Deciphering the Role of Waxy Gene Mutations in Enhancing Rice Grain Quality.

Amylose content (AC) stands as a pivotal determinant of rice grain quality, primarily governed by the Waxy gene (Wx). The allelic variation within this gene, particularly the presence of the Wxmp allele derived from the ancestral Wxmq allele, significantly influences AC and is prevalent among soft japonica rice varieties in southern China. Although both alleles are associated with lower AC, there remains a paucity of detailed understanding regarding the interplay between specific functional single nucleotide polymorphisms (SNPs) within these alleles and the overarching rice grain quality. To investigate this, we engineered three distinct transgenic rice lines, each harboring the Wxmp, Wxmq, or Wxb-5c alleles in the background of the glutinous rice cultivar Nip(wx). This suite of transgenic rice lines showcased varying degrees of grain transparency inversely correlated to AC, which in turn influenced other physicochemical properties of the rice grains, such as taste value of cooked rice, gel consistency, and starch pasting properties. Additionally, analyses of gene expression and enzyme activity revealed that the functional SNPs, Ex4-53G to A and Ex5-53T to C, lead to a decline in the activity of granule-bound starch synthase I (GBSSI) without altering expression levels.

ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH144 Module.

Abscisic acid (ABA) plays a crucial role in promoting plant stress resistance and seed dormancy. However, how ABA regulates rice quality remains unclear. This study identifies a key transcription factor SLR1-like2 (SLRL2), which mediates the ABA-regulated amylose content (AC) of rice. Mechanistically, SLRL2 interacts with NF-YB1 to co-regulate Wx, a determinant of AC and rice quality. In contrast to SLR1, SLRL2 is ABA inducible but insensitive to GA. In addition, SLRL2 exhibits DNA-binding activity and directly regulates the expression of Wx, bHLH144 and MFT2. SLRL2 competes with NF-YC12 for interaction with NF-YB1. NF-YB1 also directly represses SLRL2 transcription. Genetic validation supports that SLRL2 functions downstream of NF-YB1 and bHLH144 in regulating rice AC. Thus, an NF-YB1-SLRL2-bHLH144 regulatory module is successfully revealed. Furthermore, SLRL2 regulates rice dormancy by modulating the expression of MFT2. In conclusion, this study revealed an ABA-responsive regulatory cascade that functions in both rice quality and seed dormancy.

RGA1 regulates grain size, rice quality and seed germination in the small and round grain mutant srg5.

BACKGROUND: Generating elite rice varieties with high yield and superior quality is the main goal of rice breeding programs. Key agronomic traits, including grain size and seed germination characteristics, affect the final yield and quality of rice. The RGA1 gene, which encodes the α-subunit of rice G-protein, plays an important role in regulating rice architecture, seed size and abiotic stress responses. However, whether RGA1 is involved in the regulation of rice quality and seed germination traits is still unclear. RESULTS: In this study, a rice mutant small and round grain 5 (srg5), was identified in an EMS-induced rice mutant library. Systematic analysis of its major agronomic traits revealed that the srg5 mutant exhibited a semi-dwarf plant height with small and round grain and reduced panicle length. Analysis of the physicochemical properties of rice showed that the difference in rice eating and cooking quality (ECQ) between the srg5 mutant and its wild-type control was small, but the appearance quality was significantly improved. Interestingly, a significant suppression of rice seed germination and shoot growth was observed in the srg5 mutant, which was mainly related to the regulation of ABA metabolism. RGA1 was identified as the candidate gene for the srg5 mutant by BSA analysis. A SNP at the splice site of the first intron disrupted the normal splicing of the RGA1 transcript precursor, resulting in a premature stop codon. Additional linkage analysis confirmed that the target gene causing the srg5 mutant phenotype was RGA1. Finally, the introduction of the RGA1 mutant allele into two indica rice varieties also resulted in small and round rice grains with less chalkiness. CONCLUSIONS: These results indicate that RGA1 is not only involved in the control of rice architecture and grain size, but also in the regulation of rice quality and seed germination. This study sheds new light on the biological functions of RGA1, thereby providing valuable information for future systematic analysis of the G-protein pathway and its potential application in rice breeding programs.

Food and Nutrient Intake in Children and Adolescents with or without Overweight/Obesity.

