Natural variation of OsGluA2 is involved in grain protein content regulation in rice

Elevated atmospheric CO2 concentration enhances the cooking and eating quality of hybrid rice by modifying starch granule structure

Elevated atmospheric CO2 concentration (eCO2) is a key driver of climate change, influencing crop yield and quality. However, its effects on the cooking and eating quality (CEQ) of hybrid rice remain unclear. This study investigates eCO2's effect on CEQ by conducting a field experiment from 2015 to 2017 with three popular varieties grown in a free-air CO2 enrichment platform. eCO2 enhanced the volume and surface area of starch granule due to the formation of additional dents and holes on its surface upon eCO2, thereby altering its morphology and potentially influencing starch-protein interplay. It also induced significant changes in starch molecular structure, including increases in blue value (22.4 %), iodine binding power (5.7 %), and amylose content (5.5 %), while protein concentration decreased. These changes led to improvements in pasting (11.0 % increase in breakdown) and thermal properties (ΔHgel increased by 15.6 %), ultimately enhancing the rice taste by 8.5 %. Statistical analysis indicates that these improvements were primarily driven by eCO2-induced changes in starch granule structure. Indica-hybrid rice exhibited a greater response to eCO2, which was influenced by environmental conditions. This study provides valuable insights into how eCO2 affects hybrid rice CEQ, highlighting the need to consider varietal and environmental factors when developing climate adaptation strategies.

Unlocking the potential of wild rice to bring missing nutrition to elite grains

The domestication and artificial selection of rice involved profound genetic changes that rendered wild rice more suitable for cultivation and consumption. As a result, rice has been extensively used as a caloric source to address hunger without sufficiently considering its total nutritional value. In this review, we highlight how domestication has altered starch quality and other nutritional traits in rice, including flavonoid, protein, and lipid content, as well as digestibility and texture. Precise genetic alterations through transgenic technologies hold significant promise for the reintroduction of key nutrient biosynthesis genes that have been lost in cultivated rice. Although there is currently little concrete evidence that genome editing has improved wild rice, the de novo domestication of wild rice enables the retention of its multi-nutritional properties while enhancing its agronomic performance and grain quality. We propose that the use of accelerated breeding techniques to introgress beneficial nutritional alleles from wild rice into elite pools could advance efforts to use wild rice to improve human health.

OsGATA7 and SMOS1 cooperatively determine rice taste quality by repressing OsGluA2 expression and protein biosynthesis

Taste is crucial for the economic value of rice (Oryza sativa L.) and determines consumer preference. However, the mechanisms underlying taste formation have remained unclear. Here, we show that OsGATA7 contributes to desirable taste quality by affecting the swelling properties, texture, and taste value of cooked rice. OsGATA7 binds to the promoter of SMOS1, and activates its expression, thereby regulating taste quality. Furthermore, SMOS1 binds to the promoter of the protein biosynthesis gene OsGluA2, and recruits the PRC2 complex to repress its expression, leading to increased protein content. The overexpression of both OsGATA7 and SMOS1 reduces protein content and enhances taste quality. The haplotypes OsGATA7Hap1 and SMOS1Hap1 maintain low protein content and improve taste scores. Collectively, these findings reveal a regulatory mechanism for taste quality formation mediated by the OsGATA7-SMOS1 protein content module, and identify the elite haplotypes OsGATA7Hap1 and SMOS1Hap1 as a means to improve taste quality.

Amino acid transporter OsATL13 coordinately regulates rice yield and quality by transporting phenylalanine and methionine

Amino acids are crucial nutrients for growth in crops. In this study, we found an amino acid transporter-like 13 (OsATL13), that coordinately determined rice yield and quality. OsATL13 was primarily expressed in the root and panicle, its protein was localized on plasma membrane, and it principally transported phenylalanine and methionine. Overexpression (OE) of OsATL13 increased the tiller number by 31.4 %, resulting in a 16.18 % increase in grain yield compared to Zhonghua 11 (ZH11). It also decreased amylose content and increased protein content in OsATL13 OE lines compared to ZH11, whereas the OsATL13 mutant exhibited opposite effects. RNA-seq analysis revealed that upregulation of OsATL13 influenced the expression of genes associated with nitrogen and starch metabolism pathways. Notably, exogenous treatment with phenylalanine and methionine promoted axillary buds outgrowth, increased tiller number and rice yield, improved milled and head rice rates, and decreased chalky rice rate. Furthermore, rapid viscosity analysis supported the observation that phenylalanine and methionine treatments influenced rice eating and cooking quality. This research offers new perspectives on the synchronized enhancement of both rice yield and quality with amino acid transporter OsATL13.

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

Positional variations of rice protein compositions accumulation within a panicle during the grain filling

Grain protein is a critical quality attribute of rice that influences consumer preferences. However, the spatial variation in protein accumulation within a rice panicle remains poorly understood. This study investigated the dynamics of protein accumulation, including protein components and protein synthesis-related enzymes and genes, among grains located at the top, middle, and bottom primary rachises of a rice panicle during the grain filling. The results revealed significant variations in protein compositions across different rachis positions. The contents of albumin, globulin, prolamin, glutelin, and total protein contents exhibited fluctuations during grain filling. Notably, the grain position had a significant effect on glutelin content, with grains at the bottom primary rachis consistently having higher glutelin level than those at the top and middle rachises, except 17 days after flowering (DAF). A similar trend was observed for total protein content. Grains at the bottom rachis demonstrated dominance in the rate of protein accumulation, initiating rapid accumulation 2.0 d later and 2.2 d earlier than grains at the top and middle rachises, respectively. Furthermore, the duration of active protein accumulation was 1.9 d and 3.4 d shorter for grains at the bottom rachis compared to those at the top and middle rachises, respectively. This phenomenon was attributed to alterations in enzymatic activities. Specifically, the activities of glutamine synthetase (GS), glutamate synthase (GOGAT), glutamate pyruvate transaminase (GPT), and glutamic oxalo-acetic transaminase (GOT) in grains located at the basal rachis exhibited a marked increase from 8 DAF to 17 DAF. These activities were significantly elevated compared to those observed in grains at the top and middle rachis, although they experienced a subsequent sharp decline. The glutelin content and enzymatic activities demonstrated a strong correlation, either positive or negative, at 11 DAF and 20 DAF. These findings suggest that the positional changes of grain protein were closely associated with nitrogen assimilation and glutelin accumulation during the rice grain filling process.

