Rice

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    Rice FLOURY ENDOSPERM22, encoding a pentatricopeptide repeat protein, is involved in both mitochondrial RNA splicing and editing and is crucial for endosperm development
    Hang Yang, Yunlong Wang, Yunlu Tian, Xuan Teng, Zehui Lv, Jie Lei, Erchao Duan, Hui Dong, Xue Yang, Yuanyan Zhang, Yinglun Sun, Xiaoli Chen, Xiuhao Bao, Rongbo Chen, Chuanwei Gu, Yipeng Zhang, Xiaokang Jiang, Wenyu Ma, Pengcheng Zhang, Yi Ji, Yu Zhang, Yihua Wang and Jianmin Wan
    J Integr Plant Biol 2023, 65 (3): 755-771.  
    DOI: 10.1111/jipb.13402
    Abstract (Browse 271)  |   Save
    Most of the reported P-type pentatricopeptide repeat (PPR) proteins play roles in organelle RNA stabilization and splicing. However, P-type PPRs involved in both RNA splicing and editing have rarely been reported, and their underlying mechanism remains largely unknown. Here, we report a rice floury endosperm22 (flo22) mutant with delayed amyloplast development in endosperm cells. Map-based cloning and complementation tests demonstrated that FLO22 encodes a mitochondrion-localized P-type PPR protein. Mutation of FLO22 resulting in defective trans-splicing of mitochondrial nad1 intron 1 and perhaps causing instability of mature transcripts affected assembly and activity of complex Ⅰ, and mitochondrial morphology and function. RNA-seq analysis showed that expression levels of many genes involved in starch and sucrose metabolism were significantly down-regulated in the flo22 mutant compared with the wild type, whereas genes related to oxidative phosphorylation and the tricarboxylic acid cycle were significantly up-regulated. In addition to involvement in splicing as a P-type PPR protein, we found that FLO22 interacted with DYW3, a DYW-type PPR protein, and they may function synergistically in mitochondrial RNA editing. The present work indicated that FLO22 plays an important role in endosperm development and plant growth by participating in nad1 maturation and multi-site editing of mitochondrial messager RNA.
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    Cited: Web of Science(2)
      
    ESCRT-III component OsSNF7.2 modulates leaf rolling by trafficking and endosomal degradation of auxin biosynthetic enzyme OsYUC8 in rice
    Liang Zhou, Saihua Chen, Maohong Cai, Song Cui, Yulong Ren, Xinyue Zhang, Tianzhen Liu, Chunlei Zhou, Xin Jin, Limin Zhang, Minxi Wu, Shuyi Zhang, Zhijun Cheng, Xin Zhang, Cailin Lei, Qibing Lin, Xiuping Guo, Jie Wang, Zhichao Zhao, Ling Jiang, Shanshan Zhu and Jianmin Wan
    J Integr Plant Biol 2023, 65 (6): 1408-1422.  
    DOI: 10.1111/jipb.13460
    Abstract (Browse 337)  |   Save
    The endosomal sorting complex required for transport (ESCRT) is highly conserved in eukaryotic cells and plays an essential role in the biogenesis of multivesicular bodies and cargo degradation to the plant vacuole or lysosomes. Although ESCRT components affect a variety of plant growth and development processes, their impact on leaf development is rarely reported. Here, we found that OsSNF7.2, an ESCRT-III component, controls leaf rolling in rice (Oryza sativa). The Ossnf7.2 mutant rolled leaf 17 (rl17) has adaxially rolled leaves due to the decreased number and size of the bulliform cells. OsSNF7.2 is expressed ubiquitously in all tissues, and its protein is localized in the endosomal compartments. OsSNF7.2 homologs, including OsSNF7, OsSNF7.3, and OsSNF7.4, can physically interact with OsSNF7.2, but their single mutation did not result in leaf rolling. Other ESCRT complex subunits, namely OsVPS20, OsVPS24, and OsBRO1, also interact with OsSNF7.2. Further assays revealed that OsSNF7.2 interacts with OsYUC8 and aids its vacuolar degradation. Both Osyuc8 and rl17 Osyuc8 showed rolled leaves, indicating that OsYUC8 and OsSNF7.2 function in the same pathway, conferring leaf development. This study reveals a new biological function for the ESCRT-III components, and provides new insights into the molecular mechanisms underlying leaf rolling.
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    Cited: Web of Science(4)
      
    Histone deacetylase OsHDA706 increases salt tolerance via H4K5/K8 deacetylation of OsPP2C49 in rice
    Kai Liu, Jijin Chen, Shang Sun, Xu Chen, Xinru Zhao, Yingying Hu, Guoxiao Qi, Xiya Li, Bo Xu, Jun Miao, Chao Xue, Yong Zhou and Zhiyun Gong
    J Integr Plant Biol 2023, 65 (6): 1394-1407.  
    DOI: 10.1111/jipb.13470
    Abstract (Browse 351)  |   Save
    High salt is a major environmental factor that threatens plant growth and development. Increasing evidence indicates that histone acetylation is involved in plant responses to various abiotic stress; however, the underlying epigenetic regulatory mechanisms remain poorly understood. In this study, we revealed that the histone deacetylase OsHDA706 epigenetically regulates the expression of salt stress response genes in rice (Oryza sativa L.). OsHDA706 localizes to the nucleus and cytoplasm and OsHDA706 expression is significantly induced under salt stress. Moreover, oshda706 mutants showed a higher sensitivity to salt stress than the wild-type. In vivo and in vitro enzymatic activity assays demonstrated that OsHDA706 specifically regulates the deacetylation of lysines 5 and 8 on histone H4 (H4K5 and H4K8). By combining chromatin immunoprecipitation and mRNA sequencing, we identified the clade A protein phosphatase 2 C gene, OsPP2C49, which is involved in the salt response as a direct target of H4K5 and H4K8 acetylation. We found that the expression of OsPP2C49 is induced in the oshda706 mutant under salt stress. Furthermore, the knockout of OsPP2C49 enhances plant tolerance to salt stress, while its overexpression has the opposite effect. Taken together, our results indicate that OsHDA706, a histone H4 deacetylase, participates in the salt stress response by regulating the expression of OsPP2C49 via H4K5 and H4K8 deacetylation.
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    Young Leaf White Stripe encodes a P-type PPR protein required for chloroplast development
    Jie Lan, Qibing Lin, Chunlei Zhou, Xi Liu, Rong Miao, Tengfei Ma, Yaping Chen, Changling Mou, Ruonan Jing, Miao Feng, Thanhliem Nguyen, Yulong Ren, Zhijun Cheng, Xin Zhang, Shijia Liu, Ling Jiang and Jianmin Wan
    J Integr Plant Biol 2023, 65 (7): 1687-1702.  