OBJECTIVE: To explore the food and nutrient characteristics of children and adolescents with or without overweight/obesity and to provide scientific basis for the development of prevention strategies on overweight/obesity. METHODS: This study included children and adolescents aged 6-17 years who participated in provincial nutrition surveillance which included 90 counties (cities and districts) in Zhejiang Province with a provincial representative. Food consumption was assessed using three consecutive days of 24 h dietary recall, and nutrient intake was calculated using dietary recall in conjunction with the China Food Composition Table. Overweight/obesity was also investigated. Associations were evaluated using ordinal regression models. RESULTS: The analysis included a total of 1827 children and adolescents. The overweight prevalence was 14.0% and the obesity prevalence was 10.1%. Children and adolescents with overweight/obesity were observed to have a higher intake of carbohydrates, iron, sodium, potassium, and magnesium (F = 3.464, 5.232, 5.619, 3.469, 3.934, p < 0.05), as well as having a higher intake of the food group of cereals, tubers and beans, snacks, and salt (F = 7.348, 6.797, 3.413, p < 0.05) compared to children and adolescents without overweight/obesity. After adjusting for potential confounders via ordinal regression models, children and adolescents with overweight/obesity were observed to have a higher intake of carbohydrates (Wald χ2 = 4.325, p < 0.05). There were significant differences concerning the daily energy provided by snacks, the daily carbohydrate intake provided by snacks, the daily sodium intake provided by snacks, and the proportion of snacks to the food group of cereals, tubers, and beans (F = 8.305 6.316, 13.955, 3.692, p < 0.05). CONCLUSION: Children and adolescents with overweight/obesity have presented a high consumption of carbohydrates, which is associated with the food group of cereals, tubers, and beans. Snacks are the main factor leading to the high intake of the food group of cereals, tubers, and beans among children and adolescents with overweight/obesity.

Sedentary Activities and Food Intake among Children and Adolescents in the Zhejiang Province of China: A Cross-Sectional Study.

BACKGROUND: Sedentary behavior may affect the types of food consumed in children and adolescents' daily diets. Previous published studies are limited to local surveys. This study aimed to explore the relationship between sedentary behavior and food intake among children and adolescents. METHODS: A stratified sampling technique was employed in the present cross-sectional study. Demographic characteristics, sedentary behavior, transportation modes, and food intake were investigated. RESULTS: We found that children and adolescents who watched movies or TV programs online or on their smartphones on weekends and who chatted online on weekends, including on QQ (an instant messaging software service) and WeChat (an instant messaging software service), increased their intake of instant noodles and fried pasta (Spearman's rho = 0.468, 0.575, 0.465, and 0.323; p < 0.05). Children and adolescents who chatted online on weekends, including on QQ and WeChat, increased their intake of tofu skin (Spearman's rho = 0.461; p < 0.05), and those who browsed online on weekdays increased their intake of whole-fat liquid milk (Spearman's rho = 0.455; p < 0.05). Children and adolescents who browsed and chatted online on weekends, including on QQ and WeChat, and who played computer or smartphone games, increased their intake of fried potato chips (French fries or other fried snacks) (Spearman's rho = 0.568, 0.270, and 0.412; p < 0.05). With respect to modes of transportation used to travel to and from school, children and adolescents who took buses and subways increased their intake of rice, instant noodles, sweet potatoes, soybean milk, tofu skin, processed meat products (sausage, ham sausage, or lunch meat), fish, shrimp, vegetables, nuts, and sweet cookies (buns, cakes, Dim sum, and moon cakes) (Spearman's rho = 0.394, 0.536, 0.630, 0.408, 0.485, 0.441,0.410, 0.424, 0.444, 0.541, and 0.366; p < 0.05). CONCLUSIONS: Sedentary behavior affects the types of food consumed in children and adolescents' daily diets. Children and adolescents who browsed online on weekdays increased their intake of whole-fat liquid milk, but also increased their intake of foods with high fat, high salt, and low nutrient density. Children and adolescents taking buses and subways increased their intake of low-nutrition quality products. Public awareness efforts should focus on reducing the consumption of low-nutrition quality products and nutritional education.

