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Abstract Background Intracerebral hemorrhage (ICH) is a common subtype of stroke, characterized by a high mortality rate and a tendency to cause neurological damage. This study aims to investigate the role and mechanisms of lncRNA HCP5 in ICH. Methods We simulated ICH in vivo by injecting collagenase into rats and established an in vitro model using hemoglobin-treated BV2 cells. HCP5 and miR-195-5p levels were quantified by RT-qPCR. mNSS score was used to evaluate neurological deficits in the rats. The dry-wet weight method assessed the degree of brain edema. Cell viability and apoptosis rates were determined using the CCK-8 assay and flow cytometry, respectively. The targeting relationship between HCP5 and miR-195-5p was confirmed using dual-luciferase reporter assays and RNA immunoprecipitation. ELISA was utilized to measure inflammatory factors, and commercial kits were used to detect MDA and ROS levels. Results In the ICH model rats, HCP5 levels were significantly elevated. It was also found that silencing HCP5 significantly alleviated brain edema and neurological deficits in the ICH rats, and there was a marked improvement in ICH-induced neuroinflammation and oxidative stress. Moreover, HCP5 was found to sponge miR-195-5p, and inhibiting miR-195-5p could counteract the neuroprotective effects of silencing HCP5. Similar results were obtained in the in vitro experiments with BV2 cells. Conclusions Silencing HCP5 can alleviate brain edema, neurological dysfunction, neuroinflammation, and oxidative stress caused by ICH via miR-195-5p.

Soil and plant analyzer development (SPAD) value and leaf nitrogen concentration (LNC) based on dry weight are important indicators affecting rice yield and quality. However, there are few reports on the use of machine learning algorithms based on hyperspectral monitoring to synchronously predict SPAD value and LNC of indica rice. Meixiangzhan No. 2, a high-quality indica rice, was grown at different nitrogen rates. A hyperspectral device with an integrated handheld leaf clip-on leaf spectrometer and an internal quartz-halogen light source was conducted to monitor the spectral reflectance of leaves at different growth stages. Linear regression (LR), random forest (RF), support vector regression (SVR), and gradient boosting regression tree (GBRT) were employed to construct models. Results indicated that the sensitive bands for SPAD value and LNC were displayed to be at 350–730 nm and 486–727 nm, respectively. Normalized difference spectral indices NDSI (R497, R654) and NDSI (R729, R730) had the strongest correlation with leaf SPAD value (R = 0.97) and LNC (R = −0.90). Models constructed via RF and GBRT were markedly superior to those built via LR and SVR. For prediction of leaf SPAD value and LNC, the model constructed with the RF algorithm based on whole growth periods of spectral reflectance performed the best, with R2 values of 0.99 and 0.98 and NRMSE values of 2.99% and 4.61%. The R2 values of 0.98 and 0.83 and the NRMSE values of 4.88% and 12.16% for the validation of leaf SPAD value and LNC were obtained, respectively. Results indicate that there are significant spectral differences associated with SPAD value and LNC. The model built with RF had the highest accuracy and stability. Findings can provide a scientific basis for non-destructive real-time monitoring of leaf color and precise fertilization management of indica rice.

