Rice最新文献

{"title":"Comprehensive GWAS and Transcriptome Analysis Discovered Candidate Gene Associated with Starch Pasting Properties of Temperate japonica rice (Oryza sativa L.).","authors":"Yoon Kyung Lee, Su Jang, Jihwan Im, Hee-Jong Koh","doi":"10.1186/s12284-025-00782-8","DOIUrl":"10.1186/s12284-025-00782-8","url":null,"abstract":"<p><p>The growing market demand for high eating quality (EQ) rice, driven by improved living standards, highlights the need to better understand its complex genetic architecture. Starch pasting properties are critical determinants of rice EQ, yet their genetic basis remains incompletely understood. This study aimed to unravel the genetic factors underlying starch pasting properties in temperate japonica rice panel of 284 accessions comprising landraces and improved varieties. Genome-wide association studies conducted for two years identified 59 significant lead SNPs. Among them, consistent lead SNPs on chromosomes 2 and 8, in addition to the well-characterized Wx gene on chromosome 6 were detected from multiple traits and years. LD block analysis and transcriptome analysis of accessions with extreme phenotypes identified OsGLUTN (Os02g0224300/LOC_Os02g13130), a gene encoding a high molecular weight glutenin subunit-like protein, as a strong candidate. Clustering patterns of differential gene expressions showed higher expression of OsGLUTN in low-viscosity cultivars and lower expression in high-viscosity cultivars. Haplotype analysis revealed significant variations in viscosity traits associated to OsGLUTN alleles, and functional validation using enhancer active tagging line showed significantly reduced starch viscosity, confirming its role in EQ regulation. While the Wx accounted for most viscosity traits, the identification of novel loci on chromosomes 2 and 8 highlights additional genetic factors to EQ variation. These findings deepen our understanding of how storage protein metabolism impacts rice grain quality. The identification of OsGLUTN provides a foundation for breeding programs focused on developing rice varieties with improved cooking and eating qualities, addressing growing consumer demand for premium rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"23"},"PeriodicalIF":4.8,"publicationDate":"2025-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11961803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143764954","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Overexpression of lncRNA22524 from Dongxiang Wild Rice Reduces Drought and Salt Stress Tolerance in Cultivated Rice.","authors":"Yong Chen, Yingying Mao, Hong Xie, Xinjian Zou, Wanling Yang, Rifang Gao, Jiankun Xie, Fantao Zhang","doi":"10.1186/s12284-025-00777-5","DOIUrl":"10.1186/s12284-025-00777-5","url":null,"abstract":"<p><p>Drought and salt stresses are major challenges to rice production, and a deep understanding of the mechanisms for tolerance could help deal with the challenges. Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation. Previously, lncRNA22524 has been identified as a drought stress-responsive lncRNA from Dongxiang wild rice (DXWR). Nevertheless, its reactions to abiotic stresses in genetics and physiology remained unclear. In this study, we employed a rapid amplification of cDNA ends (RACE) to obtain the full-length cDNA of lncRNA22524 from DXWR, analyzed its cellular localization, built an overexpression vector to generate transgenic lines of cultivated rice and evaluated its impact in genetics and physiology. After treated with drought and salt stress, the overexpressed lines exhibited much more injuries and lower rates of survival, more reactive oxygen species (ROS) and malondialdehyde (MDA), lower antioxidant enzymes and lower proline (Pro) and soluble sugar (SS) than their wild-type (WT). Furthermore, transcriptome analysis of overexpressed lines with weaker tolerance than WT revealed 1,233 differentially expressed genes (DEGs), where most DEGs were involved in phenylpropanoid biosynthesis, photosynthesis and glutathione metabolism. These findings demonstrated that lncRNA22524 negatively regulated rice responses to drought and salt stress, which clear way of working from transcription to metabolic products should be worth of further study.