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

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

Momordicine I suppresses glioma growth by promoting apoptosis and impairing mitochondrial oxidative phosphorylation.

Glioblastoma (GBM) is the most common type of primary brain tumor. Patients with GBM have poor survival outcomes. Isolated components of Momordica charantia have anticancer effects. However, the bioactivity of M. charantia extracts against GBM remains unknown. We tested four major extracts of M. charantia and found that momordicine I reduced glioma cell viability without serious cytotoxic effects on astrocytes. Momordicine I suppressed glioma cell colony formation, proliferation, migration, and invasion. Momordicine I also induced apoptosis, intracellular reactive oxygen species (ROS) production, and senescence in glioma cells. Moreover, momordicine I decreased the oxidative phosphorylation capacity of glioma cells and inhibited tumor sphere formation in temozolomide (TMZ)-resistant GBM cells. We further explored whether the antiglioma effect of momordicine I may be related to cell cycle modulation and DLGPA5 expression. Our results indicate that the cytotoxic effect of momordicine I on glioma cells suggests its potential therapeutic application to GBM treatment. See also Figure 1(Fig. 1).

Antiproliferative and apoptotic effects of telmisartan in human glioma cells.

Glioblastoma is the most common primary central nervous system tumor in adults. Angiotensin II receptor blockers (ARBs) are broadly applied to treat hypertension. Moreover, research has revealed that ARBs have the capacity to suppress the growth of several cancer types. In this study, we assessed the effects of three ARBs with the ability to cross the blood brain barrier (telmisartan, valsartan and fimasartan) on cell proliferation in three glioblastoma multiforme (GBM) cell lines. Telmisartan markedly suppressed the proliferation, migration, and invasion of these three GBM cell lines. Microarray data analysis revealed that telmisartan regulates DNA replication, mismatch repair, and the cell cycle pathway in GBM cells. Furthermore, telmisartan induced G0/G1 phase arrest and apoptosis. The bioinformatic analysis and western blotting results provide evidence that SOX9 is a downstream target of telmisartan. Telmisartan also suppressed tumor growth in vivo in an orthotopic transplant mouse model. Therefore, telmisartan is a potential treatment for human GBM.

Combined effects of SSII-2RNAi and different Wx alleles on rice grain transparency and physicochemical properties.

Near-isogenic lines Nip(Wxb/SSII-2), Nip(Wxb/ss2-2), Nip(Wxmw/SSII-2), Nip(Wxmw/ss2-2), Nip(Wxmp/SSII-2) and Nip(Wxmp/ss2-2) in the Nipponbare (Nip) background containing the SSII-2RNAi cassette combined with different Waxy (Wx) alleles were investigated in terms of rice grain transparency and quality profiles. Rice lines carrying the SSII-2RNAi cassette displayed downregulation of SSII-2, SSII-3 and Wx genes. Introduction of the SSII-2RNAi cassette decreased apparent amylose content (AAC) in all transgenic lines, but grain transparency differed between low AAC rice lines. Grains from Nip(Wxb/SSII-2) and Nip(Wxb/ss2-2) were transparent, while those of rice were increasingly translucent with decreasing moisture due to cavities within starch granules. Rice grain transparency was positively correlated with grain moisture and AAC, but negatively correlated with cavity area within starch granules. Starch fine structure analysis revealed a marked increase in short amylopectin chains with DP 6-12, but a decrease in intermediate chains with DP 13-24, resulting in decreased gelatinisation temperature. Starch crystalline structure analysis showed that the transgenic rice starches have lower crystallinity and lamellar repeat distance than controls due to differences in starch fine structure. The results highlight the molecular basis underpinning rice grain transparency, and provide strategies for improving rice grain transparency.

Research progress on the role and mechanism of action of exosomes in autoimmune thyroid disease.

