Changes in Rice Grain Quality of Indica and Japonica Type Varieties Released in China from 2000 to 2014

An Evaluation of Paddy Rice as an Alternative Energy Source in Protein-Restricted Diets for Growing, Early-Finishing, and Late-Finishing Pigs

Three experiments were conducted to evaluate paddy rice as an alternative energy feedstuff in low-protein diets for pigs. In Experiment 1, a total of 400 growing pigs (20.68 ± 0.29 kg initial bodyweight), were randomly allocated four dietary treatments with 0, 10, 15, and 20% paddy rice for 30 days. Feeding 10% or 15% paddy rice had no adverse impacts on average daily gain (ADG) and feed to gain ratio (F:G), while the inclusion of 20% rice in diets significantly influenced the growth performance of pigs. In Experiment 2, 364 early-finishing pigs (42.25 ± 0.47 kg) were divided into four treatments with 0, 15, 20, and 25% paddy rice for 35 days. Feeding 15% or 20% paddy rice had no negative consequences on growth performance, while pigs fed with 25% rice had the lowest ADG and the greatest F:G. In Experiment 3, 364 late-finishing pigs (79.52 ± 1.28 kg) were divided into four treatments with 0, 20, 25, and 30% paddy rice for 60 days. Paddy rice can be included at up to 30% in diets without compromising growth performance, while feeding with 25% rice significantly improved the performance for pigs compared with the corn-fed control.

The deterioration of starch physiochemical and minerals in high-quality indica rice under low-temperature stress during grain filling

Low temperatures during the grain-filling phase have a detrimental effect on both the yield and quality of rice grains. However, the specific repercussions of low temperatures during this critical growth stage on grain quality and mineral nutrient composition in high-quality hybrid indica rice varieties have remained largely unexplored. The present study address this knowledge gap by subjecting eight high-quality indica rice varieties to two distinct temperature regimes: low temperature (19°C/15°C, day/night) and control temperature (28°C/22°C) during their grain-filling phase, and a comprehensive analysis of various quality traits, with a particular focus on mineral nutrients and their interrelationships were explored. Exposure of rice plants to low temperatures during early grain filling significantly impacts the physicochemical and nutritional properties. Specifically, low temperature increases the chalkiness rate and chalkiness degree, while decreases starch and amylopectin content, with varying effects on amylose, protein, and gelatinization temperature among rice varieties. Furthermore, crucial parameters like gelatinization enthalpy (ΔH), gelatinization temperature range (R), and peak height index (PHI) all significantly declined in response to low temperature. These detrimental effects extend to rice flour pasting properties, resulting in reduced breakdown, peak, trough, and final viscosities, along with increased setback. Notably, low temperature also had a significant impact on the mineral nutrient contents of brown rice, although the extent of this impact varied among different elements and rice varieties. A positive correlation is observed between brown rice mineral nutrient content and factors such as chalkiness, gelatinization temperature, peak viscosity, and breakdown, while a negative correlation is established with amylose content and setback. Moreover, positive correlations emerge among the mineral nutrient contents themselves, and these relationships are further accentuated in the context of low-temperature conditions. Therefore, enhancing mineral nutrient content and increasing rice plant resistance to chilling stress should be the focus of breeding efforts to improve rice quality.

Pyramiding of Low Chalkiness QTLs Is an Effective Way to Reduce Rice Chalkiness

Rice chalkiness is a key limiting factor of high-quality rice. The breeding of low chalkiness varieties has always been a challenging task due to the complexity of chalkiness and its susceptibility to environmental factors. In previous studies, we identified six QTLs for the percentage of grain chalkiness (PGC), named qPGC5, qPGC6, qPGC8.1, qPGC8.2, qPGC9 and qPGC11, using single-segment substitution lines (SSSLs) with genetic background of Huajingxian 74 (HJX74). In this study, we utilized the six low chalkiness QTLs to develop 17 pyramiding lines with 2-4 QTLs. The results showed that the PGC decreased with the increase of QTLs in the pyramiding lines. The pyramiding lines with 4 QTLs significantly reduced the chalkiness of rice and reached the best quality level. Among the six QTLs, qPGC5 and qPGC6 showed greater additive effects and were classified as Group A, while the other four QTLs showed smaller additive effects and were classified as Group B. In pyramiding lines, although the presence of epistasis, additivity remained the main component of QTL effects. qPGC5 and qPGC6 showed stronger ability to reduce rice chalkiness, particularly in the environment of high temperature (HT) in the first cropping season (FCS). Our research demonstrates that by pyramiding low chalkiness QTLs, it is feasible to develop the high-quality rice varieties with low chalkiness at the best quality level even in the HT environment of FCS.