    DOI: 10.1111/jipb.13477
    Abstract (Browse 228)  |   Save
    Pentatricopeptide repeat (PPR) proteins function in post-transcriptional regulation of organellar gene expression. Although several PPR proteins are known to function in chloroplast development in rice (Oryza sativa), the detailed molecular functions of many PPR proteins remain unclear. Here, we characterized a rice young leaf white stripe (ylws) mutant, which has defective chloroplast development during early seedling growth. Map-based cloning revealed that YLWS encodes a novel P-type chloroplast-targeted PPR protein with 11 PPR motifs. Further expression analyses showed that many nuclear- and plastid-encoded genes in the ylws mutant were significantly changed at the RNA and protein levels. The ylws mutant was impaired in chloroplast ribosome biogenesis and chloroplast development under low-temperature conditions. The ylws mutation causes defects in the splicing of atpF, ndhA, rpl2, and rps12, and editing of ndhA, ndhB, and rps14 transcripts. YLWS directly binds to specific sites in the atpF, ndhA, and rpl2 pre-mRNAs. Our results suggest that YLWS participates in chloroplast RNA group II intron splicing and plays an important role in chloroplast development during early leaf development.
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    OsWR2 recruits HDA704 to regulate the deacetylation of H4K8ac in the promoter of OsABI5 in response to drought stress
    Yalu Guo, Yiqing Tan, Minghao Qu, Kai Hong, Longjun Zeng, Lei Wang, Chuxiong Zhuang, Qian Qian, Jiang Hu and Guosheng Xiong
    J Integr Plant Biol 2023, 65 (7): 1651-1669.  
    DOI: 10.1111/jipb.13481
    Abstract (Browse 305)  |   Save
    Drought stress is a major environmental factor that limits the growth, development, and yield of rice (Oryza sativa L.). Histone deacetylases (HDACs) are involved in the regulation of drought stress responses. HDA704 is an RPD3/HDA1 class HDAC that mediates the deacetylation of H4K8 (lysine 8 of histone H4) for drought tolerance in rice. In this study, we show that plants overexpressing HDA704 (HDA704-OE) are resistant to drought stress and sensitive to abscisic acid (ABA), whereas HDA704 knockout mutant (hda704) plants displayed decreased drought tolerance and ABA sensitivity. Transcriptome analysis revealed that HDA704 regulates the expression of ABA-related genes in response to drought stress. Moreover, HDA704 was recruited by a drought-resistant transcription factor, WAX SYNTHESIS REGULATORY 2 (OsWR2), and co-regulated the expression of the ABA biosynthesis genes NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3), NCED4, and NCED5 under drought stress. HDA704 also repressed the expression of ABA-INSENSITIVE 5 (OsABI5) and DWARF AND SMALL SEED 1 (OsDSS1) by regulating H4K8ac levels in the promoter regions in response to polyethylene glycol 6000 treatment. In agreement, the loss of OsABI5 function increased resistance to dehydration stress in rice. Our results demonstrate that HDA704 is a positive regulator of the drought stress response and offers avenues for improving drought resistance in rice.
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    Auxin signaling module OsSK41-OsIAA10-OsARF regulates grain yield traits in rice
    Fuying Ma, Fan Zhang, Yu Zhu, Dengyong Lan, Peiwen Yan, Ying Wang, Zejun Hu, Xinwei Zhang, Jian Hu, Fuan Niu, Mingyu Liu, Shicong He, Jinhao Cui, Xinyu Yuan, Ying Yan, Shujun Wu, Liming Cao, Hongwu Bian, Jinshui Yang, Zhikang Li and Xiaojin Luo
    J Integr Plant Biol 2023, 65 (7): 1753-1766.  
    doi: 10.1111/jipb.13484
    Abstract (Browse 266)  |   Save
    Auxin is an important phytohormone in plants, and auxin signaling pathways in rice play key roles in regulating its growth, development, and productivity. To investigate how rice grain yield traits are regulated by auxin signaling pathways and to facilitate their application in rice improvement, we validated the functional relationships among regulatory genes such as OsIAA10, OsSK41, and OsARF21 that are involved in one of the auxin (OsIAA10) signaling pathways. We assessed the phenotypic effects of these genes on several grain yield traits across two environments using knockout and/or overexpression transgenic lines. Based on the results, we constructed a model that showed how grain yield traits were regulated by OsIAA10 and OsTIR1, OsAFB2, and OsSK41 and OsmiR393 in the OsSK41-OsIAA10-OsARF module and by OsARF21 in the transcriptional regulation of downstream auxin response genes in the OsSK41-OsIAA10-OsARF module. The population genomic analyses revealed rich genetic diversity and the presence of major functional alleles at most of these loci in rice populations. The strong differentiation of many major alleles between Xian/indica and Geng/japonica subspecies and/or among modern varieties and landraces suggested that they contributed to improved productivity during evolution and breeding. We identified several important aspects associated with the genetic and molecular bases of rice grain and yield traits that were regulated by auxin signaling pathways. We also suggested rice auxin response factor (OsARF) activators as candidate target genes for improving specific target traits by overexpression and/or editing subspecies-specific alleles and by searching and pyramiding the ‘best’ gene allelic combinations at multiple regulatory genes in auxin signaling pathways in rice breeding programs.
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    The kinase OsSK41/OsGSK5 negatively regulates amylose content in rice endosperm by affecting the interaction between OsEBP89 and OsBP5
    Zejun Hu, Fuan Niu, Peiwen Yan, Kai Wang, Lixia Zhang, Ying Yan, Yu Zhu, Shiqing Dong, Fuying Ma, Dengyong Lan, Siwen Liu, Xiaoyun Xin, Ying Wang, Jinshui Yang, Liming Cao, Shujun Wu and Xiaojin Luo
    J Integr Plant Biol 2023, 65 (7): 1782-1793.  
    doi: 10.1111/jipb.13488
    Abstract (Browse 259)  |   Save
    Amylose content (AC) is the main factor determining the palatability, viscosity, transparency, and digestibility of rice (Oryza sativa) grains. AC in rice grains is mainly controlled by different alleles of the Waxy (Wx) gene. The AP2/EREBP transcription factor OsEBP89 interacts with the MYC-like protein OsBP5 to synergistically regulate the expression of Wx. Here, we determined that the GLYCOGEN SYNTHASE KINASE 5 (OsGSK5, also named SHAGGY-like kinase 41 [OsSK41]) inhibits the transcriptional activation activity of OsEBP89 in rice grains during amylose biosynthesis. The loss of OsSK41 function enhanced Wx expression and increased AC in rice grains. By contrast, the loss of function of OsEBP89 reduced Wx expression and decreased AC in rice grains. OsSK41 interacts with OsEBP89 and phosphorylates four of its sites (Thr-28, Thr-30, Ser-238, and Thr-257), which makes OsEBP89 unstable and attenuates its interaction with OsBP5. Wx promoter activity was relatively weak when regulated by the phosphomimic variant OsEBP89E–OsBP5 but relatively strong when regulated by the nonphosphorylatable variant OsEBP89A–OsBP5. Therefore, OsSK41-mediated phosphorylation of OsEBP89 represents an additional layer of complexity in the regulation of amylose biosynthesis during rice grain development. In addition, our findings provide four possible sites for regulating rice grain AC via precise gene editing.