Exosomes are widely distributed extracellular vesicles (EVs), which are currently a major research hotspot for researchers based on their wide range of sources, stable membrane structure, low immunogenicity, and containing a variety of biomolecules. A large number of literatures have shown that exosomes and exosome cargoes (especially microRNAs) play an important role in the activation of inflammation, development of tumor, differentiation of cells, regulation of immunity and so on. Studies have found that exosomes can stimulate the immune response of the body and participate in the occurrence and development of various diseases, including autoimmune diseases. Furthermore, the potential of exosomes as therapeutic tools in various diseases has also attracted much attention. Autoimmune thyroid disease (AITD) is one of the most common autoimmune diseases, mainly composed of Graves' disease (GD) and Hashimoto's thyroiditis (HT), which affects the health of many people and has a genetic predisposition, but its pathogenesis is still being explored. Starting from the relevant biological characteristics of exosomes, this review summarizes the current research status of exosomes and the association between exosomes and some diseases, with a focus on the situation of AITD and the potential role of exosomes (including substances in their vesicles) in AITD in combination with the current published literature, aiming to provide new directions for the pathogenesis, diagnosis or therapy of AITD.Supplemental data for this article is available online at.

Co-Overexpression of Two Key Source Genes, OsBMY4 and OsISA3, Improves Multiple Key Traits of Rice Seeds.

Optimized source-sink interactions are determinants of both rice yield and quality. However, most source genes have not been well studied in rice, a major grain crop. In this study, OsBMY4 and OsISA3, the key ß-amylase and debranching enzymes that control transient starch degradation in rice leaves, were co-overexpressed in rice in order to accelerate starch degradation efficiency and increase the sugar supply for sink organs. Systematic analyses of the transgenic rice indicated that co-overexpression of OsBMY4 and OsISA3 not only promoted rice yield and quality, but also improved seed germination and stress tolerance. Moreover, since the OsBMY4 gene has not been characterized, we generated osbmy4 mutants using CRIPSR/Cas9 gene editing, which helped to reveal the roles of ß-amylase in rice yield and quality. This study demonstrated that specific modulation of the expression of some key source genes improves the source-sink balance and leads to improvements in multiple key traits of rice seeds.

[Association between dietary patterns and abdominal obesity among the adult women in Zhejiang Province].

OBJECTIVE: To explore the dietary patterns and its relationship with abdominal obesity among the adult women in Zhejiang Province. METHODS: We recruited 2915 female residents aged 18 and older by using multi-stage stratified cluster sampling method; We conducted questionnaires survey and physical examinations to understand the basic information and nutritional status of the residents. Dietary patterns were extracted with factor analysis, and the multivariate Logistic regression model was used to analyze the association between dietary patterns and abdominal obesity among the participants. RESULTS: The prevalence rate of abdominal obesity and general obesity among the subjects were 33.07% and 9.23%, respectively. The highest rate of abdominal obesity was among the female who were above 65 years old, living in rural areas with low education. On the other hand, the lowest rate of abdominal obesity was among females with higher education(P<0.0001). Four dietary patterns identified with factor analysis were grain pattern, nut-legume pattern, milk-eggs pattern and modern pattern, accounting for 38.5% of total variance. After adjusting confounding factors as age, education level, occupation, marital status, urban/rural and exercise status, the participants with the fourth quartile(Q4) score of nut-legume dietary pattern had a low risk of abdominal obesity(OR=0.720, 95% CI 0.571-0.908, P=0.0012) compared to those with the quartile(Q1) first score. CONCLUSION: The nut-legume dietary pattern is negatively associated with abdominal obesity in female adults.

Supersonic shear wave imaging of the tibial nerve for diagnosis of diabetic peripheral neuropathy: A meta-analysis.