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"22"},"PeriodicalIF":4.8,"publicationDate":"2025-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933495/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701079","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Allelic Variation of Hd17 for Rice Heading Date is Caused by Natural Selection.","authors":"Zifeng Yang, Yun Li, Jin Liu, Shuiqing Wu, Xuelin Wang, Min Guan, Yanyun Li, Haitao Zhu, Guifu Liu, Shaokui Wang, Guiquan Zhang","doi":"10.1186/s12284-025-00773-9","DOIUrl":"10.1186/s12284-025-00773-9","url":null,"abstract":"<p><p>Heading date is an important agronomic trait of rice, which directly determines adaptability and yield. Selection for natural variated alleles for heading date genes is an important manifestation of rice domestication that allows rice to spread to more broad geographic areas. In this study, three alleles of the Hd17 gene for heading date were identified by sequence analysis of 14 single-segment substitution lines, 6 wild rice species, and 2524 accessions of O. sativa. The Hd17-1 allele is an ancestral type with a middle heading date. The Hd17-2 allele was caused by the functional nucleotide polymorphism (FNP) of C to T at position 1016 of the gene and exhibits delay heading. The Hd17-3 allele was caused by the FNP of C to T in 1673 point of the gene and shows earlier heading. The Hd17-1 allele is mainly distributed in tropical regions, carrying by 5 wild rice species, O. glaberrima, and two O. sativa (Aus/Boro and tropical japonica types). The Hd17-2 allele is mainly distributed in subtropical regions, carrying by O. meridionalis, O. rufipogon, and two O. sativa (indica subspecies and Basmati/Sandri types). The Hd17-3 allele is mainly distributed in temperate regions, carrying only by temperate japonica of O. sativa. Hd17-2 and Hd17-3 had been evolved from Hd17-1, independently. Three different rice growing regions formed three alleles of Hd17, showing that the allelic variation of Hd17 is the result of natural selection. We also found that Hd17 controls heading date by up-regulating Ghd7 and down-regulating Ehd1 under long day conditions. Our findings will help to understand the evolution and the regulation of Hd17 in rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"21"},"PeriodicalIF":4.8,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933555/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143701039","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The OsZHD1 and OsZHD2, Two Zinc Finger Homeobox Transcription Factor, Redundantly Control Grain Size by Influencing Cell Proliferation in Rice.","authors":"Mingliang Guo, Chun Zheng, Chao Shi, Xiaozhuan Lu, Zeyuan She, Shuyu Jiang, Dagang Tian, Yuan Qin","doi":"10.1186/s12284-025-00774-8","DOIUrl":"10.1186/s12284-025-00774-8","url":null,"abstract":"<p><p>Grain size is vital determinant for grain yield and quality, which specified by its three-dimensional structure of seeds (length, width and thickness). The ZINC FINGER-HOMEODOMAIN (ZHD) proteins play critical roles in plant growth and development. However, the information regarding the function in reproductive development of ZHD proteins is scarce. Here, we deeply characterized the phenotype of oszhd1, oszhd2, and oszhd1oszhd2. The single mutants of OsZHD1/2 were similar with wild type. Nevertheless, the double mutant displayed dwarfism and smaller reproductive organs, and shorter, narrower, and thinner grain size. oszhd1oszhd2 revealed a significant decrease in total cell length and number, and single cell width in outer parenchyma; reducing the average width of longitudinal epidermal cells, but the length were increased in outer and inner glumes of oszhd1oszhd2 compared with wild-type, oszhd1-1, oszhd2-1, respectively. OsZHD1 and OsZHD2 encoded the nucleus protein and were distributed predominately in stem and the developing spikelets, asserting their roles in grain size. Meanwhile, yeast two-hybrid, bimolecular fluorescence complementation, and Co-immunoprecipitation assay clarified that OsZHD1 could directly interacted with OsZHD2. The differential expression analysis showed that 839 DEGs, which were down-regulated in oszhd1oszhd2 than wild type and single mutants, were mainly enriched in secondary metabolite biosynthetic, integral component of membrane, and transporter activity pathway. Moreover, it is reliable that the altered expression of cell cycle and expansion-related and grain size-related genes were observed in RNA-seq data, highly consistent with the qRT-PCR results. Altogether, our results suggest that OsZHD1/2 are functional redundancy and involved in regulating grain size by influencing cell proliferation in rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"20"},"PeriodicalIF":4.