MicroRNAs (miRNAs) are a class of small, non-coding RNAs that regulate gene expression in eukaryotes. Among them, miR396 targets GROWTH-REGULATING FACTOR (GRF) transcription factors and forms one of the most highly conserved regulatory modules in plants. Recent studies have greatly expanded the functional landscape of the miR396-GRF module, showing that, beyond its canonical role in leaf morphogenesis, it also participates in root meristem regulation, reproductive development, yield formation, tissue regeneration, and responses to diverse abiotic and biotic stresses. In crop plants, this module further controls agronomically important traits. Here, we summarize current knowledge of the evolutionary conservation and diversification of the MIR396 loci, the upstream pathways that control miR396 expression, and the developmental and stress-related outputs mediated by the miR396-GRF module. We also discuss evidence that miR396 functions as a context-dependent regulator rather than a simple growth suppressor, and highlight how precise manipulation of the miR396-GRF module may provide new opportunities for crop improvement by optimizing growth, regeneration, and stress resilience.

IntroductionDirect-seeding rice faces the prominent challenge of low seedling emergence vigor, particularly under deep-sowing mechanical resistance and hypoxic conditions. Although some physiological traits are known, the systemic molecular networks determining superior emergence remain elusive. MethodsHere, we integrated metabolomic and transcriptomic analyses to compare the elite direct-seeding variety ChongShang2022 (CS2022) with the control Huxiangruan450 (HXR450). Results and discussionWeighted gene co-expression network analysis (WGCNA) identified germination-associated metabolic modules. Hub metabolite analysis revealed that the accelerated germination of CS2022 correlates with a higher accumulation of cytokinins (zeatin and cis-zeatin-9-N-glucoside), known for antagonizing abscisic acid (ABA)-induced dormancy, alongside key amino acids (e.g., L-lysine) and structural sphingolipids. Physiological validation confirmed the functional significance of these hubs, demonstrating that exogenous trans-zeatin and L-lysine significantly promoted seed germination in a dose-dependent manner. Notably, CS2022 exhibited heightened sensitivity, achieving maximal promotion at concentrations approximately 10-fold lower than HXR450. Targeted LC-MS/MS assays further demonstrated that CS2022 maintains a significantly higher GA20/ABA ratio during germination by accumulating the key precursor GA20 and deactivating free ABA into ABA-glucosyl ester. This hormonal homeostasis couples with elevated α-amylase activity, accelerating energy mobilization. At the seedling stage, multi-omics integration suggests an optimized growth-defense trade-off in CS2022. Auxin signaling supports rapid elongation, while the upregulation of jasmonic acid (JA) precursor transcripts contrasts with restricted accumulation of bioactive signals (e.g., JA-Ile). This potential signal buffering mechanism likely mitigates growth arrest. Additionally, lipid remodeling involving sphingolipids and waxes may contribute to hypoxia tolerance. Altogether, this study delineates a correlative regulatory network where dynamic hormone buffering, redirected metabolic flux, and adaptive lipid remodeling synergistically maximize direct-seeding rice emergence vigor, providing mechanistic insights and candidate modules for breeding.

Improving plant architecture and increasing yields are the main goals of rice breeders. However, yield is a complex trait influenced by many yield-related traits. Identifying and characterizing important genes in the coordinated network regulating complex rice traits and their interactions is conducive to cultivating high-yielding rice varieties. In this study, we determined that the interaction between mitogen-activated protein kinase kinase kinase5 (OsMAPKKK5) and brassinosteroid-signalling kinase1-1 (OsBSK1-1) regulates yield-related traits in rice. Specifically, OsMAPKKK5 phosphorylates OsBSK1-1, which enhances the interaction between these two proteins, but adversely affects the OsBSK1-1-OsBRI1 (BR insensitive1) and OsBSK1-1-OsPPKL1 (protein phosphatase with two Kelch-like domains) interactions. Additionally, OsMAPKKK5 disrupts brassinosteroid signal transduction, which prevents OsBZR1 (brassinazole-resistant1) from efficiently entering the nucleus, thereby negatively modulating its function as a transcription factor regulating downstream effector genes, ultimately adversely affecting plant architecture and yield. This study revealed the relationship between the MAPK cascade and the regulatory effects of brassinosteroid on the rice grain yield involves OsMAPKKK5 and OsBSK1-1. The study data may be important for future investigations on the rice yield-regulating molecular network.

