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Seed Storability in rice: Physiological Foundations, Molecular Mechanisms, and Applications in Breeding

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rice science 2024年第4期31卷 401-416,I0023-I0024页

作者： ZHOU Tianshun YU Dong WU Liubing XU Yusheng DUAN Meijuan YUAN Dingyang Longping Branch College of BiologyHunan UniversityChangsha 410125China state key laboratory of hybrid rice Hunan Hybrid Rice Research CenterHunan Academy of Agricultural SciencesChangsha 410125China Hunan Provincial key laboratory of rice Stress Biology College of AgronomyHunan Agricultural UniversityChangsha 410128China

Long-term storage of crop seeds is critical for the conservation of germplasm resources, ensuring food supply, and supporting sustainable production. rice, as a major food staple, has a substantial stock for consumption and production worldwide. However, its food value and seed viability tend to decline during storage. Understanding the physiological responses and molecular mechanisms of aging tolerance forms the basis for enhancing seed storability in rice. This review outlines the latest progress in influential factors, evaluation methods, and identification indices of seed storability. It also discusses the physiological consequences, molecular mechanisms, and strategies for breeding aging-tolerant rice in detail. Finally, it highlights challenges in seed storability research that require future attention. This review offers a theoretical foundation and research direction for uncovering the mechanisms behind seed storability and breeding aging-tolerant rice.

关键词： rice seed storability physiological response molecular mechanism aging-tolerant breeding

RNAirport:a deep neural network-based database characterizing representative gene models inplants

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Journal of Genetics and Genomics 2024年第6期51卷 652-664页

作者： Sitao Zhu Shu Yuan Ruixia Niu Yulu Zhou Zhao Wang Guoyong Xu state key laboratory of hybrid rice Institute for Advanced Studies(IAS)Wuhan UniversityWuhanHubei 430072China Hubei Hongshan laboratory WuhanHubei 430070China

A 5'-leader,known initially as the 5'-untranslated region,contains multiple isoforms due to alternative splicing(aS)and alternative transcription start site(aTSS).Therefore,a representative 5'-leader is demanded to examine the embedded RNA regulatory elements in controlling translation ***,we develop a ranking algorithm and a deep-learning model to annotate representative 5'-leaders for five plant *** rank the intra-sample and inter-sample frequency of aS-mediated transcript isoforms using the Kruskal-Wallis test-based algorithm and identify the representative aS-5'-*** further assign a representative 5'-end,we train the deep-learning model 5'leaderP to learn aTsS-mediated 5'-end distribution patterns from cap-analysis gene expression *** model accurately predicts the 5'-end,confirmed experimentally in Arabidopsis and *** representative 5'-leader-contained gene models and 5'leaderP can be accessed at RNAirport(http:/***/leader5P/).The Stage 1 annotation of 5'-leader records 5'-leader diversity and will pave the way to Ribo-Seq open-reading frame annotation,identical to the project recently initiated by human GENCODE.

关键词： 5'-leader Transcript isoforms RNA regulatory elements UORF Deep learning Synthetic biology Translational control

Translation machinery: the basis of translational control

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Journal of Genetics and Genomics 2024年第4期51卷 367-378页

作者： Shu Yuan Guilong Zhou Guoyong Xu state key laboratory of hybrid rice Institute for Advanced Studies(IAS)Wuhan UniversityWuhanHubei 430072China Hubei Hongshan laboratory WuhanHubei 430070China

Messenger RNA(mRNA)translation consists of initiation,elongation,termination,and ribosome recycling,carried out by the translation machinery,primarily including tRNAs,ribosomes,and translation factors(TrFs).Translational regulators transduce signals of growth and development,as well as biotic and abiotic stresses,to the translation machinery,where global or selective translational control occurs to modulate mRNA translation efficiency(TrE).As the basis of translational control,the translation machinery directly determines the quality and quantity of newly synthesized peptides and,ultimately,the cellular ***,regulating the availability of diverse machinery components is reviewed as the central strategy of translational *** provide classical signaling pathways(e.g.,integrated stress responses)and cellular behaviors(e.g.,liquideliquid phase separation)to exemplify this strategy within different physiological contexts,particularly during hostemicrobe *** new technologies developed,further understanding this strategy will speed up translational medicine and translational agriculture.

关键词： Translational control Ribosome tRNA Translation machinery uORF Phase separation Immune response

Single-cell transcriptome sequencing reveals the mechanism regulating rice plumule development

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The Crop Journal 2024年第3期12卷 688-697页

作者： Mingdong Zhu Meng Zhang Kunyong Huang Feifei Lu Hong Wang Shaolu Zhao Yinghong Yu Shaoqing Tang Haining Wu Peisong Hu Xiangjin Wei state key laboratory of rice Biology and Breeding China National Center for Rice ImprovementChina National Rice Research InstituteHangzhou 310006ZhejiangChina b state key laboratory of hybrid rice Hunan Rice Research InstituteHunan Academy of Agricultural SciencesChangsha 410125HunanChina Hunan Provincial key laboratory of Plant Functional Genomics and Developmental Regulation College of BiologyHunan UniversityChangsha 410082HunanChina Hubei University Wuhan 430062HubeiChina

Seed plumules comprise multiple developing tissues and are key sites for above-ground plant organ ***,the spatial expression of genes in developing rice seed plumules was characterized by single-cell transcriptome sequencing in Zhongjiazao 17,a popular Chinese indica rice *** 15 cell clusters,13 were assigned to cell types using marker genes and cluster-specific *** genes of multiple cell types were expressed in several clusters,suggesting a complex developmental *** genes for signaling by phytohormones such as abscisic acid were highly expressed in specific *** cis-elements in the promoters of genes specifically expressed in cell clusters were calculated,and some key hormone-related motifs were frequent in certain *** expression patterns of genes involved in rapid seed germination,seedling growth,and development were *** findings enhanced our understanding of cellular diversity and specialization within plumules of rice,a monocotyledonous model crop.