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928714/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677128","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Interspecific Hybridization Enhanced Tolerance to Salinity and Cadmium Stress Through Modifying Biochemical, Physiological, and Resistance Gene Levels, Especially in Polyploid Rice: A Sustainable Way for Stress-Resilient Rice.","authors":"Lixia Sun, Fozia Ghouri, Jiacheng Jin, Minghui Zhong, Weicong Huang, Zijun Lu, Jinwen Wu, Xiangdong Liu, Muhammad Qasim Shahid","doi":"10.1186/s12284-025-00776-6","DOIUrl":"10.1186/s12284-025-00776-6","url":null,"abstract":"<p><p>Polyploid plants exhibit strong resistance to salt and cadmium (Cd) stress, which can adversely affect their growth, reducing crop quality and yield. Transcriptome analysis, antioxidant enzymatic activities, physiological measurements of reactive oxygen species, and heterosis analysis were performed on hybrids with neo-tetraploid rice and its progenitors. The results showed that diploid hybrids had fluctuating yields in early and late seasons, while tetraploid hybrids had consistent grain yield throughout. Transcriptome analysis revealed that gene expression related to sugar metabolism processes increased in tetraploid hybrids. Transcriptome analysis revealed several genes associated with heterosis and stress, including OsEAF6, which is associated with heterosis, and OsCIPK14, which is involved in defense signalling pathways. Furthermore, compared to the parents, hybrids have a much higher number of genes associated with abiotic stress. Consequently, diploid and tetraploid hybrids were treated with Cd (0 and 100 µM) and NaCl (200 mM) in the present study. Under Cd toxicity, the levels of carotenoids were reduced by 33.31% and 45.59%, while the levels of chlorophyll a declined by 16.00% and 27.81% in tetraploid and diploid hybrids, respectively, compared to the control. Tetraploid hybrids had the highest germination rate under salt stress and the lowest Cd uptake compared to diploid hybrids and their parents. In general, the activities of antioxidant enzymes exhibited a considerable drop, whereas the levels of H₂O₂ and MDA showed a remarkable increase in parents compared to hybrids. Under cadmium toxicity, the expression of OsERF1 in tetraploid rice was increased, and OsABCC1 and OsHMA3 were highly expressed in neo-tetraploid rice. Interspecific hybrid (indica and japonica) displayed enhanced tolerance to cadmium and salinity stress, potentially serving as a natural resource to improve rice resilience. These findings provide a basis for understanding polyploid rice's gene expression pattern, environmental tolerance, and heterosis.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"19"},"PeriodicalIF":4.8,"publicationDate":"2025-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11928717/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143677124","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Developmental Dynamics of Intercalary Meristem and Pith Cavity in Rice Stems.","authors":"Keisuke Nagai, Yoko Niimi, Misaki Ohsato, Motoyuki Ashikari","doi":"10.1186/s12284-025-00772-w","DOIUrl":"10.1186/s12284-025-00772-w","url":null,"abstract":"<p><p>In rice, internode elongation is a critical aspect of plant development and agricultural productivity. Previous morphological and histochemical studies using [³H]thymidine have visualized the cell division zone (intercalary meristem) in internodes. However, it has remained unclear how the intercalary meristem forms during stem development. In addition, while a pith cavity forms in the central part of the rice stem, the spatiotemporal relationship between pith cavity formation and intercalary meristem development is not well understood. Therefore, we performed histological analysis of intercalary meristem and pith cavity development using C9285, a deepwater rice variety that shows internode elongation from the vegetative growth stage. We