Mapping Genomic Regions for Grain Protein Content and Quality Traits in Milled Rice (Oryza sativa L.)

Grain protein content (GPC) is gaining attention due to increasing consumer demand for nutritious foods. The present study carried out at ICAR-IIRR, Hyderabad, focused on the identification of quantitative trait loci (QTLs) linked with GPC and other quality traits. We utilized a population of 188 F2 individuals developed from BPT 5204 (low GPC) X JAK 686 (high GPC) for QTL analysis. QTL analysis yielded four significant QTLs for GPC, three for amylose content, and multiple QTLs for other quality traits. qPC1.2, a major QTL in milled rice, was located in the marker interval RM562-RM11307 on chromosome 1 with an LOD value of 4.4. qPC1.2 explained 15.71% of the phenotypic variance (PVE). Additionally, the Interval Mapping for Epistatic QTLs (IM-EPI) method detected 332 pairs of di-genic epistatic QTLs. Fifteen QTLs exhibited a positive additive effect, indicating that the contributing allele(s) was from JAK 686. Five F2 plants, viz., F2-140, F2-12, F2-7, F2-147, and F2-41, exhibited a high GPC of 14.67%, 14.36%, 14.32%, 13.60%, and 13.36%, respectively. Additionally, these plants also exhibited high per-plant grain yield (~17.0-29.0 g) with desirable agronomic traits. The QTLs identified are valuable resources for developing high-grain-protein varieties with high grain yield and desirable quality traits.

CRISPR/Cas9-mediated editing of BADH2 and Wx genes for the development of novel aromatic and soft-textured black and red rice

Black and red rice are known for their rich nutritional content, yet most varieties suffer from a firm texture and insufficient fragrance. In this study, we aimed to develop a fragrant and soft-textured black and red rice variety using the CRISPR/Cas9 technology to knock out the OsWx gene, which is associated with amylose content (AC), and the OsBADH2 gene, responsible for rice aroma. Our results showed that, compared to wild-type, CRISPR lines of XHZ, HM, NWZ, and PGZ targeting OsWx and OsBADH2 exhibited a reduction in AC content, altered gel consistency, and a more than 50% increase in gel consistency. Headspace solid-phase microextraction gas chromatography-mass spectrometry (HS-SPME-GC-MS) analysis revealed that the 2-acetyl-1-pyrroline (2-AP) content in the grains of xhz-cBADH2 Wx and hm-cBADH2 Wx reached 189.04 μg kg-1 and 309.03 μg kg-1, respectively. Furthermore, we observed a slight increase in anthocyanins and proanthocyanidins in these co-edited lines, without significant effects on their agronomic traits. Furthermore, to investigate the genes involved in the quality formation of black and red rice for the knockout of OsBADH2 and OsWx, we conducted RNA-seq analysis. The results indicated that knockout of OsBADH2 and OsWx affected the expression of genes involved in carotenoid biosynthesis, multiple amino acid metabolism genes, and endosperm starch and sucrose metabolic pathways. These findings suggest that the CRISPR/Cas9 technology can effectively target OsBADH2 and OsWx to develop high-quality black and red rice varieties with enhanced aroma and softer texture, providing a new strategy for the improvement of colored rice.

Maize kernel nutritional quality-an old challenge for modern breeders

MAIN CONCLUSION

This article offers a comprehensive overview of the starch, protein, oil, and carotenoids content in maize kernels, while also outlining future directions for research in this area. Maize is one of the most important cereal crops globally. Maize kernels serve as a vital source of feed and food, and their nutritional quality directly impacts the dietary intake of both animals and humans. Maize kernels contain starch, protein, oil, carotenoids, and a variety of vitamins and minerals, all of which are important for maintaining life and promoting health. This review presents the current understanding of the content of starch, protein, amino acids, oil, and carotenoids in maize kernels, while also highlighting knowledge gaps that need to be addressed.

Overexpression of the general transcription factor OsTFIIB5 alters rice development and seed quality

KEY MESSAGE

Overexpression of general transcription factor OsTFIIB5 in rice affects seedling growth, plant height, flowering time, panicle architecture, and seed protein/starch levels and involves modulation of expression of associated genes. TFIIB, a key general transcription factor (GTF), plays a critical role in pre-initiation complex (PIC) formation and facilitates RNA polymerase II-mediated transcription. In humans and yeast, TFIIB is encoded by a single gene; however, in plants it is encoded by a multigene family whose products may perform specialized transcriptional functions. The role of plant TFIIBs, particularly in monocots, remains largely unexplored. This study presents the first functional characterization of the rice TFIIB gene, OsTFIIB5 (LOC_Os09g36440), during development. Expression profiling of OsTFIIB5 revealed differential patterns across various developmental stages, with pronounced transcript accumulation during seed development. Overexpression of OsTFIIB5 impacted multiple stages of plant growth and development, leading to phenotypic changes such as altered seedling growth, reduced plant height, early heading, altered panicle architecture, decreased yield, and changes in seed storage substances. Notably, there were no effects on seed germination, pollen development, and grain size. Reduction in shoot length and plant height was linked to altered expression of genes involved in gibberellin (GA) biosynthesis, signalling, and deactivation. Overexpression of OsTFIIB5 enhanced the expression of genes involved in the photoperiodic flowering pathway, resulting in early panicle emergence. Higher expression levels of OsTFIIB5 also induced the accumulation of seed storage proteins (SSPs), while reducing starch content and altering the proportions of amylose and amylopectin in seeds. These findings suggest that OsTFIIB5 functions as a transcriptional regulator, governing multiple aspects of rice growth and development.

Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC4F2 segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC4F2 population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement.

Maternally expressed FERTILIZATION-INDEPENDENT ENDOSPERM1 regulates seed dormancy and aleurone development in rice

Seed dormancy, an essential trait for plant adaptation, is determined by the embryo itself and the surrounding tissues. Here, we found that rice (Oryza sativa) FERTILIZATION-INDEPENDENT ENDOSPERM1 (OsFIE1) regulates endosperm-imposed dormancy and the dorsal aleurone thickness in a manner dependent on the parent of origin. Maternally expressed OsFIE1 suppresses gibberellin (GA) biosynthesis in the endosperm by depositing trimethylation of lysine 27 on histone H3 (H3K27me3) marks on GA biosynthesis-related genes, thus inhibiting germination and aleurone differentiation. Knockout of rice GA 20-oxidase1 (OsGA20ox1) alleviated the phenotypic defects in osfie1. The aleurone-positive determinant Crinkly 4 (OsCR4) is another target of the OsFIE1-containing Polycomb repressive complex 2 (PRC2). We found that OsFIE1 plays an important role in genomic imprinting in the endosperm of germinating seeds, particularly for paternally expressed genes associated with H3K27me3. The increased aleurone thickness of osfie1 substantially improved grain nutritional quality, indicating that the osfie1 gene may be utilized for breeding nutrient-enriched rice. The findings provide insights into the essential roles of PRC2-mediated H3K27me3 methylation in the acquisition of seed dormancy and endosperm cell differentiation in rice.

Functional nutritional rice: current progresses and future prospects

More than half of the world's population relies on rice as their staple food for three meals a day. From a dietary perspective, rice can be considered the most important grain in the world. With the continuous improvement of people's living standards, the demand for food has gradually shifted from being full and eating well to being nutritious and healthy. Developing functional nutritional rice has become an important research direction and strategic initiative for developing a major food concept. In this paper, we review the current progress in the breeding of functional nutritional rice and mineral-biofortified rice. This review focuses on the following aspects: (i) the concept, rice basic structure, nutritional components, and categorization of functional nutritional rice; (ii) genes that have been applied and identified so far, including nutritional functional rice genes, mineral bioenhancement-related genes, and their regulatory mechanisms; (iii) based on the history and technical mainline of rice breeding, research progress in nutritional functional rice using conventional breeding, a combination of conventional breeding and marker-assisted breeding, mutagenesis breeding, genetic engineering technology, and gene editing technology. Based on the current research and industrialization issues, we highlight an outlook of the problems and future developmental directions in nutritional functional rice research.

Exploring the impact of key physicochemical properties of rice on taste quality and instant rice processing

Taste quality is one of the most important indicators for assessing the quality of rice. However, there has been a lack of systematic studies investigating the impact factors of taste quality. In this study, chromosomal segment substitution lines (CSSLs) with notable differences in physicochemical properties were obtained by screening the CSSL population. A correlation analysis between the physicochemical properties and the taste qualities of rice revealed that amylose and protein content are significantly negatively correlated with the taste value of both freshly cooked and rehydrated instant rice. The alkali spreading value (ASV) had limited impact on the taste value of rice, but low-ASV rice is more resistant to cooking. Grain chalkiness played a critical role in maintaining the integrity of freshly cooked rice and instant rice grains after rehydration. In summary, our study provides crucial insights and guidance for rice breeding, with the goal of developing excellent quality and enhancing the processing of instant rice.

RAL6 encodes a seed allergenic protein that positively regulates grain weight and seed germination

The rice albumin (RAG) gene family belongs to the Tryp_alpha_amyl family. RAG2, specifically expressed in 14-21 DAP (days after pollination) seeds, regulates grain yield and quality. In this study, we identified another RAG family gene, RAL6, which exhibits specific expression in developing seeds, particularly in 7, 10, and 15 DAP seeds. Employing the CRISPR/Cas9 system, we analyzed functions of RAL6 and found that the ral6 lines (ral6-1, ral6-2, ral6-3, and ral6-4) displayed thinner seeds with significantly decreased 1000-grain weight and grain thickness compared to ZH11. Additionally, the cell width of spikelet cells, total protein and glutelin contents were significantly reduced in ral6. The germination assay and 1% TTC staining revealed a significant decrease in seed vigor among the ral6 lines. The alpha-amylase activity in ral6 mutant seeds was also markedly lower than in ZH11 seeds after 2 days of imbibition. Furthermore, co-expression analysis and GO annotation showed that co-expressed genes were involved in immune response, oligopeptide transport, and the glucan biosynthetic process. Collectively, our findings suggest that RAL6 plays a coordinating role in regulating grain weight and seed germination in rice.

