Post-genomics revolution in the design of premium quality rice in a high-yielding background to meet consumer demands in the 21st century

OsEXPA7 Encoding an Expansin Affects Grain Size and Quality Traits in Rice (Oryza sativa L.)

BACKGROUND

Yield and quality are the two most important traits in crop breeding. Exploring the regulatory mechanisms that affect both yield and quality traits is of great significance for understanding the molecular genetic networks controlling these key crop attributes. Expansins are cell wall loosening proteins that play important roles in regulating rice grain size.

RESULTS

We investigated the effect of OsEXPA7, encoding an expansin, on rice grain size and quality. OsEXPA7 overexpression resulted in increased plant height, panicle length, grain length, and thousand-grain weight in rice. OsEXPA7 overexpression also affected gel consistency and amylose content in rice grains, thus affecting rice quality. Subcellular localization and tissue expression analyses showed that OsEXPA7 is localized on the cell wall and is highly expressed in the panicle. Hormone treatment experiments revealed that OsEXPA7 expression mainly responds to methyl jasmonate, brassinolide, and gibberellin. Transcriptome analysis and RT-qPCR experiments showed that overexpression of OsEXPA7 affects the expression of OsJAZs in the jasmonic acid pathway and BZR1 and GE in the brassinosteroid pathway. In addition, OsEXPA7 regulates the expression of key quantitative trait loci related to yield traits, as well as regulates the expression levels of BIP1 and bZIP50 involved in the seed storage protein biosynthesis pathway.

CONCLUSIONS

These results reveal that OsEXPA7 positively regulates rice yield traits and negatively regulates grain quality traits by involving plant hormone pathways and other trait-related pathway genes. These findings increase our understanding of the potential mechanism of expansins in regulating rice yield and quality traits and will be useful for breeding high-yielding and high-quality rice cultivars.

Analysis of the Differences in Volatile Organic Compounds in Different Rice Varieties Based on GC-IMS Technology Combined with Multivariate Statistical Modelling

In order to investigate the flavour characteristics of aromatic, glutinous, and nonaromatic rice, gas chromatography-ion mobility spectrometry (GC-IMS) was used to analyse the differences in volatile organic compounds (VOCs) amongst different rice varieties. The results showed that 103 signal peaks were detected in these rice varieties, and 91 volatile flavour substances were identified. Amongst them, 28 aldehydes (28.89~31.17%), 24 alcohols (34.85~40.52%), 14 ketones (12.26~14.74%), 12 esters (2.30~4.15%), 5 acids (7.80~10.85%), 3 furans (0.30~0.68%), 3 terpenes (0.34~0.64%), and 2 species of ethers (0.80~1.78%) were detected. SIMCA14.1 was used to perform principal component analysis (PCA) and orthogonal partial least squares discriminant analysis, and some potential character markers (VIP > 1) were further screened out of the 91 flavour substances identified based on the variable important projections, including ethanol, 1-hexanol, hexanal, heptanal, nonanal, (E)-2-heptenal, octanal, trans-2-octenal, pentanal, acetone, 6-methyl-5-hepten-2-one, ethyl acetate, propyl acetate, acetic acid, and dimethyl sulphide. Based on the established fingerprint information, combined with principal component analysis and orthogonal partial least squares discriminant analysis, different rice varieties were also effectively classified, and the results of this study provide data references for the improvement in aromatic rice varieties.

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.

Combined effects of SSII-2RNAi and different Wx alleles on rice grain transparency and physicochemical properties

Near-isogenic lines Nip(Wx^b/SSII-2), Nip(Wx^b/ss2-2), Nip(Wx^mw/SSII-2), Nip(Wx^mw/ss2-2), Nip(Wx^mp/SSII-2) and Nip(Wx^mp/ss2-2) in the Nipponbare (Nip) background containing the SSII-2RNAi cassette combined with different Waxy (Wx) alleles were investigated in terms of rice grain transparency and quality profiles. Rice lines carrying the SSII-2RNAi cassette displayed downregulation of SSII-2, SSII-3 and Wx genes. Introduction of the SSII-2RNAi cassette decreased apparent amylose content (AAC) in all transgenic lines, but grain transparency differed between low AAC rice lines. Grains from Nip(Wx^b/SSII-2) and Nip(Wx^b/ss2-2) were transparent, while those of rice were increasingly translucent with decreasing moisture due to cavities within starch granules. Rice grain transparency was positively correlated with grain moisture and AAC, but negatively correlated with cavity area within starch granules. Starch fine structure analysis revealed a marked increase in short amylopectin chains with DP 6-12, but a decrease in intermediate chains with DP 13-24, resulting in decreased gelatinisation temperature. Starch crystalline structure analysis showed that the transgenic rice starches have lower crystallinity and lamellar repeat distance than controls due to differences in starch fine structure. The results highlight the molecular basis underpinning rice grain transparency, and provide strategies for improving rice grain transparency.