Understanding the genetic basis of elite rice varieties is conducive to the strategic utilization of genetic resources in modern breeding programs. To elucidate the genetic component and transmission across pedigrees, we investigated two elite inbred japonica varieties, Huruan1212 (HR1212) and Hugeng137 (HG137), through whole-genome sequencing with an average depth of 38.2× and pedigree analysis. We identified specific SNPs and enriched pathways underlying HR1212's excellent eating and cooking quality and HG137's stress resistance. Genomic scans traced the contributions of founder parents Xiushui04 and Wuyugeng3, revealing transmission patterns of favorable alleles across generations. Notably, the shared identity-by-descent (sIBD) segments of the two pedigrees overlapped by 74 Mb, total formed 118.42 Mb of conserved genetic segments, with validation in other founder-derived lines. This research provides valuable insights for utilizing founder parents and elite varieties and highlights the critical need to implement genome-informed breeding strategies in future breeding practice.

IntroductionHuruan1212 (HR1212) is well-regarded for its superior eating and cooking quality in the lower reaches of the Yangtze River in China. Still, its high susceptibility to rice panicle blast and lack of fragrance have limited its further spread and utilization. Pigm and Pi-ta are two dominant genes known for their stable broad-spectrum resistance against rice blast fungus Magnaporthe oryzae, while badh2 is the crucial gene that regulates rice aroma.MethodsIn this study, we utilized a molecular marker-assisted selection backcrossing strategy to introduce Pigm, Pi-ta, and badh2 into introgressed lines employing re-sequencing for precise genetic background selection.ResultsFinally, we selected three introgressed lines, including two that carry Pigm with the highest background recovery rates, showing eating and cooking qualities similar to those of HR1212, and one line that pyramids Pigm, Pi-ta, and badh2, which features a strong aroma. They all displayed significantly enhanced resistance to panicle blast and improved yield compared to HR1212.DiscussionIn conclusion, this study expanded the germplasm resources of japonica, providing a material foundation for enhancing breeding programs aimed at developing rice blast-resistant and high-quality fragrant japonica varieties. Additionally, the study demonstrated that integrating molecular markers and re-sequencing can inform breeders’ decision-making more precisely and efficiently.

The impact of the flooding-draining process on soil ecosystems is complex and dynamic. However, the specific effects of different drainage durations on soil microorganisms and metabolites remain unclear. This study adopted a multi-omics research method. After nontargeted metabolomics analysis of lipids as the main metabolite, microbial diversity analysis and lipidomics analysis were conducted to determine the main influencing factors. Subsequently, correlation analysis was performed with physiological and biochemical data to logically explore the changes in soil microorganisms and metabolites during the drainage process (Day 1 after drainage, R1; Day 2, R2; Day 3, R3; Day 4, R4; and Day 5, R5). The results revealed that S-PPO, S-POD, and S-CAT decreased with prolonged drainage time, whereas the soil redox potential (Eh-mV) and POD increased. Among the various postdrainage comparison groups, lipids and lipid-like molecules were the predominant metabolites. Among lipids, the TG subclass of glycerolipids (GLs) and the Cer subclass of sphingolipids (SPs) were the most abundant. The TG subclass was consistently present in the lipid correlation networks across all comparison groups, with TG (15:0/18:1/18:1) exhibiting significant differences between the R4 and R1 groups. Redox reactions involving lipids were associated mainly with triglycerides, with the most pronounced reduction observed on the second day postdrainage. The most pronounced lipid reduction reaction was observed on the second day after drainage. Notable differences in bacterial abundance were detected between the R4 and R5 groups. At the phylum level, the dominant bacterial communities primarily comprised Actinobacteriota and Chloroflexi, with the bacterial community structure being significantly influenced by drainage. The predominant fungal communities were composed of mainly Ascomycota and Rozellomycota. Actinobacteriota and triglyceride (TG) lipids were the major components affected during the drainage period. Correlations were identified among environmental factors, lipids, and microbial communities, indicating their cooperative interactions. The results of this study indicate that with the increase in water intake time, the redox reactions in soil lipids and the richness of bacterial communities in rice soil significantly increase. At the same time, rapid remodeling can have an impact on soil ecosystems, which helps to better understand the adaptation strategies of rice soil ecosystems under adversity.

