultivation is beneficial and economical for farmers to improve rice nutrients and quality, thus contributes to the sustainable rice production in many developing countries.

Multivariate-based classification of predicting cooking quality ideotypes in rice (Oryza sativa L.) indica germplasm

BACKGROUND

For predicting texture suited for South and South East Asia, most of the breeding programs tend to focus on developing rice varieties with intermediate to high amylose content in indica subspecies. However, varieties within the high amylose content class may still be distinguishable by consumers, who are able to distinguish texture that cannot be differentiated by proxy cooking quality indicators.

RESULTS

This study explored a suite of assays to capture viscosity, rheometric, and mechanical texture parameters for characterising cooked rice texture in a set of 211 rice accessions from a diversity panel and employed multivariate approaches to classify rice varieties into distinct cooking quality classes. Results suggest that when the amylose content range is narrowed to the intermediate to high classes, parameters determined by rheometry and RVA become diagnostic. Modeled parameters distinguishing cooking quality ideotypes within the same range of amylose classes differ in textural parameters scored by a descriptive sensory panel.

CONCLUSIONS

Our results reinforced the notion that it is important to define cooking quality classes in indica subtypes based on multidimensional parameters, by going beyond amylose predictions. These predictive cooking models will be handy in capturing cooking and eating quality properties that address consumer preferences in future breeding programs. Policy implications of such findings may lead to changes in criteria used in assessing grain quality in the intermediate to high amylose classes.