Effects of distribution, structure and interactions of starch, protein and cell walls on textural formation of cooked rice: A review

The constitution and forms of rice determine its processing and cooking properties and further control the cooked rice quality. As the two main components, starch and protein content correlations and their characteristics have been extensively explored. However, rice is mainly consumed as polished kernels, components distribution, cytoplasmic matrix, and cell walls work together, and the properties of extracted components or flour are difficult to reflect the quality of cooked rice accurately. Thus, this review summarizes the multi-scale structure changes of main components during real rice cooking conditions. The dynamic thermal changes and leaching behaviors in rice kernels are compared with pure starch or rice flour. The in situ changes and interactions of starch granules, protein bodies, and cell walls during cooking are reviewed. Based on this, different textural evaluation methods are compared, and the advantages and disadvantages are pointed out. The oral chewing perception and bionic chewing simulation for textual evaluation have gradually become hot. Both rice quality controllers and eating quality evaluators attempt to establish an accurate quality evaluation system with the increased demand for high-quality rice.

Realized Genetic Gain in Rice: Achievements from Breeding Programs

Genetic improvement is crucial for ensuring food security globally. Indeed, plant breeding has contributed significantly to increasing the productivity of major crops, including rice, over the last century. Evaluating the efficiency of breeding strategies necessitates a quantification of this progress. One approach involves assessing the genetic gain achieved through breeding programs based on quantitative traits. This study aims to provide a theoretical understanding of genetic gain, summarize the major results of genetic gain studies in rice breeding, and suggest ways of improving breeding program strategies and future studies on genetic gain. To achieve this, we present the concept of genetic gain and the essential aspects of its estimation. We also provide an extensive literature review of genetic gain studies in rice (Oryza sativa L.) breeding programs to understand the advances made to date. We reviewed 29 studies conducted between 1999 and 2023, covering different regions, traits, periods, and estimation methods. The genetic gain for grain yield, in particular, showed significant variation, ranging from 1.5 to 167.6 kg/ha/year, with a mean value of 36.3 kg/ha/year. This translated into a rate of genetic gain for grain yield ranging from 0.1% to over 3.0%. The impact of multi-trait selection on grain yield was clarified by studies that reported genetic gains for other traits, such as plant height, days to flowering, and grain quality. These findings reveal that while breeding programs have achieved significant gains, further improvements are necessary to meet the growing demand for rice. We also highlight the limitations of these studies, which hinder accurate estimations of genetic gain. In conclusion, we offer suggestions for improving the estimation of genetic gain based on quantitative genetic principles and computer simulations to optimize rice breeding strategies.

CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement

MAIN CONCLUSION

This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.

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.

Identification of Potential QTLs Related to Grain Size in Rice

Rice is a major crop, providing calories and food for most of the world's population. Currently, the global population is rapidly increasing, and securing a yield of rice that can satisfy everyone is an ongoing challenge. The yield of rice can be increased by controlling 1000-grain weight as one of the important determining factors. Grain length, grain width, grain thickness, and 1000-grain weight, which determine grain size, are controlled by QTLs. To identify QTLs related to grain size, we screened and then mapped 88 RIL individuals derived from a cross between JJ625LG, which has a long grain size, long spindle-shaped grains, and low 1000-grain weight, and Namchan, which has short grains with round shape and heavy 1000-grain weight. In 2021 and 2022, 511 SNP markers were used to map QTLs related to grain size to a physical map. The QTLs found to be related to grain size are evenly distributed on chromosomes 2, 3, 5, 10, and 11. The mapping results also show that the QTLs qGl3-2, qRlw3, and qRlw3-2 of chromosome 3, and qGt5 and qRlw5 of chromosome 5 are, respectively, associated with GS3 and qSW5, which are the major genes previously cloned and found to be related to grain size. In addition, qGw10 and qGw10-1, which were additionally detected in this study, were found to be associated with Os10g0525200 (OsCPq10), a potential candidate gene involved in controlling grain size. This gene codes for a cytochrome P450 family protein and is reported to have a positive effect on grain size by interacting with proteins related to mechanisms determining grain size. In particular, OsCPq10 was screened in the same identified QTL region for 2 consecutive years, which is expected to have a positive effect on grain size. These results will be helpful for breeding elite rice cultivars with high yields through additional fine mapping related to grain size.

