Rice最新文献

The Rice Online expression profiles Array Database version 2 (ROADv2; https://roadv2.khu.ac.kr ), an enhanced database for rice gene expression analysis, transitions from the previous microarray platforms to RNA-Seq data for improved accuracy. It encompasses 328 datasets from diverse experimental series, including anatomy, abiotic and biotic stress, hormone response, and nutrient starvation. Key updates include gene annotation (upgraded to RGAP version 7) and functional enrichment data (utilizing recent Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) versions). ROADv2 debuts protein-protein interaction (PPI) network analysis and broadens interactive visualization across all features. Gene expression data are segmented into anatomy, biotic, abiotic, nutrient, and hormone categories, with user-interactive heatmaps displaying normalized log2 expression and log2 fold change data. Coexpression correlation analysis identifies genes with similar patterns, visualized through interactive network graphs. Functional enrichment tools display GO and KEGG analyses with significant terms emphasized in various formats. PPI network analysis integrates coexpression data to enhance prediction accuracy. Validation studies affirm the database's reliability, demonstrating reproducible tissue/organ-specific expression patterns. ROADv2 provides a comprehensive resource for rice functional genomics studies.

Stigma exsertion rate (SER) is a crucial trait that influences the seed production of hybrid rice by determining the outcrossing ability of male sterile lines (MSLs). However, the molecular genetic mechanisms underlying SER are still poorly understood. In this study, we identified 14 quantitative trait loci (QTLs) using a recombinant inbred line (RIL) population derived from B805D-MR-16-8-3 (B805D) and Hua6S. Two major QTLs, qSE1 and qSE9, were validated for their effects in the residual heterozygous line (RHL) background. The RHL carrying homozygous qSE1 region from Hua6S increased dual stigma exsertion rate (DSE) by 14.67% and 15.04%, and increased total stigma exsertion rate (TSE) by 11.73% and 13.04%, in F₁₀ and F₁₁ progeny, respectively. Conversely, the RHL carrying homozygous qSE9 region from B805D showed a substantial increase of 22.72% and 14.45% in single stigma exsertion rate (SSE), an increase of 13.46% and 8.30% in TSE, and an increase in percentage of spikelets with exserted stigma (PSE) by 24.82% and 15.57%, respectively, in F₁₀ and F₁₁ progeny. Furthermore, examination of floral organ traits revealed that both the Hua6S allele of qSE1 and the B805D allele of qSE9 increased pistil size to improve SER, but they had contrasting effects on spikelet shape. Subsequently, qSE1 and qSE9 were fine-mapped to intervals of 246.5 kb and 341.4 kb, respectively. A combination of sequencing, expression and haplotype analysis revealed that a single nucleotide variation (T to C) in the 5'UTR region of LOC_Os01g72020 (OsBOP1) was likely to be the functional variation for qSE1. Collectively, our work has laid a foundation for cloning the genes responsible for SER, and demonstrated that the Hua6S allele of qSE1 and the B805D allele of qSE9 can effectively increase SER, which could make important contributions to the genetic improvement of MSLs aimed at improving hybrid seed production.

With the intensification of the greenhouse effect, a series of natural phenomena, such as global warming, are gradually recognized; when the ambient temperature increases to the extent that it causes heat stress in plants, agricultural production will inevitably be affected. Therefore, several issues associated with heat stress in crops urgently need to be solved. Rice is one of the momentous food crops for humans, widely planted in tropical and subtropical monsoon regions. It is prone to high temperature stress in summer, leading to a decrease in yield and quality. Understanding how rice can tolerate heat stress through genetic effects is particularly vital. This article reviews how rice respond to rising temperature by integrating the molecular regulatory pathways and introduce its physiological mechanisms of tolerance to heat stress from the perspective of molecular biology. In addition, genome selection and genetic engineering for rice heat tolerance were emphasized to provide a theoretical basis for the sustainability and stability of crop yield-quality structures under high temperatures from the point of view of molecular breeding.

Carbohydrate stress reduces grain size and head rice percentage and increases the chalkiness in rice. This study aims to compare low and high-quality cultivars for their milled rice and chalky grain percentages, as well as grain size, in the top, middle, and bottom panicle portions. Low-chalky and chalky long-grain rice cultivars were grown at Beaumont in 2019 and 2022. Panicles were harvested, partitioned into top, middle, and bottom portions, and phenotyped for grain size, head rice percentage, and chalkiness. Grain area reduction percentage from top to middle panicle portions is higher in the low-chalky cultivars, Presidio and Kaybonnet. This could relieve the carbohydrate stress that leads to chalkiness. The rice cultivars were also genotyped for Chalk5 and OsPPDK. The low-chalky cultivars had the same allele as the low-chalk Lemont for Chalk5. Presidio had a different allele for OsPPDK compared with the cultivars tested. Consistent with the genotyping result for Chalk5, Presidio and Kaybonnet had lower chalkiness than LaGrue and Leah. There was a positive correlation between the number of primary panicle branches and head rice percentage. The improvement in breeding efficiency for high grain quality requires phenotypic screening for a high number of primary panicle branches and for low chalky and partially chalky grain percentages.