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    The basic helix-loop-helix transcription factor gene, OsbHLH38, plays a key role in controlling rice salt tolerance
    Fengping Du, Yinxiao Wang, Juan Wang, Yingbo Li, Yue Zhang, Xiuqin Zhao, Jianlong Xu, Zhikang Li, Tianyong Zhao, Wensheng Wang and Binying Fu
    J Integr Plant Biol 2023, 65 (8): 1859-1873.  
    doi: 10.1111/jipb.13489
    Abstract (Browse 516)  |   Save
    The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination. The considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian (indica) and Geng (japonica) subspecies and between the upland-Geng and lowland-Geng ecotypes. The upland-Geng accessions were most sensitive to ABA. Genome-wide association analyses identified four major quantitative trait loci containing 21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene, OsbHLH38, was the most important for ABA sensitivity. Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses. Overexpression of OsbHLH38 increased seedling salt tolerance, while knockout of OsbHLH38 increased sensitivity to salt stress. A salt-responsive transcription factor, OsDREB2A, interacted with OsbHLH38 and was directly regulated by OsbHLH38. Moreover, OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones, transcription factor genes, and many downstream genes with diverse functions, including photosynthesis, redox homeostasis, and abiotic stress responsiveness. These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.
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    The F-box protein SHORT PRIMARY ROOT modulates primary root meristem activity by targeting SEUSS-LIKE protein for degradation in rice
    Nini Ma, Nian Li, Zhongmao Yu, Chunli Chen, Dao‐Xiu Zhou and Yu Zhao
    J Integr Plant Biol 2023, 65 (8): 1937-1949.  
    DOI: 10.1111/jipb.13492
    Abstract (Browse 274)  |   Save
    Root meristem activity is essential for root morphogenesis and adaptation, but the molecular mechanism regulating root meristem activity is not fully understood. Here, we identify an F-box family E3 ubiquitin ligase named SHORT PRIMARY ROOT (SHPR) that regulates primary root (PR) meristem activity and cell proliferation in rice. SHPR loss-of-function mutations impair PR elongation in rice. SHPR is involved in the formation of an SCF complex with the Oryza sativa SKP1-like protein OSK1/20. We show that SHPR interacts with Oryza sativa SEUSS-LIKE (OsSLK) in the nucleus and is required for OsSLK polyubiquitination and degradation by the ubiquitin 26S-proteasome system (UPS). Transgenic plants overexpressing OsSLK display a shorter PR phenotype, which is similar to the SHPR loss-of-function mutants. Genetic analysis suggests that SHPR promotes PR elongation in an OsSLK-dependent manner. Collectively, our study establishes SHPR as an E3 ubiquitin ligase that targets OsSLK for degradation, and uncovers a protein ubiquitination pathway as a mechanism for modulating root meristem activity in rice.
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    Artificial evolution of OsEPSPS through an improved dual cytosine and adenine base editor generated a novel allele conferring rice glyphosate tolerance
    Chen Zhang, Xue Zhong, Shaoya Li, Lei Yan, Jingying Li, Yubing He, Yong Lin, Yangjun Zhang and Lanqin Xia
    J Integr Plant Biol 2023, 65 (9): 2194-2203.  
    doi: 10.1111/jipb.13543
    Abstract (Browse 243)  |   Save
    Exploiting novel endogenous glyphosate-tolerant alleles is highly desirable and has promising potential for weed control in rice breeding. Here, through fusions of different effective cytosine and adenine deaminases with nCas9-NG, we engineered an effective surrogate two-component composite base editing system, STCBE-2, with improved C-to-T and A-to-G base editing efficiency and expanded the editing window. Furthermore, we targeted a rice endogenous OsEPSPS gene for artificial evolution through STCBE-2-mediated near-saturated mutagenesis. After hygromycin and glyphosate selection, we identified a novel OsEPSPS allele with an Asp-213-Asn (D213N) mutation (OsEPSPS-D213N) in the predicted glyphosate-binding domain, which conferred rice plants reliable glyphosate tolerance and had not been reported or applied in rice breeding. Collectively, we developed a novel dual base editor which will be valuable for artificial evolution of important genes in crops. And the novel glyphosate-tolerant rice germplasm generated in this study will benefit weeds management in rice paddy fields.
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    Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome
    Yarong Lin, Yiwang Zhu, Yuchao Cui, Hongge Qian, Qiaoling Yuan, Rui Chen, Yan Lin, Jianmin Chen, Xishi Zhou, Chuanlin Shi, Huiying He, Taijiao Hu, Chenbo Gu, Xiaoman Yu, Xiying Zhu, Yuexing Wang, Qian Qian, Cuijun Zhang, Feng Wang and Lianguang Shang
    J Integr Plant Biol 2023, 65 (12): 2541-2551.  
    doi: 10.1111/jipb.13568
    Abstract (Browse 231)  |   Save
    Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of cultivars. Genome evolution analysis of available rice germplasms suggested that TTL1 was selected during domestication of the indica and japonica rice subspecies, but still had much breeding potential for increasing grain length and thermotolerance. These findings provide insights into TTL1 as a novel potential target for the development of high-yield and thermotolerant rice varieties.