A Quantitative Computational Framework for Allopolyploid Single-Cell Data Integration and Core Gene Ranking in Development

Polyploidization drives regulatory and phenotypic innovation. How the merger of different genomes contributes to polyploid development is a fundamental issue in evolutionary developmental biology and breeding research. Clarifying this issue is challenging because of genome complexity and the difficulty in tracking stochastic subgenome divergence during development. Recent single-cell sequencing techniques enabled probing subgenome-divergent regulation in the context of cellular differentiation. However, analyzing single-cell data suffers from high error rates due to high dimensionality, noise, and sparsity, and the errors stack up in polyploid analysis due to the increased dimensionality of comparisons between subgenomes of each cell, hindering deeper mechanistic understandings. In this study, we develop a quantitative computational framework, called "pseudo-genome divergence quantification" (pgDQ), for quantifying and tracking subgenome divergence directly at the cellular level. Further comparing with cellular differentiation trajectories derived from single-cell RNA sequencing data allows for an examination of the relationship between subgenome divergence and the progression of development. pgDQ produces robust results and is insensitive to data dropout and noise, avoiding high error rates due to multiple comparisons of genes, cells, and subgenomes. A statistical diagnostic approach is proposed to identify genes that are central to subgenome divergence during development, which facilitates the integration of different data modalities, enabling the identification of factors and pathways that mediate subgenome-divergent activity during development. Case studies have demonstrated that applying pgDQ to single-cell and bulk tissue transcriptomic data promotes a systematic and deeper understanding of how dynamic subgenome divergence contributes to developmental trajectories in polyploid evolution.

Application of CRISPR/Cas9 system to knock out GluB gene for developing low glutelin rice mutant

The nutritional quality improvement is among the most integral objective for any rice molecular breeding programs. The seed storage proteins (SSPs) have greater role to determine the nutritional quality of any cereal grains. Rice contains relatively balanced amino acid composition and the SSPs are fractioned into albumins (ALB), globulins (GLO), prolamins (PRO) and glutelins (GLU) according to differences in solubility. GLUs are further divided into subfamilies: GluA, GluB, GluC, and GluD depending on resemblance in amino acid. The GLU protein accounts for 60-80% of total protein contents, encoded by 15 genes located on different chromosomes of rice genome. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system was employed to knockout Glu-B (LOC-Os02g15070) gene in non-basmati rice PK386 cultivar. The mutant displayed two base pair and three base pair mutation in the targeted regions. The homozygous mutant plant displayed reduction for both in total protein contents and GLU contents whereas, elevation in GLO, ALB and PRO. Moreover, the mutant plant also displayed reduction in physio-chemical properties e.g., total starch, amylose and gel consistency. The agronomic characteristics of both mutant and wild type displayed non-significant differences along with increase in higher percentage of chalkiness in mutant plants. The results obtained from scanning electron microscopy showed the loosely packed starch granules compared to wild type. The gene expression analysis displayed the lower expression of gene at 5 days after flowering (DAF), 10 DAF, 15 DAF and 20 DAF compared to wild type. GUS sub-cellular localization showed the staining in seed which further validated the results obtained from gene expression. Based on these findings it can be concluded Glu-B gene have significant role in controlling GLU contents and can be utilized in breeding programs to enhance the nutritional quality of rice, and may serve as healthy diet for patient allergic with high GLU contents.

Profiling and Improvement of Grain Quality Traits for Consumer Preferable Basmati Rice in the United States

Basmati rice is a premium aromatic rice that consumers choose primarily because of its distinct aroma and excellent grain quality. The grain quality of Basmati rice (GQBR) reflects the perspectives of producers, processors, sellers, and consumers related to the production, processing, marketing, and consumption of Basmati rice. Consumers, an invaluable part of the production demand and value chain of the Basmati rice industry, have the freedom to choose from different types of aromatic rice. Consumers expect their preferred Basmati rice to possess all superior rice grain qualities, including the physical, biochemical, and physiological properties. Gene functional analysis explained that a 10-base pair deletion in the promoter region of the OsSPL16 gene causes the slender grains in Basmati rice, whereas an 8-base-pair deletion in exon 7 of the OsBadh2 gene (located in the fgr region on rice chromosome 8) results in the distinct aroma. Furthermore, a combination of the genetic characteristics of the gw8 and gs3 genes has led to the creation of a long-grain Basmati-type rice cultivar. It has also been demonstrated that agricultural, genetic, and environmental conditions significantly influence GQBR. Hence, research on improving GQBR requires a multidimensional approach and sophisticated elements due to the complexity of its nature and preference diversity. This review covers the basic definitions of grain quality traits, consumer preference criteria, influencing factors, and strategies for producing superior-quality Basmati rice in the United States. This knowledge will be useful in improving the grain quality of Basmati and Basmati-type rice, as well as developing appropriate breeding programs that will meet the preferences of different countries and cultures.

Grain Protein Content Phenotyping in Rice via Hyperspectral Imaging Technology and a Genome-Wide Association Study

Efficient and accurate acquisition of the rice grain protein content (GPC) is important for selecting high-quality rice varieties, and remote sensing technology is an attractive potential method for this task. However, the majority of multispectral sensors are poor predictors of GPC due to their broad spectral bands. Hyperspectral technology provides a new analytical technology for bridging the gap between phenomics and genomics. However, the small size of typical datasets is a constraint for model construction for estimating GPC, limiting their accuracy and reducing their ability to generalize to a wide range of varieties. In this study, we used hyperspectral data of rice grains from 515 japonica varieties and deep convolution generative adversarial networks (DCGANs) to generate simulated data to improve the model accuracy. Features sensitive to GPC were extracted after applying a continuous wavelet transform (CWT), and the estimated GPC model was constructed by partial least squares regression (PLSR). Finally, a genome-wide association study (GWAS) was applied to the measured and generated datasets to detect GPC loci. The results demonstrated that the simulated GPC values generated after 8,000 epochs were closest to the measured values. The wavelet feature (WF1743, 2), obtained from the data with the addition of 200 simulated samples, exhibited the highest GPC estimation accuracy (R 2 = 0.58 and RRMSE = 6.70%). The GWAS analysis showed that the estimated values based on the simulated data detected the same loci as the measured values, including the OsmtSSB1L gene related to grain storage protein. This study provides a new technique for the efficient genetic study of phenotypic traits in rice based on hyperspectral technology.

