Tiller number is a crucial agronomic trait that directly influences the grain yield per unit area of rice. Alternative polyadenylation (APA), an essential post-transcriptional regulatory mechanism, plays a significant role in rice growth and development by generating transcripts with varying 3ʹ untranslated region (3ʹUTR) lengths. However, the specific role of APA in rice tillering remains poorly understood. We employed nanopore cDNA sequencing and tandem mass tag proteomics to analyze tiller axillary buds at different developmental stages in rice. Our findings revealed that genes at the early stages of tillering (effective tillering) tend to utilize longer transcripts, whereas those at the later stages (ineffective tillering) favor shorter transcripts. APA-related genes at both the effective and ineffective tillering stages are enriched in known rice tillering-associated pathways, such as the terpenoid backbone biosynthesis pathway and the carotenoid biosynthesis pathway. Additionally, APA-related genes at the ineffective tillering stage are further enriched in pathways such as leaf and organ senescence. The results demonstrate that APA-mediated gene length variation regulates rice tillering in a spatiotemporally specific pattern, and APA further impacts the protein abundance of genes involved in tillering. Genes that utilize the distal AAUAAA signal and produce longer transcripts exhibit stronger expression than those using the proximal signal, while genes using the proximal AAUAAA signal and generating shorter transcripts show stronger expression than those using the distal signal. This study clarifies the regulatory patterns of APA in rice tillering, laying a molecular foundation for the potential breeding of rice with ideal plant architecture.

Alternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism in eukaryotes that modulates gene expression by generating transcript variants. The development of young panicles in rice is a critical stage that determines grain number and weight. However, the regulatory mechanisms and inheritance patterns of APA during this process remain poorly understood. In this study, full-length isoform sequencing (Iso-seq) and metabolome were employed to investigate APA dynamics in the young panicle of hybrid rice variety Wufengyou T025 and in parent lines, Wufeng B and Changhui T025. This analysis revealed that approximately 80% of genes possessed two or more polyadenylation (pA) sites. These APA genes were predominantly enriched in the pathways associated with rice spikelet development, including response to external photoperiod changes, energy production and transportation, protein signal exchange, and amino acid metabolism. Notably, transcripts with a shortened 3'-untranslated region (3'UTR) exhibited elevated expression levels of their corresponding genes, suggesting that APA plays an important role in modulating gene expression. Furthermore, the variable 3'UTR of the 25% differentially expressed APA genes contained numerous miRNA binding sites, including osa-miR1848 and osa-miR5075, which are known to influence spikelet development. In the offspring, the expression levels of core APA factors during young panicle development were generally downregulated compared to the parental lines. Additionally, metabolomic analysis identified 209 and 164 differentially abundant metabolites in the offspring relative to Wufeng B and Changhui T025, respectively. Intriguingly, some of the enriched metabolic pathways overlapped with those of differentially expressed APA genes, implying that APA may influence small-molecule metabolites in pathways related to spike development. Collectively, these findings are valuable for understanding the regulation of APA and its genetic basis in young panicle development, offering new insights into the molecular mechanisms underlying this critical development stage.

The seedling stage is critically important for the development of rice plants, and rapid shoot growth has a major effect on plant morphology and yield potential. In this study, we identified a major and stable quantitative trait loci (QTL), qSL10, on chromosome 10, that controls shoot growth during the seedling stage using a high-resolution genetic map of recombinant inbred lines (RILs). Through differential gene expression and sequence analysis, we identified the candidate gene OsSL10 within the qSL10 region. OsSL10 was differentially expressed in the shoots of rice varieties with varying shoot growth rates. Functional validation using CRISPR/Cas9-mediated knockout and overexpression lines confirmed that OsSL10 regulates shoot length; knockout lines showed reduced shoot growth, and the growth of overexpression lines was enhanced. These findings highlight that OsSL10 is a key regulator of seedling shoot development; OsSL10 provides a promising target for improving seedling vigor in rice. Furthermore, the identification of new QTLs for seedling growth provides valuable insights into the genetic mechanisms governing early rice development, as well as opportunities for the breeding of high-yielding rice varieties.