Comprehensive Evaluation of Rice Qualities under Different Nitrogen Levels in South China

There is a need to comprehensively evaluate the rice quality of different rice varieties under different nitrogen treatments. Therefore, in this study, we used twenty-one hybrid indica rice varieties and twenty-three inbred japonica rice varieties with three nitrogen fertilizer levels to investigate differences in rice qualities. As compared with hybrid indica rice, inbred japonica rice had lower coefficient of variation values for grain shape, mild rice percentage, and head rice percentage, but relatively higher coefficient of variation values for chalkiness traits, appearance, and taste value of cooked rice. A principal component analysis and membership function method were used to comprehensively evaluate the qualities of rice. The overall eating quality value by sensory evaluation and head rice percentage explained 61.3% and 67.9% of the variations in comprehensive quality of hybrid indica rice and inbred japonica rice across different nitrogen levels, respectively. We also found that rice comprehensive quality was better under low nitrogen levels for hybrid indica rice, while for inbred japonica rice, properly increasing nitrogen application could improve the comprehensive quality.

Effects of elevated CO2 on the Cd uptake by rice in Cd-contaminated paddy soils

The rising atmospheric CO₂ is a major driver for climate change, directly affects rice production. Cadmium (Cd) in paddy soils also serves as a persistent concern. Currently, few studies consider the rice response to coupled stresses of elevated CO₂ (eCO₂) and soil Cd. Experimental evidence understanding the effects and mechanisms of eCO₂ on Cd uptake by rice is lacking yet. In a free-air CO₂ enrichment (FACE) system, a 3-year pot experiment was conducted to explore the Cd uptake by rice under two CO₂ conditions (ambient and ambient + 200 µmol·mol^-1) using combinations of in-situ Cd-contaminated soils and associated rice varieties. Results showed that more low-crystalline Fe oxides (Feh) in iron plaque (IP) were deposited on root surface with the increased dissolved Fe²⁺ due to lower soil redox status under eCO₂. The Cd accumulation in rice was hindered due to more Cd associated with Feh (Feh-Cd) rather than uptake by roots. Taken together, the relative effects of eCO₂ on Cd uptake by rice were consistent across years under different Cd-contaminated soils. Our findings will help to better understand the Cd uptake by rice under future climate conditions, and thus push the development of climate-crop-soil models and accurate prediction for food security.

Screening new breeding japonica rice varieties by rice quality, three processing characteristics, and odor characteristics

Rice's yield, cooking, and sensory quality are primary considerations in selecting new breeding rice varieties, which are determined by the rice eating quality such as processing and flavor characteristics. Thus, in this study, to advance the breed of new superior japonica rice varieties, the differences in the rice quality, processing characteristics, and flavor characteristics between 12 newly-bred varieties (H2-36, H2-42, H2-53, H2-59, H2-63, H2-73, H2-74, H2-79, H2-81, H2-82, H2-89, and H2-91) and 1 commercial variety (Kenyu38) were analyzed. The results indicated that H2-42 has a reasonable length-to-width ratio (1.51), high rice yield, good color, reasonable amylose, protein content, excellent water existence index, accessible storage, and the highest taste value. Electronic nose results showed significant differences in aldehydes, ketones, and alcohols among 13 rice varieties. Aroma analysis results showed that H2-42 had the highest n-hexanal (14.63 µg/kg), (E,E)-2,4-nonadienal (37.24 µg/kg), nonanal (19.93 µg/kg), and decanal (4.81 µg/kg); those were important aroma components in cooked rice. The Pearson correlation analysis showed that hardness, springiness, cohesiveness, trough viscosity, peak time, and pasting temperature were the crucial factors that affected rice quality. According to partial least squares regression analysis, total color change, final viscosity, setback, (E)-2-heptenal, and 2-methyl-undecanol were the most important factors that distinguished the rice quality. In conclusion, H2-42 rice was better apparent quality, processing characteristics, and aroma compounds. Therefore, H2-42 has the potential for identification and promotion. PRACTICAL APPLICATION: The results from this study will provide data support for the cultivation, application, and quality improvement of high-quality rice varieties. In addition, it gives new ideas and methods for studying rice eating quality.

