Amylose content (AC) is a key determinant of rice eating and cooking quality (ECQ). Lower AC is generally associated with improved palatability and is therefore a desirable trait in rice breeding;however,effective manipulation of AC remains a challenge.In this study,we identified AC6,a novel endosperm-specific early nodulin-like (ENODL) gene,belonging to a 32-member ENODL family.

Efficient seed germination and seedling establishment are critical for achieving high rice yields. This process is regulated by numerous metabolic pathways, including the mobilization of stored starch and the utilization of sugars. The Waxy (Wx) gene, which controls amylose content (AC) in rice grains, plays a key role in this process. Premature transcription termination of Wx determines whether the seed exhibits a waxy or non-waxy phenotype. While Wx is well established as a critical regulator of eating and cooking quality (ECQ) in rice, the present study identifies a novel role for Wx in mediating brassinosteroid (BR)-regulated seed germination. Analysis of Wx-related near-isogenic and transgenic lines revealed that seeds carrying the Wxa allele showed faster germination and superior post-germinative growth than those carrying the wx allele. This enhanced post-germinative growth was associated with increased Wx expression, which significantly boosted amylase activity and led to extensive starch degradation. Additionally, the higher expression and activity of α-amylase in Wxa seeds resulted in greater efficiency of starch-to-sugar conversion. In vitro embryo culture assays demonstrated that the Wxa allele and glucose acted synergistically to promote plumule growth. Moreover, differential Wx expression influenced ABA biosynthesis and catabolism in germinated seeds. Collectively, these findings suggest that appropriately modifying Wx expression to optimize starch composition could achieve the dual goal of improving both ECQ and germination-related traits in rice breeding.

Elevated temperatures are a major environmental stress factor that impairs rice productivity and compromises grain quality. This study investigated the effects of natural allelic variation in soluble starch synthase I (SSI) on grain quality and starch structural properties under high-temperature (HT) conditions. Four near-isogenic lines (NILs) differing in SSI alleles and carrying either the Wxb or wx backgrounds were cultivated under HT stress. A range of analytical techniques revealed that HT significantly reduced grain appearance quality, protein content, apparent amylose content (AAC), and total starch content across all NILs. In addition, rapid visco-analysis (RVA) profiles of rice flour showed a marked reduction in viscosity under HT. Starch fine structure analysis demonstrated a decrease in short-chain amylopectin and an increase in long-chain amylopectin under HT, which was associated with enhanced starch crystallinity and elevated gelatinization temperatures. Notably, rice lines carrying the SSIi allele, in both Wxb and wx backgrounds, exhibited milder declines in grain quality traits compared to those with the SSIj allele. These findings provide new insights into the role of SSI allelic variation in maintaining rice grain quality under HT stress and offer a genetic basis for breeding heat-tolerant rice varieties.

Pre-harvest sprouting (PHS), caused by weak seed dormancy and environmental stimuli, leads to significant losses in both crop yield and grain quality. Breeding crop cultivars with enhanced PHS resistance represents a promising strategy to address this challenge. However, limited useful genetic resources has hindered the progress in rice molecular breeding. Through screening of a rice mutant library, we identify the ethylene response factor115 (erf115) mutant, which exhibits enhanced PHS resistance. Genetic analysis reveals that ERF115 functions as a negative regulator of seed dormancy. Mechanistic assays show that the E3 ubiquitin-protein ligase Grain Width 2 (GW2) interacts with and ubiquitinates ERF115, thereby promoting its proteasomal degradation. Accordingly, gw2 mutants display increased PHS susceptibility. ERF115 also interacts with the transcription factor SLR1-like 2 (SLRL2) and represses its transcriptional activation activity, consequently reducing the expression of the dormancy gene Mother of FT and TFL1 like 2 (MFT2). Haplotype analysis identifies three major ERF115 haplotypes (HapI-HapIII), among which ERF115Hapl represents an elite allele associated with reduced PHS. Collectively, our findings reveal a GW2-ERF115-SLRL2 regulatory module that integrates ubiquitin-mediated regulation and hormone signaling to fine-tune rice seed dormancy, providing valuable genetic resources for breeding PHS-resistant rice varieties.