【Objective】By measuring and analyzing the physical characteristics of the basal stems of rice, the relationship between these traits and the stem breaking resistance was explored, and the core traits affecting the basal stem breaking resistance of rice were identified, providing a theoretical basis for the breeding of rice lodging-resistant varieties.【Method】The study analyzed the lodging resistance-related agronomic traits, including plant height, single plant bending resistance, basal internode breaking resistance, and stem structure, of the rice variety Yuehesimiao, the lodging-susceptible variety Xiangyaxiangzhan, and Yuehesimiao × Xiangyaxiangzhan F2 segregation populations. The influence of each trait on lodging resistance of rice was evaluated by correlation coefficient.【Result】There are significant differences in lodging resistance between the two varieties of Yuehesimiao and Xiangyaxiangzhan. The N2 (second internode from the base) breaking resistance (16.58 N), N2 wall thickness (1.02 mm), N2 filling degree (0.19 g/cm), and N2 stem diameter (6.21 mm) of Yuehesimiao are significantly larger than those of Xiangyaxiangzhan (N2 breaking resistance: 9.93 N, N2 wall thickness: 0.66 mm, N2 filling degree: 0.11 g/cm, N2 stem diameter: 4.60 mm). The N2 breaking resistance, N2 length, N2 stem diameter, stem wall thickness, fresh weight and filling degree of the F2 population show continuous distribution and are controlled by polygenes. The correlation analysis results of the F2 population show that, N2 breaking resistance is positively correlated with plant height (r=0.18), N2 breaking resistance is significantly positively correlated with N2 wall thickness (r=0.75**). N2 breaking resistance is significantly positively correlated with N2 filling degree (r=0.67*). N2 breaking resistance is positively correlated with N2 minor axis (r=0.52) and N2 stem diameter is negatively correlated with N2 length (r=-0.20).【Conclusion】The genetic mechanism of lodging resistance in the F2 population of Yuehesimiao × Xiangyaxiangzhan shows that N2 wall thickness is significantly positively correlated with N2 breaking resistance and is the core trait of stem lodging resistance, which is a quantitative trait controlled by polygenes. Taking N2 wall thickness as the research focus will greatly reduce the complexity of previous research methods for lodging resistance, which clarifies the research goals and directions for future lodging resistance-related researches.

Rice is one of the most important crops in the world, and safe production of rice is related to food safety issues. Rice blast, caused by Magnaporthe oryzae, is a worldwide fungal disease that causes serious losses to rice production. Compared with chemical pesticides control, the breeding and application of disease-resistant cultivars is the most economical and effective way to control the disease. However, the complex and diverse population of blast fungus in the field, excessive use of chemical pesticides, change of temperature environment and other factors cause rapid evolution of M. oryzae isolates, and the resistance of cultivars can only last for 3-5 years. Magnaporthe oryzae generates new races through the mutation of avirulent genes, which can escape or suppress the immune system of rice, causing infection and disease. At present, 26 avirulent genes in blast fungus have been identified, and 14 of them have been cloned, which plays an important role in the infection and colonization of pathogens and in interfering with the immune response of host plants. Further studies on the interaction mechanism of M. oryzae effector protein and rice resistance protein have also been conducted. Understanding the pathogenic mechanism of blast fungus and molecular mechanism of its interaction with rice will help to better understand the pathway of pathogens and the immune response of plant disease resistance genes, to formulate more efficient and green control measures. This review summarized the process of M. oryzae effector protein translocation and secretion in rice cells, the research advances in the interaction between effector proteins and disease-resistance proteins and the regional distribution of effector proteins. And the opportunities and challenges in current researches were discussed and prospected, with an aim to provide references for the molecular mechanism of the interaction between rice and blast fungus, disease-resistance breeding and disease prevention and control strategies.

Upland rice, an ecological type formed by the long-term domestication of rice, is mainly distributed in dry land and hilly land with stable summer rainfall but insufficient irrigation conditions. Currently, the cultivated area of upland rice in the world is about 19 million hm2, accounting for about 12.7% of the total cultivated rice area. With rich resources and a long planting history, upland rice is distributed in different rice growing areas in China. Agriculture is one of the most important sources of greenhouse gas emissions, in which the long-term water layer needs to be established in the process of rice cultivation, accounting for about 16% of the greenhouse gas emissions from agriculture. Many studies have shown that planting upland rice plays an important role in reducing greenhouse gas emissions from paddy fields, which is of great significance for ensuring national food security and achieving national carbon peak and carbon neutrality goals. Due to the relative balance of light, temperature and rainfall in Guangdong Province, double-croping rice is the main planting pattern in each ecological region, and the development of upland rice is relatively lagging. With the decrease of the rural labor force, the shortage of water resources and the continuous occurrence of extreme weather such as high temperature and drought in Guangdong and South China, the market demand for upland rice varieties has increased year by year. This review introduces the drought resistance mechanism, breeding and supporting technologies of upland rice in China and abroad, analyzes the research and planting status of upland rice in Guangdong, and puts forward suggestions on upland rice researches, providing references for molecular breeding and low-carbon cultivation technology of upland rice varieties in Guangdong Province.