Background: Diabetic peripheral neuropathy (DPN) is the most common diabetes-associated complication and imposes a significant burden to healthcare systems. Thus, early diagnosis of DPN is extremely critical for management and outcome of diabetic patients. Supersonic Shear Wave Imaging (SSI) enables the noninvasive measurement of nerve stiffness. However, previous studies on SSI in the diagnosis of DPN were limited in sample sizes and reported various results. In this meta-analysis, we aimed to obtain comprehensive evidence on the value of tibial nerve stiffness measurement by SSI in the diagnosis of DPN. Methods: A comprehensive literature search in English and Chinese electronic database was conducted for studies (published until January 25, 2022) that investigated the diagnostic performance of tibial nerve stiffness measurement by SSI for detecting DPN. Summary receiver operating characteristics (SROC) modelling was constructed to conduct the meta-analysis of diagnostic accuracy of SSI for detecting DPN. Results: Finally, a total of 12 eligible studies with 1325 subjects were included for evaluation, and a meta-analysis was conducted to evaluate the diagnostic performance of tibial nerve stiffness measurement by SSI for detecting DPN. For tibial nerve stiffness measurement by SSI, the summary sensitivity and specificity for the diagnosis of DPN were 80% (95% confidence interval [CI]: 73%-86%) and 86% (95% CI: 82%-89%), respectively. The summary area under the ROC curve (AUROC) value of the SROC was 0.90 (95% CI: 0.87-0.92), for diagnosing DPN. A subgroup analysis of 11 SSI studies from China revealed similar diagnostic performance, with a summary sensitivity of 79% (95% CI: 72%-85%), specificity of 86% (95% CI: 82%-89%) and summary AUROC value of the SROC of 0.90 (95% CI: 0.87-0.92) for diagnosing DPN. Conclusions: Our meta-analysis suggests that a tibial nerve stiffness measurement by SSI shows good performance in diagnosing DPN and has considerable potential as a noninvasive tool for detecting DPN.

Intake of Vitamin B12 and Folate and Biomarkers of Nutrient Status of Women within Two Years Postpartum.

Background: Little is known about variation in vitamin B12 and folate status among Chinese women 2 years postpartum. This study assessed intake of vitamin B12 and folate and biomarkers of nutrient status among Chinese women postpartum. Methods: Demographic information, multi-/single-nutrient supplementation, dietary data, serum vitamin B12 and serum folate were assessed in 982 women within 2 years postpartum, using ten investigation sites in Zhejiang Province from the National Nutritional Study 2016−2017, which is a nationally representative cross-sectional study, to form a representative provincial sample of Zhejiang Province. The dietary diversity score (DDS) was used for assessing the dietary pattern. Results: Vitamin B12 increased slightly at the early stage of postpartum and then dropped over time. Serum folate level elevated with postpartum time. The median serum vitamin B12 concentration was 494.59 (373.21−650.20) pg/mL, and folate was 7.58 (5.02−10.34) ng/mL. Correspondingly, vitamin B12 levels suggesting marginal deficiency (200−300 pg/mL) and deficiency (<200 pg/mL) resulted as 9.27% and 3.26%, respectively, and folate level suggesting deficiency (<3 ng/mL) was 9.16%. Multi-/single-nutrient supplementation during pregnancy was associated with log-transformed serum vitamin B12 and folate level after adjusting for potential confounders (vitamin B12: ß (SE) = 0.124 (0.028), p < 0.001; folate: 0.128 (0.035), <0.001). Additionally, postpartum nutrient supplementation was associated with log-transformed serum folate level, especially for lactating women (ß (SE) = 0.204 (0.062), p = 0.001). Increased DDS was significantly associated with elevated serum vitamin B12 and folate levels (vitamin B12: ß (SE) = 0.028 (0.011), p = 0.011; folate: 0.030 (0.014), 0.031). In addition, age and educational level were influencing factors for serum vitamin B12 and folate concentrations among postpartum women. Conclusion: Serum vitamin B12 level decreased and folate level increased with postpartum age among Chinese women. Nutrient supplementation during pregnancy was related to elevated serum vitamin B12 and folate concentrations. Postpartum nutrient supplementation was associated with the increased serum folate level of lactating women. Dietary diversity was related to increased serum vitamin B12 and folate levels, especially among postpartum women with younger age and lower educational level.

YAP1 acts as a negative regulator of pro-tumor TAZ expression in esophageal squamous cell carcinoma.