Moderate Salinity Stress Affects Rice Quality by Influencing Expression of Amylose- and Protein-Content-Associated Genes

Salinity is an environmental stress that severely impacts rice grain yield and quality. However, limited information is available on the molecular mechanism by which salinity reduces grain quality. In this study, we investigated the milling, appearance, eating and cooking, and nutritional quality among three japonica rice cultivars grown either under moderate salinity with an electrical conductivity of 4 dS/m or under non-saline conditions in a paddy field in Dongying, Shandong, China. Moderate salinity affected rice appearance quality predominantly by increasing chalkiness rate and chalkiness degree and affected rice eating and cooking and nutritional quality predominantly by decreasing amylose content and increasing protein content. We compared the expression levels of genes determining grain chalkiness, amylose content, and protein content in developing seeds (0, 5, 10, 15, and 20 days after flowering) of plants grown under saline or non-saline conditions. The chalkiness-related gene Chalk5 was up-regulated and WHITE-CORE RATE 1 was repressed. The genes Nuclear factor Y and Wx, which determine amylose content, were downregulated, while protein-content-associated genes OsAAP6 and OsGluA2 were upregulated by salinity in the developing seeds. These findings suggest some target genes that may be utilized to improve the grain quality under salinity stress conditions via gene-pyramiding breeding approaches.

Orchestrating seed storage protein and starch accumulation toward overcoming yield-quality trade-off in cereal crops

Achieving high yield and good quality in crops is essential for human food security and health. However, there is usually disharmony between yield and quality. Seed storage protein (SSP) and starch, the predominant components in cereal grains, determine yield and quality, and their coupled synthesis causes a yield-quality trade-off. Therefore, dissection of the underlying regulatory mechanism facilitates simultaneous improvement of yield and quality. Here, we summarize current findings about the synergistic molecular machinery underpinning SSP and starch synthesis in the leading staple cereal crops, including maize, rice and wheat. We further evaluate the functional conservation and differentiation of key regulators and specify feasible research approaches to identify additional regulators and expand insights. We also present major strategies to leverage resultant information for simultaneous improvement of yield and quality by molecular breeding. Finally, future perspectives on major challenges are proposed.

Effect of Fat Content on Rice Taste Quality through Transcriptome Analysis

Rice is an important crop in the word, and fat is one of the main important nutrient components of rice. The lipid content and fatty acid composition of grains significantly influences the quality of rice. In this study, 94 homozygous recombination inbred lines (RILs) were developed and the crude fat content of them displayed a normal distribution ranging from 0.44% to 2.62%. Based on their taste quality, a positive association between fat content and eating quality was revealed. Then, two lines (FH and FL) were selected with similar agronomic characteristics and different lipid content and taste quality for RNA sequencing analysis, and a total of 619 differentiable expressed genes were detected, primarily enriched in metabolic pathways such as starch and sucrose metabolism, fatty acid metabolism, and amino acid metabolism. The expression of two genes related to fatty acid synthesis and elongation was significantly up-regulated, while the expression of three genes related to fatty acid degradation was significantly down-regulated in FH grains. By using liquid chromatography, the relative levels of palmitic acid and oleic acid were discovered significantly higher in FH grains. Additionally, the comparative genomic analysis was conducted to visualize genomic differences of five genes. Ultimately, two genes (Os07g0417200 and Os12g0102100) were selected to be the key gene to affect the lipid metabolism, especially for the synthesis of unsaturated fatty acids, significantly changing the eating quality of rice. These results provide a theoretical basis for improving the taste quality of rice.

Generation of aroma in three-line hybrid rice through CRISPR/Cas9 editing of BETAINE ALDEHYDE DEHYDROGENASE2 (OsBADH2)

Aroma or fragrance in rice is a genetically controlled trait; Its high appreciation by consumers increases the rice market price. Previous studies have revealed that the rice aroma is controlled by a specific gene called BETAINE ALDEHYDE DEHYDROGENASE (OsBADH2), and mutation of this gene leads to the accumulation of an aromatic substance 2-acetyl-1-pyrroline (2-AP). The use of genetic engineering to produce aroma in commercial and cultivated hybrids is a contemporary need for molecular breeding. The current study reports the generation of aroma in the three-line hybrid restorer line Shu-Hui-313 (SH313). We created knock-out (KO) lines of OsBADH2 through the CRISPR/Cas9. The analysis of KO lines revealed a significantly increased content of 2AP in the grains compared with the control. However, other phenotypic traits (plant height, seed setting rate, and 1000-grain weight) were significantly decreased. These KO lines were crossed with a non-aromatic three-line hybrid rice male sterile line (Rong-7-A) to produce Rong-7-You-626 (R7Y626), R7Y627 and R7Y628. The measurement of 2-AP revealed significantly increased contents in these cross combinations. We compared the content of 2-AP in tissues at the booting stage. Data revealed that young spike stalk base contained the highest content of 2-AP and can be used for identification (by simple chewing) of aromatic lines under field conditions. In conclusion, our dataset offers a genetic source and illustrates the generation of aroma in non-aromatic hybrids, and outlines a straightforward identification under field conditions.

QTL detection for rice grain storage protein content and genetic effect verifications

Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01436-7.

Improving rice eating and cooking quality by enhancing endogenous expression of a nitrogen-dependent floral regulator

Improving rice eating and cooking quality (ECQ) is one of the primary tasks in rice production to meet the rising demands of consumers. However, improving grain ECQ without compromising yield faces a great challenge under varied nitrogen (N) supplies. Here, we report the approach to upgrade rice ECQ by native promoter-controlled high expression of a key N-dependent floral and circadian clock regulator Nhd1. The amplification of endogenous Nhd1 abundance alters rice heading date but does not affect the entire length of growth duration, N use efficiency and grain yield under both low and sufficient N conditions. Enhanced expression of Nhd1 reduces amylose content, pasting temperature and protein content while increasing gel consistence in grains. Metabolome and transcriptome analyses revealed that increased expression of Nhd1 mainly regulates the metabolism of carbohydrates and amino acids in the grain filling stage. Moreover, expression level of Nhd1 shows a positive relationship with grain ECQ in some local main cultivars. Thus, intensifying endogenous abundance of Nhd1 is a promising strategy to upgrade grain ECQ in rice production.