Seed germination initiates the plant life cycle, but it exhibits high sensitivity to salt stress, which is a significant environmental factor limiting rice production. Brassinosteroid (BR) is a growth-promoting phytohormone that mitigates various stresses in rice including salt, drought, and extreme temperatures. However, the mechanisms by which BR alleviates salt stress during seed germination remain inadequately characterized. This study demonstrates that seed-specific overexpression of OsDWF4, a rate-limiting gene in BR biosynthesis, enhances rice germination. The DWF4-OX lines, which have greater endogenous BR content in the seeds, showed better germination under salt stress, corroborating the results obtained through exogenous BR application. Antioxidant enzyme analyses demonstrated that BR enhances the activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT). Metabolomic analysis revealed that BR mitigates salt stress primarily through the biosynthesis of phenylpropanoids and secondary metabolites. Transcriptomic analysis indicated that both endogenous and exogenous BR share five co-regulated target genes and utilize a common biosynthetic pathway for stilbenoids, diarylheptanoids, and gingerols. These findings confirm the capacity of BR to enhance seed germination under salt stress and identified several BR-mediated targets for developing salt-tolerant rice varieties that are suitable for direct seeding cultivation.

Increasingly frequent extreme heat events threaten cereal production and food security under a changing climate. The reproductive-to-grain formation continuum of cereals is particularly vulnerable to elevated temperatures, as heat stress disrupts developmental processes from inflorescence formation and fertilization to grain filling and quality establishment. These disruptions reduce reproductive success, impair yield formation, and compromise grain quality. A comprehensive understanding of the developmental, physiological, molecular, and genetic basis of cereal heat tolerance is therefore essential for developing climate-adapted crops. This review summarizes recent advances in understanding heat stress during cereal reproduction and grain filling across major cereal crops. We first discuss how heat stress affects sequential developmental processes, including inflorescence development, gametophyte development, flowering and pollination, fertilization, and grain filling. We then integrate emerging evidence on cross-cutting mechanisms that connect stage-specific heat responses, focusing on hormonal and redox homeostasis, carbohydrate metabolism and source-sink coordination, proteostasis and endomembrane organization, and genome stability and multilayered gene regulation. Finally, we summarize the genetic basis of cereal heat tolerance by highlighting genetic determinants, favorable alleles, and their potential applications in breeding. We further discuss current bottlenecks and future opportunities for breeding heat-tolerant cereals.

Grain shape is an important trait affecting yield and quality(Ren et al.2023).Indica and japonica rice have differences in quality and yield-related traits,including grain shape.Indica rice generally has a slender grain that decreases the head rice rate and yield loss,while japonica has shorter and wider grains with high yield(Jiang et al.2022).However,grain shape and chalkiness are often correlated.Grain width is a significant factor influencing grain filling.Wider grain is often accompanied by more chalkiness,whereas slender grains can optimize grain-filling pathways,reducing the chalkiness without yield loss.

High quality stands as a pivotal competitive edge in the rice industry. Optimizing amylose content (AC) and the physicochemical properties of endosperm starch by regulating the Wx gene is crucial for enhancing rice grain quality. In this study, we created a novel Wxb-d25 allele by deleting a 25 bp segment (−26 to −2) within the Wx core promoter using CRISPR/Cas9. Compared with the wild type and the previously reported Wxb-i1, Wxb-d25 exhibited no significant changes in agronomic traits. However, its grains displayed temperature-dependent variations in AC and altered transparency and viscosity characteristics, holding the potential to synergistically improve both the eating and cooking quality (ECQ) and appearance quality (AQ) of rice. Further studies demonstrated that this promoter modification, by partially disrupting the transcription initiator, significantly downregulated the original Wx-01 transcript and generated a novel Wx transcript (ONT.7395.1) in Wxb-d25 grains. Despite its low expression abundance, the ONT.7395.1 transcript could be completely processed into mature Wx mRNA. The combined effects of the dual transcripts resulted in significantly increased Wx gene expression and AC in Wxb-d25 grains under conventional cultivation conditions. These findings provide a genetic resource and a theoretical foundation for utilizing the Wxb-d25 allele to improve rice grain quality.