Aroma is a crucial determinant of rice taste quality, with volatile organic compounds (VOCs) playing a key role in defining this characteristic. However, limited research has explored the dynamic changes in these aromatic substances during the ripening stages of rice grains. In this study, we analyzed VOCs in rice grains across four ripening stages post-flowering using headspace solid-phase microextraction combined with gas chromatography–mass spectrometry (HS-SPME-GC-MS). A total of 417 VOCs were identified, among which 65 were determined to be key aroma-active compounds based on relative odor activity value (rOAV) analysis. Most of these aroma-active compounds exhibited an accumulation pattern as the grains matured. Notably, 5-ethyl-3-hydroxy-4-methyl-2(5H)-furanone and 2-Methyloxolan-3-one had the largest rOAV values. Additionally, (Z)-6-nonenal, (Z,Z)-3,6-nonadienal, 2-thiophenemethanethiol, 5-methyl-2-furanmethanethiol, 2,2,6-trimethyl-cyclohexanone, and 3-octen-2-one were identified as potential key markers for distinguishing rice-grain maturity stages. Moreover, 2-acetyl-1-pyrroline (2-AP), heptanal, and 1-nonanol were identified as marker metabolites differentiating aromatic from non-aromatic brown rice. These findings contribute to a deeper understanding of the dynamic variation and retention of aroma compounds during rice-grain ripening, and they offer valuable insights into the improvement of fragrant rice varieties.

Grain shape in rice (Oryza sativa L.) is a complex trait governed by multiple quantitative trait loci (QTLs). To dissect the genetic basis of rice shape, QTL analysis was conducted for milled rice grain width (MGW), milled rice grain length (MGL), and milled rice length-to-width ratio (MLWR) using a recombinant inbred line (RIL) population of F10 and F11 generations derived from a cross between Yuexiangzhan and Shengbasimiao. A high-density genetic map consisting of 2412 bins was constructed by sequencing 184 RILs, spanning a total length of 2376.46 cM. A total of 19 QTLs related to MGL, MGW, and MLWR were detected under two environments. The range of phenotypic variation attributed to individual QTL ranged from 1.67% to 32.08%. Among those, a novel locus for MGL, MGW and MLWR, designated as qMLWR3.2, was pinpointed within a specific ~0.96-Mb region. Two novel loci for MGW and MLWR, qMLWR11.1 and qMLWR11.2, were verified within ~1.22-Mb and ~0.52-Mb regions using three RIL-developed populations, respectively. These findings lay the foundation for further map-based cloning and molecular design breeding in rice.

Abstract Rice quality is one of the main targets of rice breeding and is a complex trait that involves grain appearance, milling, cooking, eating and nutritional quality. For many years, rice breeding has contended with imbalances in rice yield, quality, and disease and lodging resistance. Here, the milling and appearance quality, cooking quality, starch rapid viscosity analyzer (RVA) profile, and nutritional quality of grains of Yuenongsimiao (YNSM), an indica rice variety with high yield, high quality and disease resistance, were determined. YNSM had excellent appearance and quality, with low amylose contents and high gel consistency, and these characteristics exhibited significant correlations with the RVA profile such as hot paste viscosity, cool paste viscosity, setback viscosity, and consistency. Moreover, 5 genes related to length-to-width ratio (LWR) as well as the Wx gene were used to detect the main quality genotype of YNSM. The results showed that YNSM is a semilong-grain rice with a relatively high brown rice rate, milled rice rate and head rice yield and low chalkiness. The results indicated that the LWR and food quality of YNSM might be related to gs3, gw7 and Wx b . This study also reports the quality characteristics of hybrid rice developed using YNSM as a restorer line. The quality characteristics and the genotype for grain quality determined through gene analysis in YNSM may facilitate the breeding of new rice varieties that achieve a balance of grain yield, resistance and quality.