RNA m6A modification plays a crucial role in plant growth and crop yield. Proteins that can recognize m6A modifications, known as m6A reader proteins, are essential for the regulatory functions of m6A in gene expression. Among mRNA modification, methylation of internal adenosine N6 positions (m6As) is the most prevalent. The functional impact of m6A modifications largely relies on reader proteins. In this study, we identified OsYTH10, a member of the rice YTH domain family protein, as a key player for recognizing and binding to mRNA m6A modification sites. The m6A-binding activity of OsYTH10 is mediated by its YTH structural domain. Knockout mutation of OsYTH10 results in early flowering in rice. Through FA-CLIP and m6A-seq analysis, we discovered that OsYTH10 binds to m6A in the 3'UTR region of mRNA. Our findings reveal that OsYTH10 stabilizes the mRNAs of target genes OsDTH7 and OsGI, thereby regulating the normal flowering process in rice under prolonged sunlight conditions. This study sheds light on the critical role of OsYTH10 in m6A-mediated gene regulation and its impact on flowering time in rice.Key messageA crucial RNA N6-methyladenosine (m6A) reader protein OsYTH10 in rice was identified to physically binds mRNA's 3'UTR via its YTH domain, stabilizing OsDTH7 and OsGI transcripts to accelerate flowering under long-day conditions.

Rice grain is a primary dietary source of cadmium (Cd), a heavy metal toxic to humans. Reducing Cd accumulation in rice through selecting and breeding low-Cd-accumulating cultivars is very important. However, field-based screening for low-Cd rice cultivars remains labor-intensive and time-consuming. In this study, we identified molecular marker genotypes that can distinguish high- and low-Cd-accumulating rice cultivars. We developed corresponding genotypes for marker-assisted selection of low-Cd cultivars in both early and late rice varieties. Fifty-nine locally adapted, high-yielding early rice cultivars and thirty-seven locally adapted, high-yielding late rice cultivars were grown in two fields with different soil Cd levels and genotyped using molecular markers associated with grain Cd accumulation. We identified five early rice cultivars that consistently showed low Cd accumulation, with grain Cd concentrations below the food safety threshold of 0.2 mg kg−1 across two paddy fields. For early rice, we developed two low-Cd combined molecular marker genotypes (Multi-LCL1 and Multi-LCL2) that had significantly lower grain Cd content compared to Multi-LCL3 and Multi-LCL4. For late rice, the low-Cd combined molecular marker genotype Multi-CL1 showed substantially reduced grain Cd levels relative to Multi-CL2-CL5. These findings suggest that the combined molecular marker genotypes Multi-LCL1/LCL2 for early rice and Multi-CL1 for late rice are practical tools for quickly identifying cultivars with low Cd accumulation potential.

The regulation of seed size in rice represents a significant concern within the domain of developmental biology. Nevertheless, our understanding of the mechanisms by which plants determine seed size remains limited, despite its critical importance. The transcriptome and proteome sequencing of rice kernels, derived from the recombinant inbred line (RIL) population between the large-grain line AD3 and the small-grain line AD148, were conducted at the third stage of spikelet development (stage Sp 3: formation of lemma primordium), the sixth stage of spikelet development (stage Sp 6: formation of stamen primordia), as well as nine days post anthesis (9DPA). During the stage Sp 3 and stage Sp 6, the differentially expressed genes were predominantly associated with metabolic pathways, secondary metabolite synthesis, and nitrogen metabolism. In contrast, at 9DPA, these genes were primarily involved in cysteine and methionine metabolism, biosynthesis, and protein processing. This observation indicates that the differences in grain size between the large-grain line AD3 and the small-grain line AD148 result from distinct biological processes occurring both during the early stages of glume development and the grain filling stage. Furthermore, eight genes have been identified as potential regulators of grain development, providing valuable information on the underlying mechanisms of grain development in rice.To identify the key genes, pathways, and regulatory networks controlling rice grain size by integrating transcriptomic and proteomic analyses of large-grain (AD3) and small-grain (AD148) lines at critical developmental stages.