classified the developmental stages of the stem into four stages based on the analysis of pith cavity formation using Trypan blue, Calcein-AM, and MitoRed staining, and visualized dividing cells using the Click-iT EdU imaging assay. In Stage 1, no pith cavity was formed. Vertical cell rows were observed between above the axillary bud attachment and the upper node, suggesting anticlinal divisions that lead to internode formation in the early stage of stem development. In Stage 2, the first pith cavity formed in the pith of the foot, which is the region of axillary bud attachment. Compared to cell division in the internode, that in the foot was significantly activated resulting in slight elongation from Stage 1 to Stage 2. In Stage 3, cell division in the foot ceased, while active cell division at the base of the internode led to significant vertical elongation. The second pith cavity formed due to cell death in the pith of the internode. In Stage 4, the two pith cavities connected to form a single large pith cavity. Although the intercalary meristem maintained cell division activity, the number of cell divisions decreased. Based on these results, we propose a model for stem development that involves two phases of elongation regulation: primary elongation involving slight elongation in the foot, and secondary elongation involving significant internode elongation due to the activation of cell division and cell elongation in the intercalary meristem. This is the first study to anatomically elucidate the spatiotemporal relationship between intercalary meristem development and pith cavity formation in rice stem development. It provides new insights for future research on rice stem development and studies of other grass species.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"18"},"PeriodicalIF":4.8,"publicationDate":"2025-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11920487/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143658550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Functional Analysis of Mature Activin A Produced by Enterokinase in Plant Cells.","authors":"Ki-Beom Moon, Ji-Sun Park, Han-Gyeul Kim, Jae-Heung Jeon, Tae-Ho Kwon, Kyung-Sook Chung, Hyo-Jun Lee, Hyun-Soon Kim","doi":"10.1186/s12284-025-00775-7","DOIUrl":"10.1186/s12284-025-00775-7","url":null,"abstract":"<p><p>Molecular farming for producing biopharmaceuticals in plants is considered an excellent method to replace some of the production methods currently used, and a significant number of recombinant proteins have already shown the potential to facilitate this. In particular, production of activin A, which has a variety of important biological functions in humans, is limited. The purpose of this study was to develop a safe, stable, and efficient plant-based in vitro production system for activin A, assess its biological activity in cancer cells, and demonstrate its potential for use in cancer research. We evaluated the expression and production of activin A in plant cells through a mass culture and secretion system. The formation of mature activin A homodimers, produced by enterokinase, was also assessed. Southern blot and inverse PCR were performed to investigate the gene insertion sites in the plants, and the stability of activin A was evaluated over six months under various pH conditions. The activity of plant-derived activin A was analyzed in HEK293T, Huh7, MCF7, and MDA-MB-231 cancer cell lines using luciferase reporter, migration, phosphorylation, and gelatin zymography assays. We developed cell line #71, which showed the highest levels of mature activin A expression (8.44 μg/g calli fresh weight) and had multicopy gene insertions. Pro-activin A was converted to mature activin A using enterokinase. We demonstrated that the optimal stability of plant-derived activin A was maintained for six months at pH 7 below 4 °C. Plant-derived activin A significantly enhanced activin A signaling activity in HEK293T, Huh7, and MCF7 cancer cells. Additionally, we confirmed that plant-derived activin A inhibited the growth of Huh7 cancer cells by activating the Smad pathway without affecting the MAPK pathway. Contrastingly, in MDA-MB-231 breast cancer cells, plant-derived activin A promoted cell migration. Our results confirm that plant-derived activin A, produced using a mass production system, exhibits full biological activity and affects cancer cell behavior in a manner similar to activin A derived from traditional mammalian systems. Furthermore, this study highlights the importance of considering cellular context when determining the functional outcomes of activin A treatment.