Rice is one of the most important food crops in the world. Rice disease is a major threat to its yield loss. Bacterial blight caused by the gram-negative bacterium Xanthomonas oryzae pv. oryzae (Xoo), is one of the three major diseases that seriously affect rice yield. The traditional chemical control methods have many drawbacks. The cultivation and planting of rice varieties resistant to bacterial blight is recognized worldwide as the most safe and effective means to control the disease. Identification of resistant germplasm resources and discovery of resistant genes are the premise of resistant varieties breeding. Under the pressure of both natural and artificial selections, new pathogenic varieties have emerged one after another due to the constant variation of bacterial blight pathogens, and the main varieties have gradually lost their disease resistance. Therefore, it is necessary to explore and identify more durable disease resistance genes. In the study, 16 bacterial blight resistance genes that have been cloned are briefly classified, and then three genes Xa23, Xa7 and xa5 that are broad-spectrum resistant to bacterial blight with good application are described in detail from the aspects of gene discovery, location, cloning, mechanism of action, and etc. The conventional breeding, molecular marker-assisted selection breeding, transgenic breeding and gene marker breeding for bacterial blight resistance are introduced. In addition, the prospect of molecular breeding for broad-spectrum resistance to bacterial blight is put forward based on the characteristics of different bacterial blight genes and the problems in current breeding and utilization.

Phenomics refers to the systematic study at the genomic level of all the phenotypes of an organism or cell under a variety of different environmental conditions. With the continuous improvement of plant phenotype acquisition technology and equipment as well as the rapid development of genomics, proteomics, metabolomics, bioinformatics and big data computing technology, high-throughput phenomics analysis plays an increasingly important role in germplasm identification, genetic mapping, functional gene mining and other aspects. High-throughput phenomics research is becoming a key field to break through the future research and application of crop science, providing accurate and efficient decision support for crop breeding and cultivation management. Therefore, it is of great significance to fully exploit multi-omics information and accelerate high-throughput phenotypic studies to fully understand the relationship between crop genotypes, phenotypes and environment, to discover and reveal the regulatory genes and mechanisms of important agronomic traits and to promote the researches of crop functional genomes and crop genetic improvement. In this review, the phenotypic development of phenomics were summarized, the current phenomics research platform and imaging system and its application in crop root structure, canopy structure, biological and abiotic stress were systematically discussed, with a view to providing a reference for highthroughput acquisition and analysis of crop phenotypes and accelerating the application of phenomics in crop breeding.

Yuenongsimiao is not only a conventional rice variety with high-resistance and excellent comprehensive traits, but also a good parent for high-quality rice breeding. The analysis of the characteristics of the derived varieties could provide a theoretical basis for high-quality rice breeding. With Yuenongsimiao (R1212) as the parent, there were 53 rice varieties approved or authorized, of which 43 passed national or provincial approval. These varieties were rich in type, including conventional rice, hybrid rice, aromatic rice and etc. To clarify the characteristics of varieties derived from Yuenongsimiao, the approved derived varieties were selected, and their yield, rice quality, disease and stress resistance performance in the year they participated in the national and provincial regional trials were compared and analyzed. It was found that the yields of these varieties in the regional trials were increased by 0.46%-10.98% compared with these of the control varieties. In term of quality indexes, except for the ungraded seedlings of Q Liangyouyuenongsimiao, both conventional rice and hybrid rice could reach high-quality standards. In terms of disease resistance, some derived varieties resisted blast and bacterial blight, while many derived varieties showed weak resistance to these two diseases. In the identification of lodging and heat resistance, the derived varieties showed strong lodging resistance. Furthermore, except Huiliangyouyuenongsimiao, other varieties showed strong heat resistance phenotypes. These derivatives generally possessed the characteristics of high-yielding stability, good rice quality, strong lodging and heat resistance, which fully reflected the"core"role of Yuenongsimiao as a high-quality rice parent. The main Yuenongsimiao derived varieties, such as Yuehesimiao, Yuejinnongzhan, Longjingyou1212, Jingliangyou1212, Longliangyou1212, Quanyouyuenongsimiao and Huiliangyouyuenongsimiao have been the main local varieties, with good promotion and application prospect in the approved area.