Grain yield improvement in high-quality rice varieties released in southern China from 2007 to 2017

In recent years, high-quality rice varieties have been widely cultivated for food production in southern China. However, changes in the yield performance of different high-quality rice varieties are still unclear. In this study, the yield and yield components of 710 different types (hybrid or inbred rice and japonica or indica) of high-quality rice varieties were investigated in six provinces from 2007 to 2017. The results showed that, from 2007 to 2017, the grain yield and yield traits, including the number of spikelets per panicle and seed-set percentage, of high-quality indica rice varieties increased significantly, while the number of panicles decreased only in indica inbred rice. The grain yield of high-quality japonica rice also increased significantly, whereas japonica hybrid rice increased the number of spikelets per panicle and decreased the number of panicles. Compared with inbred rice, hybrid rice had a significant increase in grain yield due to a higher number of spikelets, rather than a lower number of panicles and seed-set percentage. Meanwhile, japonica rice showed higher grain yield than indica rice, which was attributed to seed-set percentage and an optimized structure between the number of panicles and the number of spikelets. In addition, the coefficient of variation of the grain yield of japonica rice decreased, whereas that of indica rice increased over time, and those of the number of panicles and seed-set percentage remained stable. Among the six provinces, Zhejiang had the highest grain yield because the number of spikelets per panicle and seed-set percentage increased over time. Our results suggested that, based on an increase in the yield potential of high-quality rice varieties over the past 11 years, future breeding of high-quality rice should be emphasized to improve the number of panicles and seed-set percentage for hybrid rice and the number of spikelets for inbred rice, especially the grain weight for indica inbred rice.

Optimized Deep Neural Network and Its Application in Fine Sowing of Crops

Winter wheat is one of the most important food products. Increasing food demand and limited land resources have forced the development of agricultural production to be more refined and efficient. The most important part of agricultural production is sowing. With the promotion of precision agriculture, precision seeding has become the main component of modern agricultural seeding technology system, and the adoption of precision seeding technology is an important means of large-scale production and cost saving and efficiency enhancement. However, the current sowing technology and sowing equipment cannot meet the requirements of wheat sowing accuracy. In this context, a differential perturbation particle swarm optimization (DPPSO) algorithm is proposed by embedding differential perturbation into particle swarm optimization, which shows fast convergence speed and good global performance. After that the DPPSO is used to optimize the convolutional neural network (CNN) to build an optimized CNN (DPPSO-CNN) model and applied to the field of crops fine sowing. Finally, the experimental results show that the proposed method not only has a faster convergence rate but also achieves better wheat seeding performance. The research of this paper an effectively improves the accuracy and uniformity of wheat seeding and lay a foundation for improving wheat yield per unit area and promotes the intelligent development of agriculture in the future.

Development of Certified Reference Materials for the Determination of Apparent Amylose Content in Rice