Background: Alternative polyadenylation (APA) is an important pattern of post-transcriptional regulation of genes widely existing in eukaryotes, involving plant physiological and pathological processes. However, there is a dearth of studies investigating the role of APA profile in rice leaf blight. Results: In this study, we compared the APA profile of leaf blight-susceptible varieties (CT 9737-613P-M) and resistant varieties (NSIC RC154) following bacterial blight infection. Through gene enrichment analysis, we found that the genes of two varieties typically exhibited distal poly(A) (PA) sites that play different roles in two kinds of rice, indicating differential APA regulatory mechanisms. In this process, many disease-resistance genes displayed multiple transcripts via APA. Moreover, we also found five polyadenylation factors of similar expression patterns of rice, highlighting the critical roles of these five factors in rice response to leaf blight about PA locus diversity. Conclusion: Notably, the present study provides the first dynamic changes of APA in rice in early response to biotic stresses and proposes a possible functional conjecture of APA in plant immune response, which lays the theoretical foundation for in-depth determination of the role of APA events in plant stress response and other life processes.

Rice seeds of different varieties exhibited distinct metabolic profiles in our study. We analyzed the metabolites in seeds of six rice varieties (CH, HM, NX, YX, HY, and MX) using non-targeted GC–MS. Our findings revealed that amino acids, sugars, and organic acids were predominant in all varieties, with significant differences observed in CH compared to the others. Specifically phenylalanine and glycine content differed notably in NX and YX, respectively. Additionally, 1,5-anhydroglucitol content in NX, and glutamate, aspartate, and lactulose in NX, YX, HM, HY, and MX were up-regulated. Due to the biological functions of these amino acids and sugars, these indicated that compared to CH, rice of NX were more conducive to metabolism of carbohydrate and fat, and healthy growth maintenance in the human body, but mightThese variations suggest that NX rice may be more beneficial for carbohydrate and fat metabolism and overall health maintenance compared to CH. However, it may not be suitable for diabetic patients. YX rice may not be an ideal glycine supplement, rice ofwhile HM, HY, and MX rice could serve as potential lactulose sources. Furthermore, NX and YX rice exhibited higher levels of main storage proteins compared to CH. This study offers valuable insights into the metabolic differences among various rice varieties.

OsPLS4 encodes a β-ketoacyl carrier protein reductase (KAR). The role of OsPLS4 in rice sheath blight (Rhizoctonia solani) remains unclear. Our preliminary studies showed that premature leaf senescence mutants (pls4) were highly susceptive to sheath blight in the early stage of rice development. To explore the role of this gene in the development of rice sheath blight, the transcriptome profiles of the rice pls4 mutant and wild type were compared by RNA-seq. The results revealed 2,569 differentially expressed genes (DEGs). The down-regulated genes were significantly enriched in the defense response-related biological processes. These down-regulated genes included the chitinase genes and WRKY genes, which were significantly changed in pls4 mutants. Furthermore, 467 genes induced significant alternative splicing (AS) events. Among them, intron retention (IR) affected gene expression levels and functions of the vitamin B6 (VB6) metabolism pathway related to sheath blight. This result suggests that IR plays an important role in the sheath blight resistance of mutant pls4. Together, these results indicate that pls4 could be involved in the biological process of sheath blight via DEGs and the fine-tuning of IR. The present study provides a molecular basis for further investigation of the resistance of rice to sheath blight.

Anthocyanin is one of the flavonoids, which has strong antioxidant properties. Functional rice rich in anthocyanins can not only improve immunity, but also anti-radiation, beauty, anti-aging effect, very popular in the market. In this study, we used Zibaoxiangnuo 1 (ZBXN 1), a functional rice variety which is rich in total flavonoids and anthocyanins, as the experimental material to construct Recombination Inbred Lines (RILs) with Minghui63 (MH63), a variety without anthocyanins. The contents of anthocyanins and total flavonoids of RILs and two parents were determined for three consecutive generations. The average anthocyanin content of parent ZBXN 1 was 319.31 mg/kg, and the anthocyanin inheritance of RIL population was relatively stable, with 10 samples higher than ZBXN 1. In addition, there was no significant difference in the total flavonoids content between the two parents, the total flavonoids content of Z25 in RIL population was 0.33%. Based on these studies, we believe that ZBXN 1 has abundant and stable anthocyanins, which can be used as an intermediate breeding material for breeding high-quality varieties with high anthocyanins, and lay a foundation for breeding more anthocyanin-rich rice varieties.