【Objective】Rice seedling transplanting and direct seeding are the most widely used planting methods in Guangdong currently. Exploring the effects of seedling transplanting and direct seeding on rice yield and screening the rice varieties suitable for flooding direct seeding in Guangdong and South China can provide theoretical basis for variety selection and breeding application of direct seeding rice in Guangdong and South China.【Method】Twenty-five rice varieties from Guangdong Province were used as materials to simulate submergence tolerance tests, the growth period, plant height, lodging resistance and yield were measured under two different cultivation modes of seedling transplanting and direct seeding in early and late seasons, and the rice varieties suitable for direct seeding were screened.【Result】The seedling rate of 12 rice varieties, such as Yuexinyinzhan 2, Yuenongsimiao and Yuetaiyouzhan with submergence tolerance reached more than 80%.It was found that the growth period of direct seeding rice was 7-15 d shorter than that of seedling transplanting by analyzing the two cultivation modes of seedling transplanting and direct seeding in early and late seasons. As it showed in the field lodgingresistance phenotype identification, 11 rice varieties had stronger lodging resistance. Yield analysis showed that the yields of direct seeding in early and late seasons were higher than those of seedling transplanting, with an average increase of 0.99 % and 1.25 %, respectively.【Conclusion】Based on the submergence tolerance, lodging resistance and high yield of the tested varieties, 4 varieties including Yuenongsimiao, Yumeizhan, Wushansimiao and Yuteyouzhan were selected to be suitable for direct seeding cultivation pattern in South China.

Rice is one of the food crops with the largest planting area and the highest total output in China, which plays an important role in ensuring national food security. Since the "Green Revolution", China's rice yield per unit area has been greatly improved. However, the lodging problem of rice has long restricted the high and stable yield and excellent quality of rice. A large area of lodging of rice will lead to serious yield loss and rice quality decline. At present, with the continuous improvement of rice yield per unit area, the problem of rice lodging is becoming increasingly prominent, which has been one of the great hidden dangers threatening the normal rice production. Through decades of continuous research, researchers at home and abroad have made great progress in the cause, mechanism, influencing factors, evaluation methods and lodging resistance genetics and breeding of rice. The study summarizes the research progress of rice lodging resistance since the"Green Revolution", combined with the lodging resistance research work experience for many years, comprehensive analyzes the research the origin of rice lodging resistance, clarifies the properties of rice lodging, summarizes the main related factors of rice lodging resistance, and puts forward the relevant countermeasures to raise the capacity of rice lodging resistance. On the basis of the existing research, the main directions of rice lodging resistance breeding, cultivation and molecular mechanism research in the new era are prospected in order to provide references for rice lodging resistance researchers.