Apparent amylose content (AAC) is one of the most important parameters in rice quality evaluation. In this study, four rice reference materials used to test rice AAC were developed. The AAC of rice reference materials were measured by a spectrophotometric method with a defatting procedure, calibrated from potato amylose and waxy rice amylopectin at the absorption wavelengths of 620 and 720 nm. Homogeneity test (n = 20) was judged by F-test based on the mean squares of among and within bottles, and short- and long-term stability monitoring was performed by T-test to check if there was significant degradation at the delivery temperature of under 40 °C (14 days) and at 0–4 °C storage condition (18 months), respectively. After joint evaluation by ten laboratories, Dixion and Cochran statistical analyses were presented. The expanded uncertainties were calculated based on the uncertainty of homogeneity, short- and long-term stability, and inter-laboratory validation containing factor k = 2. It found that the four reference materials were homogenous and stable, and had the AAC (g/100 g, k = 2) of 2.96 ± 1.01, 10.68 ± 0.66, 17.18 ± 1.04, and 16.09 ± 1.29, respectively, at 620 nm, and 1.46 ± 0.49, 10.44 ± 0.56, 16.82 ± 0.75, and 24.33 ± 0.52, respectively, at 720 nm. It was indicated that 720 nm was more suitable for the determination of rice AAC with lower uncertainties. The determinations of the AAC of 11 rice varieties were carried out by two methods, the method without defatting and with calibration from the four rice reference materials and the method with a defatting procedure and calibrating from potato amylose and waxy rice amylopectin. It confirmed that the undefatted rice reference materials could achieve satisfactory results to test the rice samples with the AAC ranging from 1 to 25 g/100 g. It would greatly reduce the time cost and improve testing efficiency and applicability, and provide technical support for the high-quality development of the rice industry.

Rice congee as an alternative to thickened liquids for patients with swallowing disorders

OBJECTIVES

Seeing the popularity of rice congee consumption among Asian families, the present study examined the possibility of preparing thickened liquids from rice congee of different consistency levels that are commonly prescribed for individuals with swallowing disorders.

METHODS

The two most common rice varieties in Hong Kong, indica and japonica rice grains, were used to prepare rice congee from which thickened liquids were extracted. By varying the water-to-rice ratio, cooking time, optional reheating on a frying pan, and temperature, slightly thick, mildly thick, moderately thick, and extremely thick liquids were obtained.

RESULTS

Recipes for extracting thickened liquids of different consistencies from rice congee cooked with indica and japonica rice grains were established. The consistency levels were defined with reference to although not strictly following the International Dysphagia Diet Standardization Initiative (IDDSI) framework. Results revealed that the consistency of the product varied with water-to-rice ratio, cooking time and temperature.

CONCLUSION

Recipes were established for preparing thickened liquids using rice grains at both serving and room temperatures. Findings support that thickened liquids so obtained can be used as an alternative to thickened liquids preparing using commercial thickeners.

Changes in physicochemical properties of rice flour by fermentation with koji and its potential use in gluten-free noodles

To use rice flour as an ingredient in gluten-free noodles, improved texture properties such as increased hardness and reduced adhesiveness are required. We investigated the physicochemical characteristics of rice flour obtained by fermenting japonica rice with koji, determined the pasting and textural properties of the resulting gel, and suggested a method for producing gluten-free noodles. Koji-fermented rice flour was obtained by fermenting rice grains for 24 and 48 h. Koji fermentation reduced the protein and ash content of the rice and lowered the pH. The change in amylose content was not significant, but the short-to-long-chain ratio of amylopectin increased. Changes in the structural and compositional characteristics facilitated swelling of the rice flour and starch leaching. Variations in the gelatinization and hydration properties of the rice flour increased its peak viscosity and gel hardness, and reduced its gel adhesiveness. Noodles made from koji-fermented rice flour have improved physical features, such as modified textural properties resulting from a gel texture and increased whiteness, indicating that koji-fermented rice flour is a desirable noodle ingredient for gluten-free foods.

Grain chalkiness traits is affected by the synthesis and dynamic accumulation of the storage protein in rice

BACKGROUOND

Grain chalkiness lowers the market value of rice. Alleviating grain chalkiness is the most challenging issue in many rice-producing areas of the world. Nitrogen (N) metabolism has received increasing attention as a result of its relationship with grain chalkiness, although little information is available on the mechanism of N-induced grain chalk.

RESULTS

A highly chalky rice variety OM052 was used to explore the protein synthesis and its accumulation in the grain exposed to N topdressing (N+) at the panicle initiation stage and a control (N-). The results showed that chalky kernels were stimulated by the N+ treatment and more prone to occur on the top and primary rachis. The grain protein content was increased because of the increased average and maximum rates of protein accumulation during grain filling, which was related to the enhanced activities of glutamine synthetase, glutamate synthase, glutamic oxalo-acetic transaminase and glutamate pyruvate transaminase under the N+ treatment. The activities of these enzymes at 15 days after flowering (DAF) were notably positively correlated with grain chalky traits and protein content.