Brassinosteroid acts via the BZR1-SLRL2-Wx module to regulate amylose content in rice, making BZR1 a potential target for breeding rice with both superior quality and high yield.

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.

The combination of Chinsurah Boro II (BT)-type cytoplasmic male sterility (CMS) and Rf1, the main fertility restorer gene (Rf) for CMS-BT, has been extensively utilized for the production of three-line commercial japonica hybrid seeds. The identification of new Rf genes holds significance for the breeding of BT-type restorer lines, aiming to enhance the heterosis level of BT-type japonica hybrids. In the present study, ‘02428’, a wide-compatibility japonica variety, was observed to partially restore fertility to BT-type CMS lines. Genetic analysis revealed that ‘02428’ carries a dominant Rf gene, Rf21(t), responsible for the fertility restoration of BT-type CMS lines. Leveraging bulked segregant analysis (BSA) resequencing technology and molecular markers, the Rf21(t) locus was identified, and mapped within a candidate interval of 6–12.5 Mb on chromosome 2. Using the iso-cytoplasmic restorer populations, Rf21(t) was ultimately mapped to an interval of approximately 77 kb, encompassing 12 predicted genes, including LOC_Os02g17360, encoding a PPR-domain-containing protein and LOC_Os02g17380 (Rf2), a cloned Rf for Lead-rice-type CMS. A comparative sequence analysis, gene expression profiling and gene knockout experiments confirmed that LOC_Os02g17360 and LOC_Os02g17380 are the most likely candidates of Rf21(t). Furthermore, Rf21(t) showed the dosage effect on the fertility restoration of BT-type CMS lines. This newly identified Rf21(t) represents a valuable genetic resource for the breeding of BT-type japonica restorer lines. Our findings offer practical insights for breeders interested in advancing BT-type japonica hybrid development.

Identifying genes involved in folate accumulation is critical for elucidating the regulatory mechanisms of folate metabolism and breeding folate-rich crops. Here, a natural A-to-G variation at the 682nd bp is identified in the coding sequence of an identified plant gene glutamate formiminotransferase (GFT) in maize, leading to a glycine-to-asparagine substitution at the 228th in the protein sequence and contributing to the variation of folate accumulation in mature seeds of a maize inbred line population. This gene encodes a protein highly similar to the formiminotransferase domain of mammalian formiminotransferase cyclodeaminase. In vitro biochemical analysis of this protein reveals an activity of triggering 5-methyl-tetrahydrofolate (5-M-THF)-to-MeFox conversion, other than exerting an activity of formiminotransferase in mammals. Loss of ZmGFT function triples 5-M-THF levels, and overexpression of G-allele-carrying ZmGFT boosts the metabolic flow toward MeFox. Functional conservation of GFT is validated in rice and Arabidopsis. The asparagine-to-glycine substitution enhances 5-M-THF-to-MeFox conversion, as demonstrated by in vitro assays and in silico analyses. The functional characterization of the GFT gene has uncovered a new metabolic fate of 5-M-THF, apart from a C1 donor for methionine synthesis, in plants, and a distinct activity from its mammalian ortholog. The natural variation identified is useful for breeding folate-fortified maize varieties.