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    Post-transcriptional regulation of grain weight and shape by the RBP-A-J-K complex in rice
    Ding Ren, Hui Liu, Xuejun Sun, Fan Zhang, Ling Jiang, Ying Wang, Ning Jiang, Peiwen Yan, Jinhao Cui, Jinshui Yang, Zhikang Li, Pingli Lu and Xiaojin Luo
    J Integr Plant Biol 2024, 66 (1): 66-85.  
    doi: 10.1111/jipb.13583
    Abstract (Browse 199)  |   Save
    RNA-binding proteins (RBPs) are components of the post-transcriptional regulatory system, but their regulatory effects on complex traits remain unknown. Using an integrated strategy involving map-based cloning, functional characterizations, and transcriptomic and population genomic analyses, we revealed that RBP-K (LOC_Os08g23120), RBP-A (LOC_Os11g41890), and RBP-J (LOC_Os10g33230) encode proteins that form an RBP-A-J-K complex that negatively regulates rice yield-related traits. Examinations of the RBP-A-J-K complex indicated RBP-K functions as a relatively non-specific RBP chaperone that enables RBP-A and RBP-J to function normally. Additionally, RBP-J most likely affects GA pathways, resulting in considerable increases in grain and panicle lengths, but decreases in grain width and thickness. In contrast, RBP-A negatively regulates the expression of genes most likely involved in auxin-regulated pathways controlling cell wall elongation and carbohydrate transport, with substantial effects on the rice grain filling process as well as grain length and weight. Evolutionarily, RBP-K is relatively ancient and highly conserved, whereas RBP-J and RBP-A are more diverse. Thus, the RBP-A-J-K complex may represent a typical functional model for many RBPs and protein complexes that function at transcriptional and post-transcriptional levels in plants and animals for increased functional consistency, efficiency, and versatility, as well as increased evolutionary potential. Our results clearly demonstrate the importance of RBP-mediated post-transcriptional regulation for the diversity of complex traits. Furthermore, rice grain yield and quality may be enhanced by introducing various complete or partial loss-of-function mutations to specific RBP genes using clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 technology and by exploiting desirable natural tri-genic allelic combinations at the loci encoding the components of the RBP-A-J-K complex through marker-assisted selection.
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    OsNAC5 orchestrates OsABI5 to fine-tune cold tolerance in rice
    Ruiqing Li, Yue Song, Xueqiang Wang, Chenfan Zheng, Bo Liu, Huali Zhang, Jian Ke, Xuejing Wu, Liquan Wu, Ruifang Yang and Meng Jiang
    J Integr Plant Biol 2024, 66 (4): 660-682.  
    DOI: 10.1111/jipb.13585
    Abstract (Browse 371)  |   Save
    Due to its tropical origins, rice (Oryza sativa) is susceptible to cold stress, which poses severe threats to production. OsNAC5, a NAC-type transcription factor, participates in the cold stress response of rice, but the detailed mechanisms remain poorly understood. Here, we demonstrate that OsNAC5 positively regulates cold tolerance at germination and in seedlings by directly activating the expression of ABSCISIC ACID INSENSITIVE 5 (OsABI5). Haplotype analysis indicated that single nucleotide polymorphisms in a NAC-binding site in the OsABI5 promoter are strongly associated with cold tolerance. OsNAC5 also enhanced OsABI5 stability, thus regulating the expression of cold-responsive (COR) genes, enabling fine-tuned control of OsABI5 action for rapid, precise plant responses to cold stress. DNA affinity purification sequencing coupled with transcriptome deep sequencing identified several OsABI5 target genes involved in COR expression, including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1A (OsDREB1A), OsMYB20, and PEROXIDASE 70 (OsPRX70). In vivo and in vitro analyses suggested that OsABI5 positively regulates COR gene transcription, with marked COR upregulation in OsNAC5-overexpressing lines and downregulation in osnac5 and/or osabi5 knockout mutants. This study extends our understanding of cold tolerance regulation via OsNAC5 through the OsABI5-CORs transcription module, which may be used to ameliorate cold tolerance in rice via advanced breeding.
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    Knockout of a rice K5.2 gene increases Ca accumulation in the grain
    Peitong Wang, Naoki Yamaji, Namiki Mitani‐Ueno, Jun Ge and Jian Feng Ma
    J Integr Plant Biol 2024, 66 (2): 252-264.  
    DOI: 10.1111/jipb.13587
    Abstract (Browse 111)  |   Save
    Rice is a staple food for half of the world's population, but it is a poor dietary source of calcium (Ca) due to the low concentration. It is an important issue to boost Ca concentration in this grain to improve Ca deficiency risk, but the mechanisms underlying Ca accumulation are poorly understood. Here, we obtained a rice (Oryza sativa) mutant with high shoot Ca accumulation. The mutant exhibited 26%–53% higher Ca in shoots than did wild-type rice (WT) at different Ca supplies. Ca concentration in the xylem sap was 36% higher in the mutant than in the WT. There was no difference in agronomic traits between the WT and mutant, but the mutant showed 25% higher Ca in the polished grain compared with the WT. Map-based cloning combined with a complementation test revealed that the mutant phenotype was caused by an 18-bp deletion of a gene, OsK5.2, belonging to the Shaker-like K+ channel family. OsK5.2 was highly expressed in the mature region of the roots and its expression in the roots was not affected by Ca levels, but upregulated by low K. Immunostaining showed that OsK5.2 was mainly expressed in the pericycle of the roots. Taken together, our results revealed a novel role for OsK5.2 in Ca translocation in rice, and will be a good target for Ca biofortification in rice.
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    A historical review of hybrid rice breeding
    Xiaoming Zheng, Fei Wei, Cheng Cheng and Qian Qian
    J Integr Plant Biol 2024, 66 (3): 532-545.  
    doi: 10.1111/jipb.13598
    Abstract (Browse 132)  |   Save
    The development of germplasm resources and advances in breeding methods have led to steady increases in yield and quality of rice (Oryza sativa L.). Three milestones in the recent history of rice breeding have contributed to these increases: dwarf rice breeding, hybrid rice breeding, and super rice breeding. On the 50th anniversary of the success of three-line hybrid rice, we highlight important scientific discoveries in rice breeding that were made by Chinese scientists and summarize the broader history of the field. We discuss the strategies that could be used in the future to optimize rice breeding further in the hope that China will continue to play a leading role in international rice breeding.
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    A centromere map based on super pan-genome highlights the structure and function of rice centromeres
    Yang Lv, Congcong Liu, Xiaoxia Li, Yueying Wang, Huiying He, Wenchuang He, Wu Chen, Longbo Yang, Xiaofan Dai, Xinglan Cao, Xiaoman Yu, Jiajia Liu, Bin Zhang, Hua Wei, Hong Zhang, Hongge Qian, Chuanlin Shi, Yue Leng, Xiangpei Liu, Mingliang Guo, Xianmeng Wang, Zhipeng Zhang, Tianyi Wang, Bintao Zhang, Qiang Xu, Yan Cui, Qianqian Zhang, Qiaoling Yuan, Noushin Jahan, Jie Ma, Xiaoming Zheng, Yongfeng Zhou, Qian Qian, Longbiao Guo and Lianguang Shang
    J Integr Plant Biol 2024, 66 (2): 196-207.  
    doi: 10.1111/jipb.13607
    Abstract (Browse 210)  |   Save
    Rice (Oryza sativa) is a significant crop worldwide with a genome shaped by various evolutionary factors. Rice centromeres are crucial for chromosome segregation, and contain some unreported genes. Due to the diverse and complex centromere region, a comprehensive understanding of rice centromere structure and function at the population level is needed. We constructed a high-quality centromere map based on the rice super pan-genome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African rice. We showed that rice centromeres have diverse satellite repeat CentO, which vary across chromosomes and subpopulations, reflecting their distinct evolutionary patterns. We also revealed that long terminal repeats (LTRs), especially young Gypsy-type LTRs, are abundant in the peripheral CentO-enriched regions and drive rice centromere expansion and evolution. Furthermore, high-quality genome assembly and complete telomere-to-telomere (T2T) reference genome enable us to obtain more centromeric genome information despite mapping and cloning of centromere genes being challenging. We investigated the association between structural variations and gene expression in the rice centromere. A centromere gene, OsMAB, which positively regulates rice tiller number, was further confirmed by expression quantitative trait loci, haplotype analysis and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9 methods. By revealing the new insights into the evolutionary patterns and biological roles of rice centromeres, our finding will facilitate future research on centromere biology and crop improvement.