GIFTdb: a useful gene database for plant fruit traits improving

Fruit traits are critical determinants of plant fitness, resource diversity, productive and quality. Gene regulatory networks in plants play an essential role in determining fruit traits, such as fruit size, yield, firmness, aroma and other important features. Many research studies have focused on elucidating the associated signaling pathways and gene interaction mechanism to better utilize gene resources for regulating fruit traits. However, the availability of specific database of genes related to fruit traits for use by the plant research community remains limited. To address this limitation, we developed the Gene Improvements for Fruit Trait Database (GIFTdb, http://giftdb.agroda.cn). GIFTdb contains 35 365 genes, including 896 derived from the FR database 1.0, 305 derived from 30 882 articles from 2014 to 2021, 236 derived from the Universal Protein Resource (UniProt) database, and 33 928 identified through homology analysis. The database supports several aided analysis tools, including signal transduction pathways, gene ontology terms, protein-protein interactions, DNAWorks, Basic Local Alignment Search Tool (BLAST), and Protein Subcellular Localization Prediction (WoLF PSORT). To provide information about genes currently unsupported in GIFTdb, potential fruit trait-related genes can be searched based on homology with the supported genes. GIFTdb can provide valuable assistance in determining the function of fruit trait-related genes, such as MYB306-like, by conducting a straightforward search. We believe that GIFTdb will be a valuable resource for researchers working on gene function annotation and molecular breeding to improve fruit traits.

Genomic variations combined with epigenetic modifications rewire open chromatin in rice

Cis-regulatory elements (CREs) fine-tune gene transcription in eukaryotes. CREs with sequence variations play vital roles in driving plant or crop domestication. However, how global sequence and structural variations (SVs) are responsible for multilevel changes between indica and japonica rice (Oryza sativa) is still not fully elucidated. To address this, we conducted multiomic studies using MNase hypersensitivity sequencing (MH-seq) in combination with RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), and bisulfite sequencing (BS-seq) between the japonica rice variety Nipponbare (NIP) and indica rice variety 93-11. We found that differential MNase hypersensitive sites (MHSs) exhibited some distinct intrinsic genomic sequence features between NIP and 93-11. Notably, through MHS-genome-wide association studies (GWAS) integration, we found that key sequence variations may be associated with differences of agronomic traits between NIP and 93-11, which is partly achieved by MHSs harboring CREs. In addition, SV-derived differential MHSs caused by transposable element (TE) insertion, especially by noncommon TEs among rice varieties, were associated with genes with distinct functions, indicating that TE-driven gene neo- or subfunctionalization is mediated by changes of chromatin openness. This study thus provides insights into how sequence and genomic SVs control agronomic traits of NIP and 93-11; it also provides genome-editing targets for molecular breeding aiming at improving favorable agronomic properties.

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

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

Gene editing of non-coding regulatory DNA and its application in crop improvement

The development of the clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas) system has provided precise and efficient strategies to edit target genes and generate transgene-free crops. Significant progress has been made in the editing of protein-coding genes; however, studies on the editing of non-coding DNA with regulatory roles lags far behind. Non-coding regulatory DNAs, including those which can be transcribed into long non-coding RNAs (lncRNAs), and miRNAs, together with cis-regulatory elements (CREs), play crucial roles in regulating plant growth and development. Therefore, the combination of CRISPR/Cas technology and non-coding regulatory DNA has great potential to generate novel alleles that affect various agronomic traits of crops, thus providing valuable genetic resources for crop breeding. Herein, we review recent advances in the roles of non-coding regulatory DNA, attempts to edit non-coding regulatory DNA for crop improvement, and potential application of novel editing tools in modulating non-coding regulatory DNA. Finally, the existing problems, possible solutions, and future applications of gene editing of non-coding regulatory DNA in modern crop breeding practice are also discussed.

Knocking Out OsAAP11 to Improve Rice Grain Quality Using CRISPR/Cas9 System

The demand for rice grain quality, particularly in terms of eating and cooking quality, is increasingly concerning at present. However, the limited availability of rice-quality-related gene resources and time-consuming and inefficient traditional breeding methods have severely hindered the pace of rice grain quality improvement. Exploring novel methods for improving rice grain quality and creating new germplasms is an urgent problem that needs to be addressed. In this study, an amino-acid-transporter-encoding gene OsAAP11 (Os11g0195600) mainly expressed in endosperm was selected as the target for gene editing using the CRISPR/Cas9 system in three japonica genetic backgrounds (Wuyungeng30, Nangeng9108, and Yanggeng158, hereafter referred to as WYG30, NG9108, and YG158). We successfully obtained homozygous osaap11 mutants without transgenic insertion. Subsequently, we conducted comprehensive investigations on the agronomic traits, rice grain quality traits, and transcriptomic analysis of these mutants. The results demonstrate that loss of OsAAP11 function led to a reduced amino acid content and total protein content in grains without affecting the agronomic traits of the plants; meanwhile, it significantly increased the peak viscosity, holding viscosity, and final viscosity values during the cooking process, thereby enhancing the eating and cooking quality. This study not only provides valuable genetic resources and fundamental materials for improving rice grain quality but also provides novel technical support for the rapid enhancement of rice grain quality.

Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice

Improving grain quality is a primary objective in contemporary rice breeding. Japanese modern rice breeding has developed two different types of rice, eating and sake-brewing rice, with different grain characteristics, indicating the selection of variant gene alleles during the breeding process. Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding, we conducted genome scans for divergence, genome-wide association studies, and map-based cloning. Consequently, we successfully identified two genes, OsMnS and OsWOX9D, both contributing to rice grain traits. OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm, a desirable trait for sake brewing but decreases the grain appearance quality. OsWOX9D encodes a grass-specific homeobox-containing transcription factor, which enhances grain width for better sake brewing. Furthermore, haplotype analysis revealed that their defective alleles were selected in East Asia, but not Europe, during modern improvement. In addition, our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection. This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits, based on the concept of "breeding-assisted genomics" in plants.

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.

Comparisons of rice taste and starch physicochemical properties in superior and inferior grains of rice with different taste value

The difference in grain yield between superior grains (SG) on the upper part and inferior grains (IG) on the lower part of the same panicle was widely reported. To date, variations in rice taste quality between SG and IG and the related starch physicochemical properties remained poorly understood. Here, rice cultivars with different taste quality (NT, normal taste; GT, good taste) were grown to investigate the mechanism underlying taste difference between SG and IG and the correlation between cooked rice taste and starch properties. In this study, the taste value of GT rice was 32.2% higher than that of NT rice across the cultivars. The GT rice comprised a series of typical taste qualities of larger stickiness, smaller hardness, lower apparent amylose content (AAC), and lower protein content (PC). The taste quality differed among rice grains on the same panicle; SG achieved 21.9% and 17.0% higher taste value than IG in GT rice and NT rice, respectively. The higher taste value in SG was owing to the larger stickiness and lower PC. Meanwhile, SG of GT rice achieved the lowest PC (8.2%) and gluten content (5.6%), which might indicate a better health value. Additionally, larger and smoother granules, more fa (DP < 12), lower crystallinity, and larger 1045/1022 cm^-1 ratios were found in SG starch compared to IG starch. These led to a weaker swelling power and lower gelatinization enthalpy in SG starch, while gelatinization temperature and retrogression enthalpy were the opposite. Moreover, SG starch exhibited higher storage modulus, loss modulus, slowly digestible starch contents, and resistant starch contents than IG. Our results revealed a great difference in taste quality between SG and IG in rice. The larger and smoother starch granules and shorter chain length could increase the ordered structure of starch, thus improving swelling power, gelatinization properties, and rheological characteristics and facilitating better taste quality of SG over IG. Besides, the lower PC (especially gluten content), higher slowly digestible starch, and higher resistant starch content indicated a more promising health value of SG in the food industry.

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.

Metabolomic profiles reveals the dose-dependent effects of rice grain yield and nutritional quality upon exposure zero-valent iron nanoparticles

Zero-valent iron nanoparticles (nZVI) were widely used material in environmental remediation, which has attracted increasing concern for their safety. Previous studies have shown that the addition of nZVI could inhibit rice seedling growth. However, the effect of nZVI on the soil-rice system during the entire life cycle was not reported. Furthermore, the effect of nZVI on the quality of rice grain has also not been studied. Therefore, we investigated the effects of rice grain yield and nutritional quality upon exposure nZVI. The results showed that the soil pH value, redox potential and Fe (II) content in the nZVI-treated group were decreased in a dose-dependent manner. Interestingly, 2500 mg/kg nZVI significantly decreased the relative abundance of several functional microbial communities (10.52-73.53 %) associated with carbon and nitrogen cycles in response to plants compared to the control. Meanwhile, the nZVI treatment clearly reduced grain yield (8.71-18.21 %). Furthermore, the content of protein (51.72-57.79 %) and several essential nutrients (Zn, Cu, Mn and Mo) in the nZVI-treated grains was also decreased in a dose-dependent manner. The results of grain metabolomics indicated that nZVI could interfere with the relative expression of lysine and glutathione by regulating the metabolic pathways of antioxidant and protein synthesis in rice.

Tailoring crops with superior product quality through genome editing: an update

In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.

Can the Wild Perennial, Rhizomatous Rice Species Oryza longistaminata be a Candidate for De Novo Domestication?

As climate change intensifies, the development of resilient rice that can tolerate abiotic stresses is urgently needed. In nature, many wild plants have evolved a variety of mechanisms to protect themselves from environmental stresses. Wild relatives of rice may have abundant and virtually untapped genetic diversity and are an essential source of germplasm for the improvement of abiotic stress tolerance in cultivated rice. Unfortunately, the barriers of traditional breeding approaches, such as backcrossing and transgenesis, make it challenging and complex to transfer the underlying resilience traits between plants. However, de novo domestication via genome editing is a quick approach to produce rice with high yields from orphans or wild relatives. African wild rice, Oryza longistaminata, which is part of the AA-genome Oryza species has two types of propagation strategies viz. vegetative propagation via rhizome and seed propagation. It also shows tolerance to multiple types of abiotic stress, and therefore O. longistaminata is considered a key candidate of wild rice for heat, drought, and salinity tolerance, and it is also resistant to lodging. Importantly, O. longistaminata is perennial and propagates also via rhizomes both of which are traits that are highly valuable for the sustainable production of rice. Therefore, O. longistaminata may be a good candidate for de novo domestication through genome editing to obtain rice that is more climate resilient than modern elite cultivars of O. sativa.

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.