Rice false smut（RFS） is a rice fungal disease caused by the biotrophic fungus Ustilaginoidea virens（Cooke） Takahashi. The pathogenic fungus specifically infects rice spikelets at the booting stage and coverts the infected spikelets into false smut balls consisting of hyphae and chlamydospores(Ashizawa et al., 2012; Sun et al.,

Cadmium (Cd) pollution and uptake into the grains of developing rice plants represent a major threat to human health. Studies of specific genes can offer new insights into the functional roles of particular genes, highlighting candidate alleles that can be leveraged as DNA markers. Accordingly, the identification of novel Cd-related traits and sequence variants can provide new molecular markers for Cd resistance in rice. In the present study, a genetic diversity analysis was carried out on 85 rice varieties exhibiting varied Cd accumulation, and 436 single polymorphic sites (SNP) corresponding to 43 haplotypes were detected across 12 Cd-associated genes (CAL1, OsCADT1, Oscd1, OsHMA4, OsHMA9, OsNRAMP1, OsNRAMP2, OsNRAMP5, OsHMA2, OsHSMA3, OsPCR1, and OsABCG43). By utilizing the information of the SNPs, 85 rice varieties was classified the into 2 clusters with different source categories and Cd contents. Among the variants, 45 sites in 5 genes were significantly associated with the Cd content in rice grains, of which 8 alleles in OsPCR1, CAL1, and Oscd1 were negatively correlated with Cd accumulation. The results of haplotype aggregation analysis for OsPCR1, Oscd1, and CAL1 showed that 85 rice varieties were divided into 5 clusters. Interestingly, most of the varieties in Cluster A belonged to tropical type, which contained the aggregation of three favorable alleles, whereas the temperate varieties constituted the majority of Cluster B lacking favorable alleles. This observation suggests that the allelic combination found in tropical rice varieties may hold promise for reducing Cd accumulation levels in rice grains. The Cd-associated alleles identified in the present study can not only be used to check the Cd tolerance of rice varieties, but also serve as functional molecular markers to differentiate the source of the rice varieties, which provides a better understanding of the relationship between the sequence variation in Cd-related genes and Cd accumulation in rice.

Zaoxian 14 is a new early rice variety developed by the Jiangxi Agricultural University.It was approved in Jiangxi Province in April 2022.It was characterized by early maturity,high yield,stable yield and lodging resistance,suitable for direct seeding,seedling throwing,machine transplanting and other light and simplified cultivation.This paper briefly introduced the breeding process of Zaoxian 14 and its light and simplified cultivation techniques.

: Plant architecture is a compound trait integrated with multiple morphological and physiological traits, and it is closely related to rice yield. Deciphering excellent plant architecture alleles or QTLs is of great significance for high-yield rice breeding. In this study, we constructed a set of Changhui 121/Koshihikari chromosome segment substitution lines (CSSLs) with the size of 208 in our laboratory. QTLs controlling plant height, flag leaf morphology, and tiller numbers were detected under three environments. A total of 35 QTLs for rice architecture were identified on 11 chromosomes except chromosome 9, and the range of the phenotypic variation explaining was 2.00%–22.86%. It was worth noting that qPH-1-1 , qFLW-6 , and qFLA-3 could be detected in three environments, among which qFLW-6 was a newly identified QTL of the flag leaf width. Phenotypic identification verified that the additive effects and environmental stability of the two locus alleles by the replacement lines carrying qPH-1-1 and sites. The results of this study laid the foundation for further fine mapping and cloning of QTLs for rice plant architecture and the molecular marker-assisted selection (MAS) in rice breeding.

[目的]糯稻"航天稻"是经空间技术育种所得,籼稻"昌恢871"是江西省常规的水稻品种.通过比较糯稻"航天稻"与籼稻"昌恢871"的果糖和氨基酸代谢,探究两种水稻间代谢组的差异.[方法]运用气相色谱-质谱联用仪(GC-MS),对两种水稻的化学成分进行了非靶向代谢组学分析.[结果](1)共鉴定出221个代谢物;(2)基于主成分分析(PCA),样本间差异明显;(3)基于偏最小二乘判别分析(PLS-DA)的重要投影性值(VIP>1)和t检验(P<0.05)筛选出81个差异代谢物,其中上调和下调幅度前20的差异代谢物主要是糖类(尤其是果糖)、有机酸和氨基酸;(4)基于KEGG通路分析,将差异代谢物注释到52个代谢通路,其中12条显著富集的通路(P<0.05).[结论]构建了两种水稻材料的果糖和氨基酸代谢网络,为进一步探究糯稻"航天稻"和籼稻"昌恢871"主要营养成分及其代谢途径提供了理论参考,也为稻米营养品质的研究提供依据.