Cold stress has a significantly negative effect on the growth, development, and yield of rice. However, the genetic basis for the differences in the cold tolerance of Xian/indica and Geng/japonica rice seedlings is still largely unknown. In this study, an RIL population was generated by crossing of the cold-tolerant japonica variety Nipponbare and the cold-sensitive indica variety WD16343 for BSA-seq analysis, and a major cold tolerance QTL qCTS11 was identified on chromosome 11. This locus was narrowed to the 584 kb region through fine mapping. Sequence alignment and expression analysis identified the cloned gene COLD11 and a novel cold-related gene OsCTS11. According to the reported functional variation of COLD11, Nipponbare (TCG + 3GCG)×2 presented more GCG repeats in the 1st exon than WD16343 (TCG + 3GCG), partially explaining the difference in cold tolerance between the parents. OsCTS11, encoding a stress enhanced protein based on phylogenetic analysis, was strongly induced by cold stress and located in the chloroplast and the nucleus. oscts11-mutant lines generated via CRISPR/Cas9 system improved the cold tolerance of rice seedlings. Our study not only reveals novel genetic loci associated with cold tolerance, but also provides potentially valuable gene resources for the cultivation of cold-tolerant rice.

Ghd7 is a central regulator to multiple growth and development processes in rice. While it is not clear how Ghd7 is regulated by upstream factors. To identify its upstream regulator, the truncated Ghd7 promoter fragments were used to screen cis elements binding to rice total nuclear proteins. Electrophoretic mobility shift assays screened one truncated fragment f3 binding to the proteins. Subsequently, the fragment f3 was employed to screen a yeast one-hybrid library, and a transcription factor OsIAA23 was screened as a direct upstream regulator of Ghd7. Dual-luciferase transient assay demonstrated the transcriptional repression effect of OsIAA23 on the activity of Ghd7, and the location of the cis elements binding to OsIAA23 in the region 1264 to 1255 bp upstream of ATG. Genetic analysis between the wild type Ghd7-OsIAA23 and single/double mutants further verified that OsIAA23 downregulated Ghd7 expression and led to a delayed heading under long day conditions. Moreover, natural variations in fragment f3 were associated with heading and geographic distribution in rice. This study sheds light on the direct regulatory mechanism of OsIAA23 on Ghd7, which enriches the understanding of the Ghd7 involved flowering regulatory network in rice.

The roles of plant-specific transcription factor family YABBY may vary among different members. OsYABBY6 is a rice YABBY gene, whose function is not well elucidated so far. In this paper, we show that OsYABBY6 is a nucleus-localized protein with transcriptional activation activity. OsYABBY6 is predominantly expressed in the palea and lemma, as well as in the sheath, culm and node. OsYABBY6 RNA interference (RNAi) plants exhibited altered plant height and larger grain size. Under cold treatment, OsYABBY6 overexpression (OE) plants had up-regulated expression of cold responsive genes, and accumulated less reactive oxygen species but more proline compared to wild type, resulting in improved cold tolerance. On the other hand, RNAi plants showed enhanced drought tolerance compared to the wild type by slower water loss, less reactive oxygen species but more proline and soluble sugar accumulation. In addition, endogenous abscisic acid (ABA) level was reduced in OsYABBY6 RNAi plants, and RNAi and OE plants were more and less sensitive to ABA treatment, respectively. Accordingly, we deduce that OsYABBY6 positively regulates cold response but negatively regulates drought response through different pathways. Our study reveals the crucial roles of OsYABBY6 in plant architecture and grain development, as well as in abiotic stress response, providing new insights into the functions of YABBYs in rice.

Phosphatidylinositol signaling system plays a crucial role in plant physiology and development, phosphatidylinositol phosphate kinases (PIPKs) are one of the essential enzymes responsible for catalyzing the synthesis of phosphatidylinositol bisphosphate (PIP2) within this signaling pathway. However, its mechanism of signal transduction remains poorly exploited in plants. OsMBL1, a jacalin-related mannose-binding lectin in rice, plays a crucial role in plant defense mechanisms, acting as a key component of the pattern-triggered immunity (PTI) pathway. Here, a rice phosphatidylinositol-phosphate kinase FAB (OsPIPK-FAB), a member of the rice PIPKs family, as an interacting protein of OsMBL1 through yeast-two-hybrid (Y2H) screening assay. And this interaction was confirmed by using co-immunoprecipitation (Co-IP) and pull-down assay techniques. Furthermore, we demonstrated that the deletion of OsPIPK-FAB gene in plant enhanced resistance against rice blast while overexpression of OsPIPK-FAB increases sensitivity to the fungal infection. Additionally, through determination and measurement of the plant inositol 1,4,5-trisphosphate (IP3) contents and the plant phosphatidylinositol 4-phosphate 5-kinase (PIP5K) activity, we revealed that OsMBL1 inhibits the PIP5K kinase activity of OsPIPK-FAB as well as the plant IP3 contents in rice. Conclusively, these findings indicated that OsPIPK-FAB serves as a novel and critical component that is negatively involved in PTI activation and was inhibited by OsMBL1.

The yield potential of large-panicle rice is often limited by grain-filling barriers caused by the development of inferior spikelets (IS). Photoassimilates, which are the main source of rice grain filling, mainly enter the caryopsis through the dorsal vascular bundle. The distribution of assimilates between superior spikelets (SS) and IS is influenced by auxin-mediated apical dominance; however, the mechanism involved is still unclear. In this study, the effect of auxin signaling on the grain filling of SS and IS was investigated in two large-panicle japonica rice varieties, W1844 and CJ03. Compared to SS, IS displayed delayed initiation of filling and a significantly lower grain weight. Furthermore, the endosperm development in IS remained stagnant at the coenocytic stage. The development of the dorsal vascular bundle in the IS was also slow, and poor sucrose-unloading was observed during the initial grain filling stage. However, the endosperm development in IS immediately started after the improvement of dorsal vascular bundle development. GUS activity staining further revealed that indole-3-acetic (IAA) was localized in the dorsal vascular bundle and surrounding areas, suggesting that the low IAA content observed in the IS during the initial grain filling stage may have delayed the development of the dorsal vascular bundle. Therefore, these results demonstrate that IAA may control sugar transport and unloading by regulating dorsal vascular bundle development, consequently affecting endosperm development in IS.