Since 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus causing COVID-19, has been spreading and mutating globally despite the expedited approval of many commercial vaccines. Therefore, developing safe, effective and affordable vaccines remains essential to meet the global demand, particularly in developing countries. Transgenic plants have emerged as a promising platform to express recombinant proteins for pharmaceutical and vaccine applications. Two binary vectors, pCAMBIA1300Gt1-S1 and pCAMBIA1300Actin-S1, containing distinct promoters, were constructed and transformed into rice via Agrobacterium. Overall, 56 independent transgenic rice lines were regenerated. Expression analysis revealed that the rice-derived S1 (rS1) protein could be expressed in pGt1::S1 transgenic rice seeds. rS1 protein expression levels reached up to 282 μg/g dry weight, with S1 gene insertion having no effect on grain size and weight. The rS1 protein exhibited a high affinity for human angiotensin-converting enzyme 2 (ACE2) in vitro. Moreover, the immunogenicity of purified rS1 protein co-administered with various adjuvants demonstrated that mice vaccinated with Alum-adjuvant rS1 generated enhanced humoral immune responses with high serum IgG, IgG1 and neutralizing antibody levels. Salmonella Typhimurium flagellin (FliC)-adjuvanted rS1 elicited stronger S1-specific IgG2a levels, promoted splenocyte proliferation and induced mixed Th1/Th2/Th17 cytokine responses. This was evidenced by increased proportions of antigen-specific interferon (IFN)-γ, interleukin-4 (IL-4) and IL-17A-positive CD4+ T lymphocytes, suggesting its potential to induce both humoral and cellular immune responses. These findings suggest that rS1 protein offers a promising approach for affordable COVID-19 subunit vaccine production, and this strategy can be universally applied to other viral vaccines.

A promising ethylene sensor based on Sb2MoO6 (SMO) with a permeable lamellar structure and tunable W dopants is proposed. The optimal 5 mol% W-doped SMO featuring atomically distributed heterovalent doping sites enables the ideal combination of high response (121.26/2.6 for 10/0.5 ppm), short response/recovery time (180 s/54 s for 10 ppm), low limit of detection (LoD) (23.18 ppb), excellent selectivity, good long-term stability (45 days), and robust performance in high humidity (LoD of 31.5 ppb at 80 % relative humidity). The rich W4+ doping-induced active sites are primarily responsible for the strengthened gas-sensing performances. Theoretical simulations reveal that W doping modulates the SMO lattice through substitutional and interstitial mechanisms, optimizing adsorption energy and charge transfer between ethylene and Mo sites, thereby resolving the trade-off between high response and recovery speed. Furthermore, the real-world application in detecting and differentiating moldy rice across storage periods underscores its potential for on-site quality monitoring in the grain industry. This work highlights the significant role of heteroatom doping in tailoring material properties, positioning W-doped SMO as a highly effective gas-sensing material for agricultural and environmental applications.

Rice grain size influences both grain yield and quality, making it a significant target for rice genetic improvement. In recent years, numerous genes related to grain size with differential effects have been cloned. The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) gene editing system is a convenient tool for modifying genes. The use of the CRISPR/Cas9 tool for the genetic improvement of grain size-related genes is worth exploring. This paper summarizes the known grain size-related genes and the use of CRISPR/Cas9 for grain size modification and discusses the potential applications of CRISPR/Cas9 for improving rice grain size.

Staple crops such as rice, wheat, and maize are crucial for global food security; however, improving their quality remains a significant challenge. This review summarizes recent advances in enhancing crop quality, focusing on key areas such as the molecular mechanisms underlying endosperm filling initiation, starch granule synthesis, protein body formation, and the interactions between carbon and nitrogen metabolism. It also highlights ten unresolved questions related to starch-protein spatial distribution, epigenetic regulation, and the environmental impacts on quality traits. The integration of multi-omics approaches and rational design strategies presents opportunities to develop high-yield "super-crop" varieties with enhanced nutritional value, better processing characteristics, and attributes preferred by consumers. Addressing these challenges is crucial to promote sustainable agriculture and achieve the dual objectives of food security and environmental conservation.