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    Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway
    Chaoqing Ding, Zhengji Shao, Yuping Yan, Guangheng Zhang, Dali Zeng, Li Zhu, Jiang Hu, Zhenyu Gao, Guojun Dong, Qian Qian and Deyong Ren
    J Integr Plant Biol 2024, 66 (2): 172-175.  
    doi: 10.1111/jipb.13617
    Abstract (Browse 190)  |   Save
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    Structural insights into the Oryza sativa cation transporters HKTs in salt tolerance
    Ran Gao, Yutian Jia, Xia Xu, Peng Fu, Jiaqi Zhou and Guanghui Yang
    J Integr Plant Biol 2024, 66 (4): 700-708.  
    DOI: 10.1111/jipb.13632
    Abstract (Browse 101)  |   Save
    The high-affinity potassium transporters (HKTs), selectively permeable to either Na+ alone or Na+/K+, play pivotal roles in maintaining plant Na+/K+ homeostasis. Although their involvement in salt tolerance is widely reported, the molecular underpinnings of Oryza sativa HKTs remain elusive. In this study, we elucidate the structures of OsHKT1;1 and OsHKT2;1, representing two distinct classes of rice HKTs. The dimeric assembled OsHKTs can be structurally divided into four domains. At the dimer interface, a half-helix or a loop in the third domain is coordinated by the C-terminal region of the opposite subunit. Additionally, we present the structures of OsHKT1;5 salt-tolerant and salt-sensitive variants, a key quantitative trait locus associated with salt tolerance. The salt-tolerant variant of OsHKT1;5 exhibits enhanced Na+ transport capability and displays a more flexible conformation. These findings shed light on the molecular basis of rice HKTs and provide insights into their role in salt tolerance.
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    OsWRKY78 regulates panicle exsertion via gibberellin signaling pathway in rice
    Enyang Mei, Mingliang He, Min Xu, Jiaqi Tang, Jiali Liu, Yingxiang Liu, Zhipeng Hong, Xiufeng Li, Zhenyu Wang, Qingjie Guan, Xiaojie Tian and Qingyun Bu
    J Integr Plant Biol 2024, 66 (4): 771-786.  
    DOI: 10.1111/jipb.13636
    Abstract (Browse 250)  |   Save
    Panicle exsertion is one of the crucial agronomic traits in rice (Oryza sativa). Shortening of panicle exsertion often leads to panicle enclosure and severely reduces seed production. Gibberellin (GA) plays important roles in regulating panicle exsertion. However, the underlying mechanism and the relative regulatory network remain elusive. Here, we characterized the oswrky78 mutant showing severe panicle enclosure, and found that the defect of oswrky78 is caused by decreased bioactive GA contents. Biochemical analysis demonstrates that OsWRKY78 can directly activate GA biosynthesis and indirectly suppress GA metabolism. Moreover, we found OsWRKY78 can interact with and be phosphorylated by mitogen-activated protein kinase (MAPK) kinase OsMAPK6, and this phosphorylation can enhance OsWRKY78 stability and is necessary for its biological function. Taken together, these results not only reveal the critical function of OsWRKY78, but also reveal its mechanism via mediating crosstalk between MAPK and the GA signaling pathway in regulating panicle exsertion.
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    Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating OsGA2ox7 in rice
    Peng Zeng, Ting Xie, Jiaxin Shen, Taokai Liang, Lu Yin, Kexin Liu, Ying He, Mingming Chen, Haijuan Tang, Sunlu Chen, Sergey Shabala, Hongsheng Zhang and Jinping Cheng
    J Integr Plant Biol 2024, 66 (4): 731-748.  
    doi: 10.1111/jipb.13642
    Abstract (Browse 146)  |   Save
    Soil salinity has a major impact on rice seed germination, severely limiting rice production. Herein, a rice germination defective mutant under salt stress (gdss) was identified by using chemical mutagenesis. The GDSS gene was detected via MutMap and shown to encode potassium transporter OsHAK9. Phenotypic analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt stress. OsHAK9 is highly expressed in germinating seed embryos. Ion contents and non-invasive micro-test technology results showed that OsHAK9 restricted K+ efflux in salt-exposed germinating seeds for the balance of K+/Na+. Disruption of OsHAK9 significantly reduced gibberellin 4 (GA4) levels, and the germination defective phenotype of oshak9a was partly rescued by exogenous GA3 treatment under salt stress. RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress, and the expression of OsGA2ox7 was significantly inhibited by salt stress. Null mutants of OsGA2ox7 created using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt stress. Overall, our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7, which provides a novel clue about the relationship between GA and OsHAKs in rice.
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    OsATL32 ubiquitinates the reactive oxygen species-producing OsRac5–OsRbohB module to suppress rice immunity
    Yuqing Yan, Hui Wang, Yan Bi, Jiajing Wang, Muhammad Noman, Dayong Li, Fengming Song
    J Integr Plant Biol 2024, 66 (7): 1459-1480.  
    DOI: 10.1111/jipb.13666
    Abstract (Browse 151)  |   Save
    Ubiquitination-mediated protein degradation is integral to plant immunity, with E3 ubiquitin ligases acting as key factors in this process. Here, we report the functions of OsATL32, a plasma membrane-localized Arabidopsis Tóxicos En Levadura (ATL)-type E3 ubiquitin ligase, in rice (Oryza sativa) immunity and its associated regulatory network. We found that the expression of OsATL32 is downregulated in both compatible and incompatible interactions between rice and the rice blast fungus Magnaporthe oryzae. The OsATL32 protein level declines in response to infection by a compatible M. oryzae strain or to chitin treatment. OsATL32 negatively regulates rice resistance to blast and bacterial leaf blight diseases, as well as chitin-triggered immunity. Biochemical and genetic studies revealed that OsATL32 suppresses pathogen-induced reactive oxygen species (ROS) accumulation by mediating ubiquitination and degradation of the ROS- producing OsRac5–OsRbohB module, which enhances rice immunity against M. oryzae. The protein phosphatase PHOSPHATASE AND TENSIN HOMOLOG enhances rice blast resistance by dephosphorylating OsATL32 and promoting its degradation, preventing its negative effect on rice immunity. This study provides insights into the molecular mechanism by which the E3 ligase OsATL32 targets a ROS-producing module to undermine rice immunity.