Elemental Composition and Implications on Brown Rice Flour Biofortified with Selenium

Rice (Oryza sativa L.) is one of the most economically and socially important cereals in the world. Several strategies such as biofortification have been developed in a way eco-friendly and sustainable to enhance crop productivity. This study implemented an agronomic itinerary in Ariete and Ceres rice varieties in experimental fields using the foliar application of selenium (Se) to increase rice nutritional value. At strategic phases of the plant's development (at the end of booting, anthesis, and at the milky grain stage), they were sprayed with sodium selenate (Na₂SeO₄) and sodium selenite (Na₂SeO₃). In the first foliar application plants were sprayed with 500 g Se·ha^-1 and in the remaining two foliar applications were sprayed with 300 g Se·ha^-1. The effects of Se in the level of micro and macronutrients in brown grains, the localization of Se in these grains, and the subsequent quality parameters such as colorimetric characteristics and total protein were considered. After grain harvesting, the application of selenite showed the highest enrichment in all grain with levels reaching 17.06 µg g^-1 Se and 14.28 µg g^-1 Se in Ariete and Ceres varieties, respectively. In the Ceres and Ariete varieties, biofortification significantly affected the K and P contents. Regarding Ca, a clear trend prevailed suggesting that Se antagonizes the uptake of it, while for the remaining elements in general (except Mn) no significant differences were noted. Protein content increased with selenite treatment in the Ariete variety but not in Ceres. Therefore, it was possible to conclude, without compromising quality, that there was an increase in the nutritional content of Se in brown rice grain.

Generation of new rice germplasms with low amylose content by CRISPR/CAS9-targeted mutagenesis of the FLOURY ENDOSPERM 2 gene

FLOURY ENDOSPERM 2 (FLO2), encoding a tetratricopeptide repeat domain (TPR)-containing protein located in the nucleus, is considered to be a regulatory protein that controls the biosynthesis of seed storage substances. The diversity of flo2 allele is attributable for the variations in grain appearance, amylose content (AC), and physicochemical properties, influencing the eating and cooking quality (ECQ) of rice. In this study, we used CRISPR/Cas9 to introduce loss-of-function mutations into the FLOURY ENDOSPERM 2 gene in Suken118 (SK118), a widely cultivated elite japonica rice variety in Jiangsu, China. Physiochemical analyses of the flo2 mutants were congruent with previous studies, exhibiting lowered AC and viscosity, risen gel consistency (GC) and gelatinization temperature (GT) values, which were all instrumental to the improvement of ECQ. However, the wrinkled opaque appearance and the decrease in grain width, grain thickness and grain weight imply trade-offs in grain yield. Despite the ex-ante estimation for low yielding, the superior ECQ in these novel genotypes generated by using genome editing approach may have the potential for formulating high value specialty food.

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.

Novel PCR-Based Multiplex Assays for Detecting Major Quality and Biotic Stress in Commercial and Weedy Rice

While previous research has demonstrated that multiplex polymerase chain reaction (PCR) can be a cost-effective approach to detect various genes in crops, the availability of multiplex assays to simultaneously screen both grain quality and biotic stress resistance traits in rice (Oryza sativa) is limited. In this work, we report six novel multiplex assays that use a universal protocol to detect major rice grain quality (amylose content and fragrance) and biotic stress (blast, sheath blight, and bacterial leaf blight) traits with amplified products consisting of up to four primer pairs that can be analyzed using a standard agarose-based gel electrophoresis system. Recent studies have suggested that weedy rice has novel sources of disease resistance. However, an intensive screening of weedy biotypes has not been reported in Malaysia. Accordingly, we employed one of the developed multiplex assays to screen reported genes or quantitative trait loci (QTLs) associated with blast, sheath blight, and bacterial leaf blight diseases in 100 weedy rice biotypes collected from five local fields, with phenotyping performed to validate the genotyping results. In conclusion, our universal multiplex protocol is effective for the large-scale genotyping of rice genetic resources, and it can be employed in routine molecular laboratories with limited resources.

The Underlying Physicochemical Properties and Starch Structures of indica Rice Grains with Translucent Endosperms under Low-Moisture Conditions

Rice grain quality is a complex trait that includes processing, appearance, eating, cooking, and nutrition components. The amylose content (AC) in the rice endosperm affects the eating and cooking quality along with the appearance of milled rice. In this study, four indica rice varieties with different ACs were used to study the factors affecting endosperm transparency along with the physical and chemical characteristics and eating quality of translucent endosperm varieties. Endosperm transparency was positively correlated with water content and negatively correlated with the cumulative area of cavities within starch granules. The indica landrace 28Zhan had a translucent endosperm and exhibited good taste. Based on starch fine structure analysis, long-chain amylopectin and the B2 chain of amylopectin might be major contributors to the good taste and relatively slow digestion of this landrace.