PURPOSE: Although YAP1 and TAZ are believed to be equivalent downstream effectors of the Hippo pathway, differential expression of YAP1 or TAZ suggests distinct functions during cancer progression. The exact role of YAP1 and TAZ in esophageal cancer, the 6th leading cancer-related mortality in the world, remains elusive. METHODS: Following single or double manipulation of YAP1 or TAZ expression, we subjected these manipulated cells to proliferation, migration, invasion, and xenograft tumorigenesis assays. We used RT-qPCR and Western blotting to examine their expression in the manipulated cells with or without inhibition of transcription or translation. We also examined the impact of YAP1 or TAZ deregulation on clinical outcome of esophageal cancer patients from the TCGA database. RESULTS: We found that YAP1 functions as a tumor suppressor whereas TAZ exerts pro-tumor functions in esophageal cancer cells. We also found a significant increase in TAZ mRNA expression upon YAP1 depletion, but not vice versa, despite the downregulation of CTGF and CYR61, shared targets of YAP1 and TAZ, in xenografted tissue cells. In addition to transcriptional regulation, YAP1-mediated TAZ expression was found to occur via protein synthesis. Restored TAZ expression mitigated YAP1-mediated suppression of cellular behavior. By contrast, TAZ silencing reduced the promoting effect exerted by YAP1 depletion on cellular behaviors. The observed anti-tumor function of YAP1 was further supported by a better overall survival among esophageal cancer patients with a high YAP1 expression. CONCLUSION: From our data we conclude that YAP1 functions as a suppressor and negatively regulates pro-tumor TAZ expression via transcriptional and translational control in esophageal cancer.

Serum microRNAs as biomarkers for the diagnosis of papillary thyroid carcinoma: a meta-analysis.

Papillary thyroid carcinoma (PTC) is the most common form of thyroid cancer. Several studies have proposed serum microRNAs (miRNAs) as novel biomarkers for diagnosing PTC. In this study, we conducted a meta-analysis aiming to investigate the overall diagnostic accuracy of serum miRNAs in PTC detection. Three online databases including PubMed, EMBASE and Cochrane Library were searched up to 1 May 2021. We systematically reviewed studies evaluating the value of serum miRNAs in diagnosing PTC, and then summarized the area under receiver operating characteristics curve (AUROC), sensitivity, specificity, and diagnostic odds ratio to assess the accuracy of serum miRNAs for the discrimination between patients with PTC and patients with benign thyroid nodules and healthy controls. We included 32 studies from 6 articles. Overall, there were 463 PTC patients, 334 patients with benign thyroid nodules, and 104 healthy controls. The results showed that the summary sensitivity and specificity were 76% (95% confidence interval [CI]: 68%‒83%) and 86% (95% CI: 80%‒91%), respectively, and that the summary AUROC was 0.89 (95% CI: 0.86‒0.91), when serum miRNAs were used for discriminating between PTC patients and those with benign nodules. On the other hand, the summary sensitivity and specificity of serum miRNAs for discriminating between PTC patients and healthy controls were 82% (95% CI: 77%‒86%) and 84% (95% CI: 76%‒90%), respectively, and the summary AUROC was 0.89 (95% CI: 0.86‒0.92). We found that serum miRNAs have good diagnostic performance for the discrimination between patients with PTC and patients with benign nodules and healthy controls, and thus have considerable potential as novel minimally invasive tools for detecting PTC.

The Long Read Transcriptome of Rice (Oryza sativa ssp. japonica var. Nipponbare) Reveals Novel Transcripts.

BACKGROUND: High-throughput next-generation sequencing technologies offer a powerful approach to characterizing the transcriptomes of plants. Long read sequencing has been shown to support the discovery of novel isoforms of transcripts. This approach enables the generation of full-length sequences revealing splice variants that may be important in regulating gene action. Investigation of the diversity of transcripts in the rice transcriptome including splice variants was conducted using PacBio long-read sequence data to improve the annotation of the rice genome. RESULTS: A cDNA library was prepared from RNA extracted from leaves, roots, seeds, inflorescences, and panicles of O. sativa ssp. japonica var Nipponbare and sequenced on a PacBio Sequel platform. This produced 346,190 non-redundant full-length non-chimeric reads (FLNC) resulting in 33,504 high-quality transcripts. Half of the transcripts were multi-exonic and entirely matched with the reference transcripts. However, 14,874 novel isoforms were also identified resulting predominantly from intron retention and at least one novel splice site. Intron retention was the prevalent alternative splicing event and exon skipping was the least observed. Of 73,659 splice junctions, 12,755 (17%) represented novel splice junctions with canonical and non-canonical intron boundaries. The complexity of the transcriptome was examined in detail for 19 starch synthesis-related genes, defining 276 spliced isoforms of which 94 splice variants were novel. CONCLUSION: The data reveal the great complexity of the rice transcriptome. The novel transcripts provide new insights that may be a key input in future research to improve the annotation of the rice genome.