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    An orchestrated ethylene–gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding
    Yusong Lyu, Xinli Dong, Shipeng Niu, Ruijie Cao, Gaoneng Shao, Zhonghua Sheng, Guiai Jiao, Lihong Xie, Shikai Hu, Shaoqing Tang, Xiangjin Wei, Peisong Hu
    J Integr Plant Biol 2024, 66 (7): 1427-1439.  
    doi: 10.1111/jipb.13671
    Abstract (Browse 106)  |   Save
    A mechanized direct seeding of rice with less labor and water usage, has been widely adopted. However, this approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME) offers the main drive of fast emergence of rice seedlings from soils; nevertheless, its genetic basis remains unknown. Here, we identify a major rice quantitative trait locus Mesocotyl Elongation1 (qME1), an allele of the Green Revolution gene Semi-Dwarf1 (SD1), encoding GA20-oxidase for gibberellin (GA) biosynthesis. ME1 expression is strongly induced by soil depth and ethylene. When rice grains are direct-seeded in soils, the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription, accelerating bioactive GA biosynthesis. The GAs further degrade the DELLA protein SLENDER RICE 1 (SLR1), alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13 (OsPIL13) to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence. The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process, and an elite ME1-R allele (D349H) is found in some modern Geng varieties (long mesocotyl lengths) in northern China, which can be used in the direct seeding and dwarf breeding of Geng varieties. Furthermore, the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield penalties. Collectively, we reveal the molecular mechanism of rice ME, and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.
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    Sporophytic control of tapetal development and pollen fertility by a mitogen-activated protein kinase cascade in rice
    Jianguo Zeng, Manman Duan, Yiqing Wang, Guangtao Li, Yujing You, Jie Shi, Changhao Liu, Jinyang Zhang, Juan Xu, Shuqun Zhang, Jing Zhao
    J Integr Plant Biol 2024, 66 (7): 1500-1516.  
    DOI: 10.1111/jipb.13673
    Abstract (Browse 104)  |   Save
    Tapetum, the innermost layer of the anther wall, provides essential nutrients and materials for pollen development. Timely degradation of anther tapetal cells is a prerequisite for normal pollen development in flowering plants. Tapetal cells facilitate male gametogenesis by providing cellular contents after highly coordinated programmed cell death (PCD). Tapetal development is regulated by a transcriptional network. However, the signaling pathway(s) involved in this process are poorly understood. In this study, we report that a mitogen-activated protein kinase (MAPK) cascade composed of OsYDA1/OsYDA2-OsMKK4-OsMPK6 plays an important role in tapetal development and male gametophyte fertility. Loss of function of this MAPK cascade leads to anther indehiscence, enlarged tapetum, and aborted pollen grains. Tapetal cells in osmkk4 and osmpk6 mutants exhibit an increased presence of lipid body-like structures within the cytoplasm, which is accompanied by a delayed occurrence of PCD. Expression of a constitutively active version of OsMPK6 (CA-OsMPK6) can rescue the pollen defects in osmkk4 mutants, confirming that OsMPK6 functions downstream of OsMKK4 in this pathway. Genetic crosses also demonstrated that the MAPK cascade sporophyticly regulates pollen development. Our study reveals a novel function of rice MAPK cascade in plant male reproductive biology.
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    Natural variation in MORE GRAINS 1 regulates grain number and grain weight in rice
    Yingchun Han, Qianfeng Hu, Nuo Gong, Huimin Yan, Najeeb Ullah Khan, Yanxiu Du, Hongzheng Sun, Quanzhi Zhao, Wanxi Peng, Zichao Li, Zhanying Zhang, Junzhou Li
    J Integr Plant Biol 2024, 66 (7): 1440-1458.  
    doi: 10.1111/jipb.13674
    Abstract (Browse 114)  |   Save
    Grain yield is determined mainly by grain number and grain weight. In this study, we identified and characterized MORE GRAINS1 (MOG1), a gene associated with grain number and grain weight in rice (Oryza sativa L.), through map-based cloning. Overexpression of MOG1 increased grain yield by 18.6%-22.3% under field conditions. We determined that MOG1, a bHLH transcription factor, interacts with OsbHLH107 and directly activates the expression of LONELY GUY(LOG), which encodes a cytokinin-activating enzyme and the cell expansion gene EXPANSIN-LIKE1(EXPLA1), positively regulating grain number per panicle and grain weight. Natural variations in the promoter and coding regions of MOG1 between Hap-LNW and Hap-HNW alleles resulted in changes in MOG1 expression level and transcriptional activation, leading to functional differences. Haplotype analysis revealed that Hap-HNW, which results in a greater number and heavier grains, has undergone strong selection but has been poorly utilized in modern lowland rice breeding. In summary, the MOG1-OsbHLH107 complex activates LOG and EXPLA1 expression to promote cell expansion and division of young panicles through the cytokinin pathway, thereby increasing grain number and grain weight. These findings suggest that Hap-HNW could be used in strategies to breed high-yielding temperate japonica lowland rice.
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    Transcription factor OsWRKY11 induces rice heading at low concentrations but inhibits rice heading at high concentrations
    Lirong Zhao, Yunwei Liu, Yi Zhu, Shidie Chen, Yang Du, Luyao Deng, Lei Liu, Xia Li, Wanqin Chen, Zhiyu Xu, Yangyang Xiong, You Ming, Siyu Fang, Ligang Chen, Houping Wang, Diqiu Yu
    J Integr Plant Biol 2024, 66 (7): 1385-1407.  