CONCLUSION

N topdressing regulates the synthesis and accumulation of the protein by affecting the key enzymes, especially at 15 DAF, which is attributed to grain chalkiness in rice. © 2021 Society of Chemical Industry.

Genotype-dependent and heat-induced grain chalkiness in rice correlates with the expression patterns of starch biosynthesis genes

Starch biosynthesis is a complex process underlying grain chalkiness in rice in a genotype-dependent manner. Coordinated expression of starch biosynthesis genes is important for producing translucent rice grains, while disruption in this process leads to opaque or chalky grains. To better understand the dynamics of starch biosynthesis genes in grain chalkiness, six rice genotypes showing variable chalk levels were subjected to gene expression analysis during reproductive stages. In the chalky genotypes, peak expression of the large subunit genes of ADP-glucose pyrophosphorylase (AGPase), encoding the first key step in starch biosynthesis, occurred in the stages before grain filling commenced, creating a gap with the upregulation of starch synthase genes, granule bound starch synthase I (GBSSI) and starch synthase IIA (SSIIA). Whereas, in low-chalk genotypes, AGPase large subunit genes expressed at later stages, generally following the expression patterns of GBSSI and SSIIA. However, heat treatment altered the expression in a genotype-dependent manner that was accompanied by transformed grain morphology and increased chalkiness. The suppression of AGPase subunit genes during early grain filling stages was observed in the chalky genotypes or upon heat treatment, which could result in a limited pool of ADP-Glucose for synthesizing amylose and amylopectin, the major components of the starch. This suboptimal starch biosynthesis process could subsequently lead to inefficient grain filling and air pockets that contribute to chalkiness. In summary, this study suggests a mechanism of grain chalkiness based on the expression patterns of the starch biosynthesis genes in rice.

Genetic and Molecular Factors Determining Grain Weight in Rice

Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.

Genomic Prediction of Yield Traits in Single-Cross Hybrid Rice (Oryza sativa L.)

Hybrid rice varieties can outyield the best inbred varieties by 15 – 30% with appropriate management. However, hybrid rice requires more inputs and management than inbred rice to realize a yield advantage in high-yielding environments. The development of stress-tolerant hybrid rice with lowered input requirements could increase hybrid rice yield relative to production costs. We used genomic prediction to evaluate the combining abilities of 564 stress-tolerant lines used to develop Green Super Rice with 13 male sterile lines of the International Rice Research Institute for yield-related traits. We also evaluated the performance of their F₁ hybrids. We identified male sterile lines with good combining ability as well as F₁ hybrids with potential further use in product development. For yield per plant, accuracies of genomic predictions of hybrid genetic values ranged from 0.490 to 0.822 in cross-validation if neither parent or up to both parents were included in the training set, and both general and specific combining abilities were modeled. The accuracy of phenotypic selection for hybrid yield per plant was 0.682. The accuracy of genomic predictions of male GCA for yield per plant was 0.241, while the accuracy of phenotypic selection was 0.562. At the observed accuracies, genomic prediction of hybrid genetic value could allow improved identification of high-performing single crosses. In a reciprocal recurrent genomic selection program with an accelerated breeding cycle, observed male GCA genomic prediction accuracies would lead to similar rates of genetic gain as phenotypic selection. It is likely that prediction accuracies of male GCA could be improved further by targeted expansion of the training set. Additionally, we tested the correlation of parental genetic distance with mid-parent heterosis in the phenotyped hybrids. We found the average mid-parent heterosis for yield per plant to be consistent with existing literature values at 32.0%. In the overall population of study, parental genetic distance was significantly negatively correlated with mid-parent heterosis for yield per plant (r = −0.131) and potential yield (r = −0.092), but within female families the correlations were non-significant and near zero. As such, positive parental genetic distance was not reliably associated with positive mid-parent heterosis.