Small auxin-up-regulated RNAs (SAURs) are genes rapidly activated in response to auxin hormones, significantly affecting plant growth and development. However, there is limited information available about the specific functions of SAURs in rice due to the presence of extensive redundant genes. In this study, we found that OsSAUR10 contains a conserved downstream element in its 3′ untranslated region that causes its transcripts to be unstable, ultimately leading to the immediate degradation of the mRNA in rice. In our investigation, we discovered that OsSAUR10 is located in the plasma membrane, and its expression is regulated in a tissue-specific, developmental, and hormone-dependent manner. Additionally, we created ossaur10 mutants using the CRISPR/Cas9 method, which resulted in various developmental defects such as dwarfism, narrow internodes, reduced tillers, and lower yield. Moreover, histological observation comparing wild-type and two ossaur10 mutants revealed that OsSAUR10 was responsible for cell elongation. However, overexpression of OsSAUR10 resulted in similar phenotypes to the wild-type. Our research also indicated that OsSAUR10 plays a role in regulating the expression of two groups of genes involved in auxin biosynthesis (OsYUCCAs) and auxin polar transport (OsPINs) in rice. Thus, our findings suggest that OsSAUR10 acts as a positive plant growth regulator by contributing to auxin biosynthesis and polar transport.

Rice quality is a comprehensive quantitative trait greatly influenced by heredity and environment. Here, 11 rice quality traits and Rapid Visco-Analyser (RVA) profiles of 30 indica rice germplasms were detected and analyzed. In addition, we used grain size genes and starch synthesis gene Wx to detect the rice quality genotypes of rice. The results showed different degrees of correlation among rice quality traits. In addition, principal component analysis (PCA) divided rice quality traits into four principal components, and the cumulative contribution rate reached 82.478%. Cluster analysis divided 30 rice varieties into five categories. The first four types had better rice quality. Identification of rice quality genes indicated that most of the genotypes were GS3, GS9, GW5, GW8 and Wxb, and a few were GW7 and Wxa. Identifying rice quality characteristics and genotypes of rice varieties may lay a theoretical foundation for promoting the cultivation of new rice varieties, enabling breeders andresearchers to develop better rice varieties.

Abstract Leaf senescence is one of the most precisely modulated developmental process and affects various agronomic traits of rice. Anti-senescence rice varieties are important for breeding application. However, little is known about the mechanisms underlying the metabolic regulatory process of leaf senescence in rice. In this study, we performed transcriptomic and metabolomic analyses of the flag leaves in Yuenong Simiao (YN) and YB, two indica rice cultivars that differ in terms of their leaf senescence. We found 8524 genes/204 metabolites were differentially expressed/accumulated in YN at 30 days after flowering (DAF) compared to 0 DAF, and 8799 genes/205 metabolites were differentially expressed in YB at 30 DAF compared to 0 DAF. Integrative analyses showed that a set of genes and metabolites involved in flavonoid pathway were significantly enriched. We identified that relative accumulation of PHENYLALANINE AMMONIA-LYASE (PAL), CINNAMATE 4-HYDROXYLASE (C4H), 4-COUMAROYL-COA LIGASE (4CL), CHALCONE SYNTHASE (CHS) and CHALCONE ISOMERASE (CHI) in YN30/0 was higher than that in YB30/0. Three flavonoid derivatives, including phloretin, luteolin and eriodictyol, showed lower abundances in YB than in YN at 30 DAF. We further revealed a MYB transcription factor, which is encoded by OsR498G0101613100 gene, could suppress the expression of CHI and CHS. Our results suggested a comprehensive analysis of leaf senescence in a view of transcriptome and metabolome and would contribute to exploring the molecular mechanism of leaf senescence in rice.

Bacterial blight (BB) is an important constraint on achieving a high and stable rice grain yield. An increasing number of BB resistance (R) genes have been identified and cloned to increase the available options for rice disease resistance breeding. However, it is necessary to understand the distribution of R genes in rice varieties for rational distribution and breeding. Here, we genotyped five R genes, i.e. Xa4, Xa7, Xa21, Xa23, and Xa27, in seventy main cultivars from Guangdong Province, South China using the corresponding specific markers. Our results showed that 61 varieties carried Xa4, only three varieties carried Xa27, and Xa7, Xa21, or Xa23 was not detected in all tested varieties. Notably, only 33 varieties exhibited resistance to pathotype IV Xoo strains. These results indicate that Xa4 is no longer suitable for widespread use in rice breeding, although Xa4 is widely present in tested varieties. Remarkably, the strongly virulent BB strains of pathotype IX evolved quickly in southern China, and Xa23 was found to effectively confer resistance against the pathotype IX strains. Subsequently, we successfully bred two novel inbred rice varieties as also being restorer lines and two photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines using the broad-spectrum resistance gene Xa23 through marker-assisted selection (MAS) combined with phenotypic selection. All of the developed lines and derived hybrids exhibited enhanced resistance to BB with excellent yield performance. Our research may potentially facilitate both of the inbred and hybrid rice disease resistance breeding.