    DOI: 10.1111/jipb.13679
    Abstract (Browse 132)  |   Save
    The heading date of rice is a crucial agronomic characteristic that influences its adaptability to different regions and its productivity potential. Despite the involvement of WRKY transcription factors in various biological processes related to development, the precise mechanisms through which these transcription factors regulate the heading date in rice have not been well elucidated. The present study identified OsWRKY11 as a WRKY transcription factor which exhibits a pivotal function in the regulation of the heading date in rice through a comprehensive screening of a clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated nuclease 9 mutant library that specifically targets the WRKY genes in rice. The heading date of oswrky11 mutant plants and OsWRKY11-overexpressing plants was delayed compared with that of the wild-type plants under short-day and long-day conditions. Mechanistic investigation revealed that OsWRKY11 exerts dual effects on transcriptional promotion and suppression through direct and indirect DNA binding, respectively. Under normal conditions, OsWRKY11 facilitates flowering by directly inducing the expression of OsMADS14 and OsMADS15. The presence of elevated levels of OsWRKY11 protein promote formation of a ternary protein complex involving OsWRKY11, Heading date 1 (Hd1), and Days to heading date 8 (DTH8), and this complex then suppresses the expression of Ehd1, which leads to a delay in the heading date. Subsequent investigation revealed that a mild drought condition resulted in a modest increase in OsWRKY11 expression, promoting heading. Conversely, under severe drought conditions, a significant upregulation of OsWRKY11 led to the suppression of Ehd1 expression, ultimately causing a delay in heading date. Our findings uncover a previously unacknowledged mechanism through which the transcription factor OsWRKY11 exerts a dual impact on the heading date by directly and indirectly binding to the promoters of target genes.
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    Rice stripe mosaic virus hijacks rice heading‐related gene to promote the overwintering of its insect vector
    Siping Chen, Xinyi Zhong, Zhiyi Wang, Biao Chen, Xiuqin Huang, Sipei Xu, Xin Yang, Guohui Zhou and Tong Zhang
    J Integr Plant Biol 2024, 66 (9): 2000-2016.  
    DOI: 10.1111/jipb.13722
    Abstract (Browse 138)  |   Save
    Rice stripe mosaic virus (RSMV) is an emerging pathogen which significantly reduces rice yields in the southern region of China. It is transmitted by the leafhopper Recilia dorsalis, which overwinters in rice fields. Our field investigations revealed that RSMV infection causes delayed rice heading, resulting in a large number of green diseased plants remaining in winter rice fields. This creates a favorable environment for leafhoppers and viruses to overwinter, potentially contributing to the rapid spread and epidemic of the disease. Next, we explored the mechanism by which RSMV manipulates the developmental processes of the rice plant. A rice heading‐related E3 ubiquitin ligase, Heading date Associated Factor 1 (HAF1), was found to be hijacked by the RSMV‐encoded P6. The impairment of HAF1 function affects the ubiquitination and degradation of downstream proteins, HEADING DATE 1 and EARLY FLOWERING3, leading to a delay in rice heading. Our results provide new insights into the development regulation‐based molecular interactions between virus and plant, and highlights the importance of understanding virus‐vector‐plant tripartite interactions for effective disease management strategies.
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    BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice
    Zhen Li, Junhua Ye, Qiaoling Yuan, Mengchen Zhang, Xingyu Wang, Jing Wang, Tianyi Wang, Hongge Qian, Xinghua Wei, Yaolong Yang, Lianguang Shang and Yue Feng
    J Integr Plant Biol 2024, 66 (9): 1966-1982.  
    doi: 10.1111/jipb.13726
    Abstract (Browse 134)  |   Save
    Tiller angle is a key agricultural trait that establishes plant architecture, which in turn strongly affects grain yield by influencing planting density in rice. The shoot gravity response plays a crucial role in the regulation of tiller angle in rice, but the underlying molecular mechanism is largely unknown. Here, we report the identification of the BIG TILLER ANGLE2 (BTA2), which regulates tiller angle by controlling the shoot gravity response in rice. Loss-of-function mutation of BTA2 dramatically reduced auxin content and affected auxin distribution in rice shoot base, leading to impaired gravitropism and therefore a big tiller angle. BTA2 interacted with AUXIN RESPONSE FACTOR7 (ARF7) to modulate rice tiller angle through the gravity signaling pathway. The BTA2 protein was highly conserved during evolution. Sequence variation in the BTA2 promoter of indica cultivars harboring a less expressed BTA2 allele caused lower BTA2 expression in shoot base and thus wide tiller angle during rice domestication. Overexpression of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting conditions. Our findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity response. Our work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.
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    D53 represses rice blast resistance by directly targeting phenylalanine ammonia lyases
    Haitao Ye, Qingqing Hou, Haitao Lv, Hui Shi, Duo Wang, Yujie Chen, Tangshuai Xu, Mei Wang, Min He, Junjie Yin, Xiang Lu, Yongyan Tang, Xiaobo Zhu, Lijuan Zou, Xuewei Chen, Jiayang Li, Bing Wang and Jing Wang
    J Integr Plant Biol 2024, 66 (9): 1827-1830.  
    DOI: 10.1111/jipb.13734
    Abstract (Browse 156)  |   Save
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    A NAC transcription factor MNAC3-centered regulatory network negatively modulates rice immunity against blast disease
    Hui Wang, Yan Bi, Yuqing Yan, Xi Yuan, Yizhou Gao, Muhammad Noman, Dayong Li and Fengming Song
    J Integr Plant Biol 2024, 66 (9): 2017-2041.  
    DOI: 10.1111/jipb.13727
    Abstract (Browse 100)  |   Save
    NAC transcription factors (TFs) are pivotal in plant immunity against diverse pathogens. Here, we report the functional and regulatory network of MNAC3, a novel NAC TF, in rice immunity. MNAC3, a transcriptional activator, negatively modulates rice immunity against blast and bacterial leaf blight diseases and pathogen-associated molecular pattern (PAMP)-triggered immune responses. MNAC3 binds to a CACG cis-element and activates the transcription of immune-negative target genes OsINO80, OsJAZ10, and OsJAZ11. The negative function of MNAC3 in rice immunity depends on its transcription of downstream genes such as OsINO80 and OsJAZ10. MNAC3 interacts with immunity-related OsPP2C41 (a protein phosphatase), ONAC066 (a NAC TF), and OsDjA6 (a DnaJ chaperone). ONAC066 and OsPP2C41 attenuate MNAC3 transcriptional activity, while OsDjA6 promotes it. Phosphorylation of MNAC3 at S163 is critical for its negative functions in rice immunity. OsPP2C41, which plays positive roles in rice blast resistance and chitin-triggered immune responses, dephosphorylates MNAC3, suppressing its transcriptional activity on the target genes OsINO80, OsJAZ10, and OsJAZ11 and promoting the translocation of MNAC3 from nucleus to cytoplasm. These results establish a MNAC3-centered regulatory network in which OsPP2C41 dephosphorylates MNAC3, attenuating its transcriptional activity on downstream immune-negative target genes in rice. Together, these findings deepen our understanding of molecular mechanisms in rice immunity and offer a novel strategy for genetic improvement of rice disease resistance.