Semi-dwarfing improves the lodging resistance and yield of rice, and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height, resulting in reduced genetic diversity and negative agronomic traits. Thus, exploring alternative sources of dwarfism is imperative for rice breeding. Here, we identified a novel RGA1 allele, d1-w, from a local indica variety Xiaolixiang (XLX) using a map-based cloning approach. Compared with other rice varieties, RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript level. The RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice breeding. Compared with transgenic XLX plants (XLXD1), XLX exhibited reduced plant height, increased stem strength, lower reactive oxygen species accumulation, delayed senescence, stronger photosynthesis, higher grain yield and quality (including external, milling and nutritional qualities), and enhanced resistance to drought and Rhizoctonia solani. Therefore, we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

宏S是萍乡市农业科学研究所与江西农业大学农学院共同选育的籼型水稻两系不育系,来源于深08S/内香3B.宏S具有株型紧凑、分蘖力较强、茎秆粗壮、异交习性好、配合力较好、米质优且有香味等优点,可用于测配杂交晚稻和一季中稻组合,2021年1月通过江西省农作物品种审定委员会审定,同年6月获得植物新品种权.用宏S配组的杂交晚稻组合宏两优瑞占于2021年通过江西省农作物品种审定委员会审定,其米质达部颁2级优质稻谷标准.

随着人们生活水平的日益提高,富含各种营养成分且具有保健功效的功能稻也越来越受到关注.挖掘和利用功能稻中的相关内源基因来用于育种实践显得尤为重要.本研究利用富含天然维生素A(VA)的功能稻品种'紫宝香糯1号'作为实验材料,通过与93-11进行正反交构建遗传群体,并测定其F1代及F2代群体的VA含量,表明VA合成是隐形核基因控制的数量性状.为了进一步对控制水稻含VA性状的基因进行QTL定位分析,利用'紫宝香糯1号'与'明恢63'通过单粒传构建重组自交系(RIL)并绘制遗传图谱,最终定位了 3个与VA性状相关的QTL,这些结果为调控VA合成相关基因的精细定位和富含VA新型功效稻选育提供依据.

BACKGROUND:Phytochromes are important photoreceptors in plants, and play essential roles in photomorphogenesis. The functions of PhyA and PhyB in plants have been fully analyzed, while those of PhyC in plant are not well understood.RESULTS:A rice mutant, late heading date 3 (lhd3), was characterized, and the gene LHD3 was identified with a map-based cloning strategy. LHD3 encodes phytochrome C in rice. Animo acid substitution in OsphyC disrupted its interaction with OsphyB or itself, restraining functional forms of homodimer or heterodimer formation. Compared with wild-type plants, the lhd3 mutant exhibited delayed flowering under both LD (long-day) and SD (short-day) conditions, and delayed flowering time was positively associated with the day length via the Ehd1 pathway. In addition, lhd3 showed a pale-green-leaf phenotype and a slower chlorophyll synthesis rate during the greening process. The transcription patterns of many key genes involved in photoperiod-mediated flowering and chlorophyll synthesis were altered in lhd3.CONCLUSION:The dimerization of OsPhyC is important for its functions in the regulation of chlorophyll synthesis and heading. Our findings will facilitate efforts to further elucidate the function and mechanism of OsphyC and during light signal transduction in rice.

使用5个转Bt基因水稻恢复系作为父本,以12个不育系作为母本,根据5×12(NCII)不完全双列杂交设计配制60个组合,分析了这些组合的9个稻米品质性状的配合力及遗传参数.结果表明:精米率主要受基因加性效应的影响,整精米率、垩白粒率、碱消值、胶稠度主要受基因非加性效应互作的影响;除精米率主要受母本影响外,其余8个性状均受双亲交互作用的影响;垩白粒率和垩白度在后代遗传中主要受基因遗传作用的影响,可以在早代直接选择.配合力方差分析结果表明:精米率、垩白度及碱消值受环境因素的影响较大;昌恢891T为一般配合力较好的父本,华1165S为一般配合力较好的母本;原香39A/昌恢891T、泰乡1209A/昌恢T025T、昌盛843A/昌恢T025T为较优的组合,其中原香39A/昌恢891T的特殊配合力的综合评价最好.