Nuclear factor Y (NF-Y) is a ubiquitous transcription factor that regulates important physiological and developmental processes. In this study, we identified 34 OsNF-Y genes in rice, including 6 newly identified genes. Expression profile analysis covering the whole life cycle revealed that transcripts of OsNF-Y differentially accumulated in a tissue-specific, preferential or constitutive manner. In addition, gene duplication studies and expression analyses were performed to determine the evolutionary origins of the OsNF-Y gene family. Nine OsNF-Y genes were differentially expressed after treatment of seedlings with one or more abiotic stresses such as drought, salt and cold. Analysis of expression correlation and Gene Ontology annotation suggested that OsNF-Y genes were co-expressed with genes that participated in stress, accumulation of seed storage reserves, and plant development. Co-expression analysis also revealed that OsNF-Y genes might interact with each other, suggesting that NF-Y subunits formed complexes that take part in transcriptional regulation. These results provide useful information for further elucidating the function of the NF-Y family and their regulatory pathways.

BACKGROUND: SET domain is responsible for the catalytic activity of histone lysine methyltransferases (HKMTs) during developmental process. Histone lysine methylation plays a crucial and diverse regulatory function in chromatin organization and genome function. Although several SET genes have been identified and characterized in plants, the understanding of OsSET gene family in rice is still very limited. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a systematic analysis was performed and revealed the presence of at least 43 SET genes in rice genome. Phylogenetic and structural analysis grouped SET proteins into five classes, and supposed that the domains out of SET domain were significant for the specific of histone lysine methylation, as well as the recognition of methylated histone lysine. Based on the global microarray, gene expression profile revealed that the transcripts of OsSET genes were accumulated differentially during vegetative and reproductive developmental stages and preferentially up or down-regulated in different tissues. Cis-elements identification, co-expression analysis and GO analysis of expression correlation of 12 OsSET genes suggested that OsSET genes might be involved in cell cycle regulation and feedback. CONCLUSIONS/SIGNIFICANCE: This study will facilitate further studies on OsSET family and provide useful clues for functional validation of OsSETs.

Background: The anthers and pollen grains are critical for male fertility and hybrid rice breeding. The development of rice mature anther and pollen consists of multiple continuous stages. However, molecular mechanisms regulating mature anther development were poorly understood. Results: In this study, we have identified 291 mature anther-preferentially expressed genes (OsSTA) in rice based on Affymetrix microarray data. Gene Ontology (GO) analysis indicated that OsSTA genes mainly participated in metabolic and cellular processes that are likely important for rice anther and pollen development. The expression patterns of OsSTA genes were validated using real-time PCR and mRNA in situ hybridizations. Cis-element identification showed that most of the OsSTA genes had the cis-elements responsive to phytohormone regulation. Co-expression analysis of OsSTA genes showed that genes annotated with pectinesterase and calcium ion binding activities were rich in the network, suggesting that OsSTA genes could be involved in pollen germination and anther dehiscence. Furthermore, OsSTA RNAi transgenic lines showed male-sterility and pollen germination defects. Conclusions: The results suggested that OsSTA genes function in rice male fertility, pollen germination and anther dehiscence and established molecular regulating networks that lay the foundation for further functional studies. [ABSTRACT FROM AUTHOR]