MOTHER-OF-FT-AND-TFL1 regulates the seed oil and protein content in soybean

Soybean is a major crop that produces valuable seed oil and protein for global consumption. Seed oil and protein are regulated by complex quantitative trait loci (QTLs) and have undergone intensive selections during the domestication of soybean. It is essential to identify the major genetic components and understand their mechanism behind seed oil and protein in soybean. We report that MOTHER-OF-FT-AND-TFL1 (GmMFT) is the gene of a classical QTL that has been reported to regulate seed oil and protein content in many studies. Mutation of MFT decreased seeds oil content and weight in both Arabidopsis and soybean, whereas increased expression of GmMFT enhanced seeds oil content and weight. Haplotype analysis showed that GmMFT has undergone selection, which resulted in the extended haplotype homozygosity in the cultivated soybean and the enriching of the oil-favorable allele in modern soybean cultivars. This work unraveled the GmMFT-mediated mechanism regulating seed oil and protein content and seed weight, and revealed a previously unknown function of MFT that provides new insights into targeted soybean improvement and breeding.

The genetic basis of grain protein content in rice by genome-wide association analysis

The grain protein content (GPC) of rice is an important factor that determines its nutritional, cooking, and eating qualities. To date, although a number of genes affecting GPC have been identified in rice, most of them have been cloned using mutants, and only a few genes have been cloned in the natural population. In this study, 135 significant loci were detected in a genome-wide association study (GWAS), many of which could be repeatedly detected across different years and populations. Four minor quantitative trait loci affecting rice GPC at four significant association loci, qPC2.1, qPC7.1, qPC7.2, and qPC1.1, were further identified and validated in near-isogenic line F2 populations (NIL-F2), explaining 9.82, 43.4, 29.2, and 13.6% of the phenotypic variation, respectively. The role of the associated flo5 was evaluated with knockdown mutants, which exhibited both increased grain chalkiness rate and GPC. Three candidate genes in a significant association locus region were analyzed using haplotype and expression profiles. The findings of this study will help elucidate the genetic regulatory network of protein synthesis and accumulation in rice through cloning of GPC genes and provide new insights on dominant alleles for marker-assisted selection in the genetic improvement of rice grain quality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-022-01347-z.

Rapid improvement of rice eating and cooking quality through gene editing toward glutelin as target

Rice eating and cooking quality (ECQ) is a major concern of breeders and consumers, determining market competitiveness worldwide. Rice grain protein content (GPC) is negatively related to ECQ, making it possible to improve ECQ by manipulating GPC. However, GPC is genetically complex and sensitive to environmental conditions; therefore, little progress has been made in traditional breeding for ECQ. Here, we report that CRISPR/Cas9-mediated knockout of genes encoding the grain storage protein glutelin rapidly produced lines with downregulated GPC and improved ECQ. Our finding provides a new strategy for improving rice ECQ.

Using transcriptomic and metabolomic data to investigate the molecular mechanisms that determine protein and oil contents during seed development in soybean

Soybean [Glycine max (L.) Merri.] is one of the most valuable global crops. And vegetable soybean, as a special type of soybean, provides rich nutrition in people's life. In order to investigate the gene expression networks and molecular regulatory mechanisms that regulate soybean seed oil and protein contents during seed development, we performed transcriptomic and metabolomic analyses of soybean seeds during development in two soybean varieties that differ in protein and oil contents. We identified a total of 41,036 genes and 392 metabolites, of which 12,712 DEGs and 315 DAMs were identified. Analysis of KEGG enrichment demonstrated that DEGs were primarily enriched in phenylpropanoid biosynthesis, glycerolipid metabolism, carbon metabolism, plant hormone signal transduction, linoleic acid metabolism, and the biosynthesis of amino acids and secondary metabolites. K-means analysis divided the DEGs into 12 distinct clusters. We identified candidate gene sets that regulate the biosynthesis of protein and oil in soybean seeds, and present potential regulatory patterns that high seed-protein varieties may be more sensitive to desiccation, show earlier photomorphogenesis and delayed leaf senescence, and thus accumulate higher protein contents than high-oil varieties.

Effects of Wx Genotype, Nitrogen Fertilization, and Temperature on Rice Grain Quality

Quality is a complex trait that is not only the key determinant of the market value of the rice grain, but is also a major constraint in rice breeding. It is influenced by both genetic and environmental factors. However, the combined effects of genotypes and environmental factors on rice grain quality remain unclear. In this study, we used a three-factor experimental design to examine the grain quality of different Wx genotypes grown under different nitrogen fertilization and temperature conditions during grain development. We found that the three factors contributed differently to taste, appearance, and nutritional quality. Increased Wx function and nitrogen fertilization significantly reduced eating quality, whereas high temperature (HT) had almost no effect. The main effects of temperature on appearance quality and moderate Wx function at low temperatures (LTs) contributed to better appearance, and higher nitrogen fertilization promoted appearance at HTs. With regard to nutritional quality, Wx alleles promoted amylose content (AC) as well as starch-lipids content (SLC); nitrogen fertilization increased storage protein content (PC); and higher temperature increased lipid content but decreased the PC. This study helps to broaden the understanding of the major factors that affect the quality of rice and provides constructive messages for rice quality improvement and the cultivation of high-quality rice varieties.

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

The eating and cooking quality (ECQ) of rice is critical for determining its economic value in the marketplace and promoting consumer acceptance. It has therefore been of paramount importance in rice breeding programs. Here, we highlight advances in genetic studies of ECQ and discuss prospects for further enhancement of ECQ in rice. Innovations in gene- and genome-editing techniques have enabled improvements in rice ECQ. Significant genes and quantitative trait loci (QTLs) have been shown to regulate starch composition, thereby affecting amylose content and thermal and pasting properties. A limited number of genes/QTLs have been identified for other ECQ properties such as protein content and aroma. Marker-assisted breeding has identified rare alleles in diverse genetic resources that are associated with superior ECQ properties. The post-genomics-driven information summarized in this review is relevant for augmenting current breeding strategies to meet consumer preferences and growing population demands.

Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality

Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.

Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice (Oryza sativa L.)

The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.

Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics

Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.

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

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