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"16"},"PeriodicalIF":4.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906942/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625827","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Variations in the N₂ Fixation and CH₄ Oxidation Activities of Type I Methanotrophs in the Rice Roots in Saline-Alkali Paddy Field Under Nitrogen Fertilization.","authors":"Jumei Liu, Jiahui Cao, Rina Su, Lei Yan, Kexin Wang, Haiyang Hu, Zhihua Bao","doi":"10.1186/s12284-025-00766-8","DOIUrl":"10.1186/s12284-025-00766-8","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The root-associated methanotrophs contribute to N&lt;sub&gt;2&lt;/sub&gt; fixation and CH&lt;sub&gt;4&lt;/sub&gt; oxidation in paddy fields under N-limited conditions. However, the impact of nitrogen inputs on N₂ fixation and CH₄ oxidation by methanotrophs is largely unknown, especially in saline-alkali paddy fields with higher nitrogen application. This study explored the impact of nitrogen fertilization on N₂ fixation and CH₄ oxidation by root-associated active diazotrophic and methanotrophic communities in a saline-alkali paddy field using &lt;sup&gt;15&lt;/sup&gt;N-N&lt;sub&gt;2&lt;/sub&gt; and &lt;sup&gt;13&lt;/sup&gt;C-CH&lt;sub&gt;4&lt;/sub&gt; isotope feeding experiments along with RNA-based sequencing. The &lt;sup&gt;15&lt;/sup&gt;N and &lt;sup&gt;13&lt;/sup&gt;C isotope feeding experiments showed that the CH₄ oxidation-dependent nitrogen fixation rate of methanotrophs (&lt;sup&gt;15&lt;/sup&gt;N and &lt;sup&gt;13&lt;/sup&gt;C) in the roots of two rice cultivars was significantly higher than the CH₄ oxidation-independent nitrogen fixation rate of heterotrophic diazotrophs (only &lt;sup&gt;15&lt;/sup&gt;N) under nitrogen fertilization (SN) in a saline-alkali environment (P &lt; 0.05). For Kongyu131 rice, the CH₄ oxidation-dependent nitrogen fixation rate ranged from 1.17 to 4.15 μmol/h/g, while the CH₄ oxidation-independent nitrogen fixation rate was determined to be 1.10 to 3.17 μmol/h/g. In J3 rice, these rates were 7.30 to 9.22 μmol/h/g and 5.76 to 4.85 μmol/h/g, respectively (P &lt; 0.05). Moreover, both N&lt;sub&gt;2&lt;/sub&gt; fixation and CH&lt;sub&gt;4&lt;/sub&gt; oxidation rates of methanotrophs in the roots of salt-alkali tolerant J3 cultivar (9.22 μmol/h/g for N&lt;sub&gt;2&lt;/sub&gt; fixation; 0.09 μmol/h/g for CH&lt;sub&gt;4&lt;/sub&gt; oxidation) were significantly higher than those in the roots of the common rice cultivar Kongyu131 (4.15 μmol/h/g for N₂ fixation; 0.03 μmol/h/g for CH₄ oxidation) under nitrogen fertilization (P &lt; 0.01). Thus, methanotrophs associated with J3 rice roots demonstrated improved N&lt;sub&gt;2&lt;/sub&gt; fixation and CH&lt;sub&gt;4&lt;/sub&gt; oxidation activities under saline-alkali stress in the presence of nitrogen fertilizer. Even heterotrophic diazotrophs in J3 rice roots showed enhanced N&lt;sub&gt;2&lt;/sub&gt; fixation with (SN) or without (LN) nitrogen inputs. The RNA-based amplicon sequencing showed that nitrogen fertilizer had a greater influence on diazotrophic and methanotrophic communities than the differences between rice cultivars. Further, active Methylomonas (type I methanotrophs) dominated the root-associated diazotrophic (9.8-20.9%) and methanotrophic (46.8-80.3%) communities. Within these, Methylomonas methanica (13.3 vs. 3.8%) and Methylomonas paludis (8.8 vs. 27.4%) were determined as the common genera in the diazotrophic and methanotrophic communities, respectively, with both proportions undergoing significant shifts under SN conditions. Whereas the LN condition led to high CH&lt;sub&gt;4&lt;/sub&gt; oxidation activity and a relatively high abundance of Methylocystis (26.0%) in the roots of Kongyu131 rice, which sharply decreased under the SN condition (0.3%). The findings revealed that CH&lt;sub&gt;","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"17"},"PeriodicalIF":4.8,"publicationDate":"2025-03-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11909318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143633634","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Revealing