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    PE6c greatly enhances prime editing in transgenic rice plants
    Zhenghong Cao, Wei Sun, Dexin Qiao, Junya Wang, Siyun Li, Xiaohan Liu, Cuiping Xin, Yu Lu, Syeda Leeda Gul, Xue-Chen Wang, Qi-Jun Chen
    J Integr Plant Biol 2024, 66 (9): 1864-1870.  
    doi: 10.1111/jipb.13738
    Abstract (Browse 95)  |   Save
    Prime editing is a versatile CRISPR/Cas-based precise genome-editing technique for crop breeding. Four new types of prime editors (PEs) named PE6a–d were recently generated using evolved and engineered reverse transcriptase (RT) variants from three different sources. In this study, we tested the editing efficiencies of four PE6 variants and two additional PE6 constructs with double-RT modules in transgenic rice (Oryza sativa) plants. PE6c, with an evolved and engineered RT variant from the yeast Tf1 retrotransposon, yielded the highest prime-editing efficiency. The average fold change in the editing efficiency of PE6c compared with PEmax exceeded 3.5 across 18 agronomically important target sites from 15 genes. We also demonstrated the feasibility of using two RT modules to improve prime-editing efficiency. Our results suggest that PE6c or its derivatives would be an excellent choice for prime editing in monocot plants. In addition, our findings have laid a foundation for prime-editing-based breeding of rice varieties with enhanced agronomically important traits.
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    The actin motor protein OsMYA1 associates with OsExo70H1 and contributes to rice secretory defense by modulating OsSyp121 distribution
    Yuan‐Bao Li, Chengyu Liu, Ningning Shen, Shuai Zhu, Xianya Deng, Zixuan Liu, Li‐Bo Han and Dingzhong Tang
    J Integr Plant Biol 2024, 66 (9): 2058-2075.  
    DOI: 10.1111/jipb.13744
    Abstract (Browse 99)  |   Save
    Magnaporthe oryzae (M. oryzae) is a devastating hemibiotrophic pathogen. Its biotrophic invasive hyphae (IH) are enclosed in the extrainvasive hyphal membrane produced by plant cells, thus generating a front line of the battlefield between the pathogen and the host plants. In plants, defense-related complexes such as proteins, callose-rich materials and vesicles, are directionally secreted to this interface to confer defense responses, but the underlying molecular mechanism is poorly understood. In this study, we found that a Myosin gene, Myosin A1 (OsMYA1), contributed to rice defense. The OsMYA1 knockout mutant exhibited decreased resistance to M. oryzae infection. OsMYA1 localizes to the actin cytoskeleton and surrounds the IH of M. oryzae. OsMYA1 interacts with an exocyst subunit, OsExo70H1, and regulates its accumulation at the plasma membrane (PM) and pathogen–plant interface. Furthermore, OsExo70H1 interacted with the rice syntaxin of the plants121 protein (OsSyp121), and the distribution of OsSyp121 to the PM or the pathogen–plant interface was disrupted in both the OsMYA1 and OsExo70H1 mutants. Overall, these results not only reveal a new function of OsMYA1 in rice blast resistance, but also uncover a molecular mechanism by which plants regulate defense against M. oryzae by OsMYA1-initiated vesicle secretory pathway, which originates from the actin cytoskeleton to the PM.
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    A QTL GN1.1, encoding FT-L1, regulates grain number and yield by modulating polar auxin transport in rice
    Huai-Yu Zhao, Jun-Xiang Shan, Wang-Wei Ye, Nai-Qian Dong, Yi Kan, Yi-Bing Yang, Hong-Xiao Yu, Zi-Qi Lu, Shuang-Qin Guo, Jie-Jie Lei, Ben Liao, Hong-Xuan Lin
    J Integr Plant Biol 2024, 66 (10): 2158-2174.  
    DOI: 10.1111/jipb.13749
    Abstract (Browse 92)  |   Save
    Rice grain number is a crucial agronomic trait impacting yield. In this study, we characterized a quantitative trait locus (QTL), GRAIN NUMBER 1.1 (GN1.1), which encodes a Flowering Locus T-like1 (FT-L1) protein and acts as a negative regulator of grain number in rice. The elite allele GN1.1B, derived from the Oryza indica variety, BF3-104, exhibits a 14.6% increase in grain yield compared with the O. japonica variety, Nipponbare, based on plot yield tests. We demonstrated that GN1.1 interacted with and enhanced the stability of ADP-ribosylation factor (Arf)-GTPase-activating protein (Gap), OsZAC. Loss of function of OsZAC results in increased grain number. Based on our data, we propose that GN1.1B facilitates the elevation of auxin content in young rice panicles by affecting polar auxin transport (PAT) through interaction with OsZAC. Our study unveils the pivotal role of the GN1.1 locus in rice panicle development and presents a novel, promising allele for enhancing rice grain yield through genetic improvement.
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    The OsAGO2–OsNAC300OsNAP module regulates leaf senescence in rice
    Shaoyan Zheng, Junyu Chen, Ying He, Jingqin Lu, Hong Chen, Zipeng Liang, Junqi Zhang, Zhenlan Liu, Jing Li, Chuxiong Zhuang
    J Integr Plant Biol 2024, 66 (11): 2395-2411.  
    doi: 10.1111/jipb.13766
    Abstract (Browse 101)  |   Save
    Leaves play a crucial role in the growth and development of rice (Oryza sativa) as sites for the production of photosynthesis. Early leaf senescence leads to substantial drops in rice yields. Whether and how DNA methylation regulates gene expression and affects leaf senescence remains elusive. Here, we demonstrate that mutations in rice ARGONAUTE 2 (OsAGO2) lead to premature leaf senescence, with chloroplasts in Osago2 having lower chlorophyll content and an abnormal thylakoid structure compared with those from wild-type plants. We show that OsAGO2 associates with a 24-nt microRNA and binds to the promoter region of OsNAC300, which causes DNA methylation and suppressed expression of OsNAC300. Overexpressing OsNAC300 causes the similar premature leaf senescence as Osago2 mutants and knocking out OsNAC300 in the Osago2 mutant background suppresses the early senescence of Osago2 mutants. Based on yeast one-hybrid, dual-luciferase, and electrophoresis mobility shift assays, we propose that OsNAC300 directly regulates transcription of the key rice aging gene NAC-like, activated by APETALA3/PISTILLATA (OsNAP) to control leaf senescence. Our results unravel a previously unknown epigenetic regulatory mechanism underlying leaf senescence in which OsAGO2–OsNAC300–OsNAP acts as a key regulatory module of leaf senescence to maintain leaf function.
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    OsFAD1OsMYBR22 modulates clustered spikelet through regulating BRD3 in rice
    Mingxing Cheng, Huanran Yuan, Ruihua Wang, Fengfeng Fan, Fengfeng Si, Xiong Luo, Wei Liu, Shaoqing Li
    J Integr Plant Biol 2024, 66 (11): 2325-2328.  
    DOI: 10.1111/jipb.13775
    Abstract (Browse 105)  |   Save
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