Variability in waxy (Wx) allele, in-vitro starch digestibility, glycemic response and textural behaviour of popular Northern Himalayan rice varieties

Eight commonly cultivated and consumed rice varieties of Northern Himalayan regions and a popular high amylose rice variety were characterized at Wx locus and evaluated for resistant starch (RS), in-vitro starch digestibility, predicted glycemic index (pGI), glycemic load (GL) and textural parameters. Cytosine and thymine repeats (CT)n at waxy locus (Wx) showed high association with apparent amylose content (AAC). Both pGI and GL varied substantially within the selected varieties. The pGI was relatively lower in high and intermediate amylose Indica varieties compared to low amylose Japonica ones. However, Koshikari despite being a low amylose variety showed relatively lower pGI and GL, due to its higher RS, dietary fiber, protein and fat content. It was thus presumed that in addition to AAC, RS and other grain components also affect the glycemic response. Inherent resistance to enzymatic hydrolysis was also found to be higher in firm textured and less sticky rice varieties. The genotypes-Lalat, Basmati-1509 and Koshikari, in view of their low to moderate pGI and relatively higher RS content, can be explored in future breeding programmes to develop rice varieties whose consumption will help to prevent hyper/hypo glycemic responses in Northern Himalayan regions, where daily staple diet is rice.

Characteristics of Grain Physicochemical Properties and the Starch Structure in Rice Carrying a Mutated ALK/SSIIa Gene

The gelatinization temperature (GT) of endosperm starch influences rice eating and the cooking quality (ECQ). ALK encoding soluble starch synthase IIa (SSIIa) is the major gene determining grain GT in rice. Herein, we identified a spontaneous ALK mutant named ALK^d, which resulted from a G/T single-nucleotide polymorphism (SNP) in exon 1 of the ALK^c allele from the high-GT indica rice cultivar. Compared with grains from the ALK^c near-isogenic line (NIL), NIL(ALK^d) grains exhibited a high GT (2.3 °C) and improved retrogradation properties. The NIL(ALK^d) grain starch contained an increased proportion of amylopectin intermediate chains (DP 13-24) at the expense of short chains (DP < 12), resulting in enhancements in both the crystallinity and the lamellar peak intensity compared with low-GT rice grains. Moreover, both NIL(ALK^d) and NIL(ALK^c) grains also featured a significantly lower apparent amylose content (AAC), harder gel consistency (GC), higher pasting curve, and poorer taste values in comparison to Nip(ALK^a) grains. Taken together, this work provides novel insights underlying the allelic variation of the ALK gene in rice.

Robustification of Linear Regression and Its Application in Genome-Wide Association Studies

Regression analysis is one of the most popular statistical techniques that attempt to explore the relationships between a response (dependent) variable and one or more explanatory (independent) variables. To test the overall significance of regression, F-statistic is used if the parameters are estimated by the least-squares estimators (LSEs), while if the parameters are estimated by the maximum likelihood estimators (MLEs), the likelihood ratio test (LRT) statistic is used. However, both procedures produce misleading results and often fail to provide good fits to the reasonable space of the dataset in the presence of outlying observations. Moreover, outliers occur very frequently in any real datasets as well as in the molecular OMICS datasets. Hence, an effort is made in this study to robustify MLE based regression analysis by maximizing the β-likelihood function. The tuning parameter β is selected by cross-validation. For β = 0, the proposed method reduces to the classical MLE based regression analysis. We inspect the performance of the proposed method using both synthetic and real data analysis. The results of simulations indicate that the proposed method performs better than traditional methods in both outliers and high leverage points to estimate the parameters and mean square errors. The results of relative efficiency analysis show that the proposed estimator is relatively less affected than the popular estimators, including S, MM, and fast-S for normal error distribution in case high dimension and outliers. Also, real data analysis results demonstrated that the proposed method shows robust properties with respect to data contaminations, overcome the drawback of the traditional methods. Genome-wide association studies (GWAS) by the proposed method identify the vital gene influencing hypertension and iron level in the liver and spleen of mice. Furthermore, we have identified 15 and 21 significant SNPs for chalkiness degree and chalkiness percentage, respectively, by GWAS based on the proposed method. The variant of the SNPs might be provided the new resources for grain quality traits and could be used for further molecular and physiological analysis to enhance the better quality of rice grain. These results offer an important basis for further understanding of the robust regression analysis, which might be applied in various fields, including business, genetics, and bioinformatics.