Genomic Traits and Evolutionary Insights of Oryza officinalis from Southern China Through Genome Assembly and Transcriptome Analysis.","authors":"Can Chen, Haifei Hu, Hui Guo, Xiuzhong Xia, Zongqiong Zhang, Baoxuan Nong, Rui Feng, Shuhui Liang, Boheng Liu, Jianhui Liu, Danting Li, Junliang Zhao, Xinghai Yang","doi":"10.1186/s12284-025-00769-5","DOIUrl":"10.1186/s12284-025-00769-5","url":null,"abstract":"<p><p>Wild rice, as the ancestor of cultivated rice, has accumulated a wide range of beneficial traits through prolonged natural selection and evolution. Oryza officinalis, belonging to the CC genome, differs significantly from the AA genome. In this study, we utilized second- and third-generation sequencing, along with Hi-C technology, to assemble the genome of MT10 (O. officinalis). The assembled genome is 552.58 Mb, with contigs and scaffold N50 values of 40.04 and 44.48 Mb, respectively, and 96.73% of the sequences anchored to 12 chromosomes. A total of 33,813 genes were annotated, and repetitive sequences account for 54.24% of the MT10 genome. The number of unique genes in MT10 exceeds that in the O. officinalis genome from Thailand, and their divergence time is estimated at 1.6 million years ago. The MT10 genome exhibits fewer expanded gene families compared to contracted ones, with the expanded families predominantly associated with disease and pest resistance. Comparative genomic analysis of MT10 and Nipponbare reveals sequence variations in biotic and abiotic resistance-related genes. In particular, the presence of R genes and cystatin gene families in MT10 may contribute to its unique insect resistance. Transcriptome analyses indicate that flavonoid biosynthesis and MAPK-related genes are expressed in response to brown planthopper infestation. This study represents the first chromosome-level genome assembly of MT10, providing a reference sequence for the efficient cloning of beneficial genes from O. officinalis, which holds significant potential for the genetic improvement of cultivated rice.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"15"},"PeriodicalIF":4.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11906960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143625829","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"OsPRDA1 Interacts With OsFSD2 To Promote Chloroplast Development by Regulating Chloroplast Gene Expression in Rice.","authors":"Chao Zhang, Lengjing Wang, Zirui Wang, Qiang Dai, Haiyang Feng, Shu Xu, Xueju Liu, Jiaqi Tang, Hengxiu Yu","doi":"10.1186/s12284-025-00771-x","DOIUrl":"10.1186/s12284-025-00771-x","url":null,"abstract":"<p><p>Chloroplasts are vital for photosynthesis, and their development necessitates proper expression of chloroplast genes. However, the regulatory mechanisms underlying rice chloroplast gene expression have not been fully elucidated. In this study, we obtained an albino mutant of rice, white seedling and lethal 1 (wsl1), which displays significantly decreased chlorophyll contents and impaired chloroplast ultrastructure. The causal gene Oryza sativa PEP-RELATED DEVELOPMENT ARRESTED 1 (OsPRDA1) was isolated using Mutmap + and verified by gene editing and complementary assays. The expression of OsPRDA1 is induced by light, and OsPRDA1 is localized in chloroplasts. Transcription sequencing revealed that genes related to photosynthesis were differentially expressed in wsl1. The expression levels of the examined plastid-encoded RNA polymerase (PEP)-dependent chloroplast genes are downregulated due to the mutation of OsPRDA1. Moreover, OsPRDA1 interacts with OsFSD2, a member of PEP-associated proteins (PAPs). Knockout of OsFSD2 leads to the albino and seedling-lethal phenotype and downregulation of PEP-dependent chloroplast genes. Together, our results demonstrated that OsPRDA1 plays essential roles in rice chloroplast development, probably by facilitating the function of the PAP complex and chloroplast gene expression.</p>","PeriodicalId":21408,"journal":{"name":"Rice","volume":"18 1","pages":"14"},"PeriodicalIF":4.8,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11896912/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143606191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}