Soft Japonica rice is popular in Yangtze River Delta of China in recent years because of its high eating quality. In this study, high eating quality soft Japonica rice with early and late maturity was used to analyze their eating quality traits. The appearance, texture, and physicochemical characteristics, gelatinization and pasting properties, and fine structures between early and late maturing soft rice were compared. Early maturing soft rice had higher whiteness, chalkiness, gelatinization temperature, peak viscosity, breakdown viscosity, long branch-chain amylopectin, amylopectin chains (DP > 25), and molecular weight than late maturing soft rice. The higher gelatinization and pasting properties in early maturing soft rice probably be attributed to its higher amount of long branch-chain amylopectin, proportions of amylopectin chains (DP > 25) and molecular weight, compared with late maturing soft rice. Late maturing soft rice had higher amylose content, gel consistency, short branch-chain amylopectin, amylopectin short chains (DP 6–12), setback viscosity, and consistence viscosity than early maturing soft rice. The appearance and eating quality of late maturing soft rice were significantly higher than those of early maturing soft rice.

Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin (OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic lines. Based on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling pathways. We also suggested rice auxin response factor (OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the 'best' gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.

Grain size, characterized by a combination of grain length, width, and thickness, is one of the major determinants of yield in rice. The present study identified TATA-box binding protein-associated factor 2 (TAF2) as an essential component regulating transcription and determining grain size in rice. Map-based cloning showed that a G/T substitution in TAF2 resulted in a naturally occurring mutant called reduced grain size and plant height 1 (rgh1). The mutants, with weak edited rgh1 alleles, exhibited a small grain phenotype with reduced grain length and width, while the severe knockout mutant (rgh1-2s) was dwarf and completely sterile. Allelic test performed between rgh1 and several edited alleles confirmed that the mutation in TAF2 caused the rgh1 phenotype. GUS staining showed that TAF2 was mainly expressed in the vascular bundles of roots, stems, leaves, and grains. The cytological analysis revealed that reduced cell division in the glumes resulted in the small grain phenotype of rgh1. Further RNA-sequencing detected altered expression of genes involved in the basic biological processes in rgh1 mutant. These findings provide novel insights into the TAF2-mediated genetic mechanism regulating grain size in rice.

Amylose content (AC) is the main factor determining the palatability, viscosity, transparency, and digestibility of rice (Oryza sativa) grains. AC in rice grains is mainly controlled by different alleles of the Waxy (Wx) gene. The AP2/EREBP transcription factor OsEBP89 interacts with the MYC-like protein OsBP5 to synergistically regulate the expression of Wx. Here, we determined that the GLYCOGEN SYNTHASE KINASE 5 (OsGSK5, also named SHAGGY-like kinase 41 [OsSK41]) inhibits the transcriptional activation activity of OsEBP89 in rice grains during amylose biosynthesis. The loss of OsSK41 function enhanced Wx expression and increased AC in rice grains. By contrast, the loss of function of OsEBP89 reduced Wx expression and decreased AC in rice grains. OsSK41 interacts with OsEBP89 and phosphorylates four of its sites (Thr-28, Thr-30, Ser-238, and Thr-257), which makes OsEBP89 unstable and attenuates its interaction with OsBP5. Wx promoter activity was relatively weak when regulated by the phosphomimic variant OsEBP89E -OsBP5 but relatively strong when regulated by the nonphosphorylatable variant OsEBP89A -OsBP5. Therefore, OsSK41-mediated phosphorylation of OsEBP89 represents an additional layer of complexity in the regulation of amylose biosynthesis during rice grain development. In addition, our findings provide four possible sites for regulating rice grain AC via precise gene editing.

为快速选育优质抗稻瘟病粳稻新品种,以优质粳稻新品系沪香软16-18为母本,抗稻瘟病粳稻新品系沪香粳16-44为父本进行杂交配组,利用花药培养和分子标记辅助选择相结合的方法快速育成了聚合香味等位基因badh2-E7、低直链淀粉含量基因Wxmp和抗稻瘟病基因Pita的粳稻新品种'崇尚2022'.该品种在上海地区作移栽稻全生育期145 d左右;株高90 cm左右,每667 m2平均产量为600 kg;抗倒性强,病害轻,2021年稻瘟病鉴定综合指数为4.7,田间发病少;稻米具有明显香味,米饭油润透亮,口感柔软有弹性,冷饭不回生.