In-Frame and Frame-Shift Editing of the Ehd1 Gene to Develop Japonica Rice With Prolonged Basic Vegetative Growth Periods

Japonica rice has become increasingly popular in China owing to its superior grain quality. Over the past decades, "indica to japonica" projects have been proposed to promote cultivation of japonica rice in low latitudes in China. Traditionally, japonica varieties were planted mainly in mid latitudes in the northeast plain and Yangtze River region. The key obstacle for introducing elite mid-latitude japonica varieties to low latitudes is the severe shortening of growth period of the japonica varieties due to their sensitivity to low-latitude short photoperiod and high temperature. Here we report development of new japonica rice with prolonged basic vegetative growth (BVG) periods for low latitudes by targeted editing the Early heading date 1 (Ehd1) gene. Using CRISPR/Cas9 system, we generated both frame-shift and/or in-frame deletion mutants in four japonica varieties, Nipponbare, Longdao16, Longdao24, and Xiushui134. When planting at low-latitude stations, the frame-shift homozygous lines exhibited significantly longer BVG periods compared with wild-types. Interestingly, we observed that minor deletion of the first few residues within the receiver domain could quantitatively impair the function of Ehd1 on activation of Hd3a and RFT1, resulting in an intermediate-long BVG period phenotype in the homozygous in-frame deletion ehd1 lines. Field investigation further showed that, both the in-frame and frame-shift lines exhibited significantly improved yield potential compared with wild-types. Our study demonstrates an effective approach to rapid breeding of elite japonica varieties with intermediate-long and long BVG periods for flexible cropping systems in diverse areas or under different seasons in southern China, and other low-latitude regions.

How Does the Control of Grain Purchase Price Affect the Sustainability of the National Grain Industry? One Empirical Study from China

As one of the most important grain protection policies in China, the minimum purchase price policy prevents the fluctuation of grain output and protects the interests of farmers by regulating the prices of major grain varieties. For developing countries with a shortage of agricultural resources, represented by China, an in-depth study on the implementation effect and public satisfaction of this policy is of great significance for promoting the sustainable development of the grain industry. Based on the interest demands of the government, farmers, grain enterprises and consumers, this paper constructs a policy satisfaction evaluation model based on the Analytic Hierarchy Process and Fuzzy Comprehensive Evaluation. The research shows that the implementation effect of this policy has promoted the sustainable development of China’s grain in four aspects: improving farmers’ enthusiasm for planting, optimizing the structure of supply and demand, reducing the adverse impact of disasters, and ensuring the steady increase of output. However, due to the differences in natural resources and folk customs, the implementation effect of this policy varies in different regions.

The Amino Acid Permease 5 (OsAAP5) Regulates Tiller Number and Grain Yield in Rice

As fundamental nutrients, amino acids are important for rice (Oryza sativa) growth and development. Here, we identified the amino acid permease 5 (OsAAP5), that regulates tiller number and grain yield in rice. The OsAAP5 promoter sequence differed between indica and japonica rice varieties. Lower expression of OsAAP5 in the young leaf blade in indica varieties than in japonica varieties was associated with more tillers in indica than in japonica Down-regulation of OsAAP5 expression in japonica using RNA interference (RNAi) and clustered regularly interspaced short palindromic repeats led to increases in tiller number and grain yield, whereas OsAAP5 overexpression (OE) had the opposite effect. Both a protoplast amino acid uptake assay and HPLC analysis indicated that more basic (Lys, Arg) and neutral (Val, Ala) amino acids were transported and accumulated in the OE lines than in the wild type, but the opposite was observed in the RNAi lines. Furthermore, exogenous application of Lys, Arg, Val, and Ala in the OE lines substantially inhibited tiller bud elongation, but the effect was lost in the RNAi lines. Notably, concentrations of the cytokinins cis-zeatin and dihydrozeatin were much lower in the OE lines than in the wild type, whereas concentrations in the RNAi lines were higher. Thus, OsAAP5 could regulate tiller bud outgrowth by affecting cytokinin levels, and knockout of OsAAP5 could be valuable for japonica breeding programs seeking high yield and grain quality.