已克隆的抗稻瘟病基因Pi9、Pib、Pi5、Pita、Pi2、Pikh、Pikm和Pigm对稻瘟病菌表现广谱抗性,这些基因已广泛应用于水稻抗稻瘟病育种.为了明确长三角地区粳稻的抗稻瘟病基因分布及其抗性表现,利用上述8个抗病基因的功能标记对52份粳稻种质进行抗病基因检测.同时,利用江苏省2019年稻瘟病菌代表菌株2019-746、2019-587、2019-924、2019-16-3、2019-522和2019-863的孢子混合液对供试种质进行抗性鉴定.结果表明,在供试种质中分布频率较高的抗稻瘟病基因是Pib和Pita,分别达到78.85％和50.00％,其余基因分布频率依次为38.46％(Pikh)、34.62％(Pi9)、23.08％(Pikm)、21.15％(Pi2)、5.77％(Pi5),供试种质都不携带基因Pigm.进一步研究结果表明,携带抗病基因Pita、Pi5、Pi2和Pikm的种质表现抗病的比例高;Pita、Pi5、Pi2和Pikm可以作为今后改良粳稻稻瘟病抗性的主要基因.本研究结果为长三角地区抗稻瘟病基因的利用提供了科学依据.

Eating quality is the important trait of rice, and rice breeders also employ eating quality in breeding selection for advanced generations. Therefore, to better understand the factors affecting the eating quality of japonica rice in China, the physicochemical indices [apparent amylose content (AAC), gel consistency (GC), protein content (PC), and gelatinization temperature (GT)], rapid visco analyzer parameters, and cooked rice taste values of 141 rice cultivars were analyzed. The rice cultivars were divided into low, medium, and total AAC groups. Association and principal component analyses of these indices were performed. In total AAC rice, cooked rice taste value showed a significant negative correlation with AAC, final viscosity (CPV), setback viscosity (SBV), consistence viscosity (CSV), and a positive correlation with GC, peak viscosity (PKV), holding strength (HPV), and breakdown viscosity (BDV). PC showed a significant negative correlation with cooked rice taste value in low, medium, and total AAC rice. For both low and medium AAC rice, the factor load matrix of PC and cooked rice taste value in factor 1 was remarkably higher than that of the other indices, indicating that PC was the most important factor for the eating quality of low and medium AAC rice. For total AAC rice, the factor load matrix of AAC, GC, and cooked rice taste value in factor 1 was remarkably higher than that of the other indices, indicating that AAC and GC were important factors for the eating quality of different type rice cultivars. The results showed that AAC and GC were more important for the eating quality of different type rice cultivars, while PC was more important for the eating quality of similar type rice cultivars. Our findings offer new insight into target traits in breeding rice with high eating quality.

为了培育优良食味粳稻新品种,先以优质晚粳品种'金丰'与优质早粳品种'大华香粳'进行杂交,收获F1种子,并以其为母本,再与含有抗条纹叶枯病基因Stv-bi及低直链淀粉含量基因Wxmq的优良食味晚粳品种'南粳46'为父本进行杂交,从F2世代开始利用与两个目标基因共分离的分子标记进行辅助选择.通过连续多世代的标记辅助选择结合品质鉴定最终育成了同时含有Stv-bi和Wxmq基因的优良食味粳稻新品种'沪软1212',并于2018年通过上海市品种审定.凭借突出的食味口感,2018年5月获得首届全国优质粳稻品种食味品质鉴评金奖.

BACKGROUND Rice eating quality largely dictates consumer preference and the demand of new rice varieties with excellent eating quality from farmers is increasing. Identification of the factors contributing to eating quality is helpful for developing high-quality rice varieties. RESULTS Two groups of rice with different apparent amylose contents (AACs) were used in this study. One group contained four varieties with low AACs (8.8-9.4%), whereas the other contained four traditional varieties with medium AACs (17.2-17.5%). The physicochemical properties, starch fine structure and crystallinity, and storage protein composition of the two groups were analyzed. We found that, in both groups, the rice varieties with high eating quality had more short-chain amylopectin, lower glutelin and prolamin contents, and a higher albumin content. In addition, the low-AAC varieties produced opaque endosperms, which may result from the increased pores in the center of starch granules. CONCLUSIONS Both the fine structure of starch and the storage protein composition were closely related to rice eating quality. In both groups, short branch-chain amylopectin, short-chain amylopectin [degree of polymerization (DP) 6-12], and albumin had positive effects on eating quality. By contrast, long branch-chain amylopectin, long-chain amylopectin (DP 35-60), glutelin and prolamin had adverse effects on eating quality of rice. This article is protected by copyright. All rights reserved.

Heading date is an important agronomic trait in rice (Oryza sativa L.). We previously fine-mapped two complementary genes, Late Heading Date 1 and Late Heading Date 2 (LH2), that control the late heading trait in rice. Here, we cloned and analyzed the function of LH2. LH2 was fine-mapped to a 53-kb genomic region. Sequencing analysis revealed that there were differences in the coding sequence of LOC_Os08g07740 between the varieties 'Bo B' and 'Yuefeng B'. Therefore, LOC_Os08g07740 was identified as a candidate gene for LH2 and subsequently determined that LH2 is a Type 3 allele of Days To Heading 8. Transgenic plants of Yuefeng B carrying LH2 from Bo B significantly delayed the heading date under short-day and long-day conditions. A yeast two-hybrid analysis revealed that LH2 physically interacted with Heme Activator Protein (HAP) 5A, -H, -I, -L, -K, and HAP5-LIKE. The HAP5 domain of HAP5 family members has various functions. Further analysis revealed that LH2 represses photoperiodic flowering by controlling the expression of Early Heading Date 1, Heading date 3a, and Rice Flowering Locus T1 in rice.

Plant architecture is an important agronomic trait that affects crop yield. Here, we report that a gene involved in programmed cell death, OsPDCD5, negatively regulates plant architecture and grain yield in rice. We used the CRISPR/Cas9 system to introduce loss-of-function mutations into OsPDCD5 in 11 rice cultivars. Targeted mutagenesis of OsPDCD5 enhanced grain yield and improved plant architecture by increasing plant height and optimizing panicle type and grain shape. Transcriptome analysis showed that OsPDCD5 knockout affected auxin biosynthesis, as well as the gibberellin and cytokinin biosynthesis and signaling pathways. OsPDCD5 interacted directly with OsAGAP, and OsAGAP positively regulated plant architecture and grain yield in rice. Collectively, these findings demonstrate that OsPDCD5 is a promising candidate gene for breeding super rice cultivars with increased yield potential and superior quality.

Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.

Leaf-color mutants have been extensively studied in rice (Oryza sativa L.) and many corresponding genes have been identified and cloned. However, the mechanism of complex leaf-color mutations requires further study. In this study, we obtained an introgression line (TIL22) from a set of introgression lines raised using African cultivated rice (O. glaberrima Steud.) as the donor parent and O. sativa subsp. indica Teqing as the recipient. Compared with Teqing, TIL22 showed a yellow-green leaf phenotype at the seedling stage, but the leaves gradually changed to green after the five-leaf stage. The photosynthetic pigment contents of yellow-green leaves at the seedling stage were significantly reduced and chloroplast development was retarded compared with those of Teqing. Genetic analysis indicated that the introgression line phenotype was controlled by a single nuclear gene, temporarily designated YGL22. Map-based cloning and sequence analysis suggested that the candidate gene was likely to be LOC_Os01g15390, which encodes a chloroplast protein. Real-time quantitative polymerase chain reaction (qPCR) analysis revealed that the YGL22 transcript level was significantly lower in TIL22 than that of Teqing at the seedling stage. We generated the ygl22 knockout mutant using the CRISPR/Cas9 system. The ygl22 mutants showed a similar phenotype to that of TIL22 at the seedling stage, suggesting that YGL22 may be involved in the early development of chloroplasts in rice. In addition, plant height, number of panicles per plant, and grain yield per plant of ygl22 were not significantly affected. The results indicate that YGL22 can be used as a trait marker gene in hybrid rice production.

测定了42个粳稻品种(系)的米饭食味值、食味品质理化指标和RVA谱特征值,并根据米饭食味值筛选出优质食味组[13个品种(系)]和普通食味组[13个品种(系)].同时测定了42个粳稻品种(系)的倒伏指数和影响植株倒伏的相关性状,通过相关性分析,筛选出影响品种倒伏的代表性状,并对优质食味组和普通食味组粳稻品种(系)的这些代表性状进行比较分析.结果 表明:优质食味粳稻品种(系)较普通食味粳稻品种(系)的株高高、茎秆壁薄、茎秆中硅含量少、基部第1伸长节间短且第3伸长节间长,倒伏指数较大,易发生倒伏;优质食味粳稻品种(系)的直链淀粉含量(AC)较低,胶稠度(GC)较高,崩解值(BDV)较大,消减值(SBV)、最终黏度(CPV)、峰值时间(PeT)和回复值(CSV)均较小;抗倒伏能力较强的粳稻品种(系)株高较矮、茎秆壁较厚、茎秆中硅含量较多、基部第1伸长节间较长且第3伸长节间较短.