关键词： rice Plumule Single-cell sequencing Regulatory network

A bacterial protein Rhp-PSP inhibits plant viral proliferation through endoribonuclease activity

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Journal of Integrative Agriculture 2024年第6期23卷 1967-1978页

作者： Lijie Chen Qianze Peng Xiaohua Du Weixing Zhang Ju’e Cheng Shu’e Sun Deyong Zhang Pin Su Yong Liu Longping Branch College of BiologyHunan UniversityChangsha 410082China state key laboratory of hybrid rice/Institute of Plant Protection Hunan Academy of Agricultural SciencesChangsha 410125China

Plant virus causes massive crop losses ***,there is currently no effective measure to control plant viral ***,we identify an antiviral protein Rhp-PSP,produced by the bacterial Rhodopseudomonas palustris strain *** this study,we discover that the antiviral activity of Rhp-PSP relies on its endoribonuclease *** the arginine(R)residue at position 129 onto alanine(A)abolishs its endoribonuclease activity on coat protein(CP)RNA of tobacco mosaic virus(TMV),consequentially,compromises the antiviral activity of *** investigation demonstrates that,the mutant Rhp-PSP^(R129A)is unable to form the homotrimer as the wild type,indicating the importance of quaternary junction for the endoribonuclease *** of Rhp-PSP in Nicotiana benthamiana significantly enhances the resistance against TMV of seedlings,while expression of Rhp-PSP^(R129A)did not,confirming that endoribonuclease activity is responsible for the antiviral activity of *** addition,foliar spray of Rhp-PSP solution on tomato and pepper plants significantly reduces the disease index of viral diseases,indicating that Rhp-PSP shows potential to develop antiviral agent in practice.

关键词： Rhodopseudomonas palustris Rhp-PSP tobacco mosaic virus endoribonuclease antiviral activity

Genetic analysis and fine mapping of a grain size QTL in the smallgrain sterile rice line Zhuo201S

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Journal of Integrative Agriculture 2024年第7期23卷 2155-2163页

作者： Bin Lei Jiale Shao Feng Zhang Jian Wang Yunhua Xiao Zhijun Cheng Wenbang Tang Jianmin Wan College of Agronomy Hunan Agricultural UniversityChangsha 410128China National key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijing 100081China state key laboratory for Crop Genetics and Germplasm Enhancement/Jiangsu Plant Gene Engineering Research Center Nanjing Agricultural UniversityNanjing 210095China state key laboratory of hybrid rice Hunan Hybrid Rice Research CenterChangsha 410125China

The development and application of the small-grain rice sterile line Zhuo201S(Z201S)has demonstrated its potential for mechanized hybrid rice seed production,leading to significant cost ***,the molecular mechanism responsible for the small-grain size characteristic of Z201S remains *** this study,we conducted a genetic analysis using near-isogenic lines constructed from Z210S,a small-grain rice sterile line,and R2115,a normal-grain *** results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain *** mapping,we localized the causal gene to the short arm of chromosome 2,within a 113 kb physical region delimited by the molecular markers S2-4-1 and *** analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene,suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.

关键词： rice grain size map-based cloning

Carbon Catabolite Repressor UvCreA is Required for Development and Pathogenicity in Ustilaginoidea virens

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rice science 2024年第2期31卷 203-214,I0029-I0031页

作者： XIE Shuwei SHI Huanbin WEN Hui LIU Zhiquan QIU Jiehua JIANG Nan KOU Yanjun state key laboratory of rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China

The rice false smut disease, caused by Ustilaginoidea virens, has emerged as a significantglobal threat to rice production. The mechanism of carbon catabolite repression plays a crucial role in theefficient utilization of carbon nutrients and enzyme regulation in the presence of complex nutritionalconditions. Although significant progress has been made in understanding carbon catabolite repression infungi such as Aspergillus nidulans and Magnaporthe oryzae, its role in U. virens remains unclear. Toaddress this knowledge gap, we identified UvCreA, a pivotal component of carbon catabolite repression,in U. virens. Our investigation revealed that UvCreA localized to the nucleus. Deletion of UvCreA resultedin decreased growth and pathogenicity in U. virens. Through RNA-seq analysis, it was found that theknockout of UvCreA led to the up-regulation of 514 genes and down-regulation of 640 genes. Moreover,UvCreA was found to be involved in the transcriptional regulation of pathogenic genes and genesassociated with carbon metabolism in U. virens. In summary, our findings indicated that UvCreA isimportant in fungal development, virulence, and the utilization of carbon sources through transcriptionalregulation, thus making it a critical element of carbon catabolite repression.

关键词： Ustilaginoidea virens virulence carbon catabolite repression Oryza sativa rice false smut

Gapless Genome Assembly of ZH8015 and Preliminary Multi-Omics Analysis to Investigate ZH8015's Responses Against Brown Planthopper Infestation

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rice science 2024年第3期31卷 317-327,I0042-I0045页

作者： LI Dian DUAN Wenjing LIU Qun’en WU Weixun ZHAN Xiaodeng SUN Lianping ZHANG Yingxin CHENG Shihua state key laboratory of rice Biology and Breeding China National Rice Research InstituteHangzhou 310006China

Accurate genomic information is essential for advancing genetic breeding research in specific rice *** study presented a gapless genome assembly of the indica rice cultivar Zhonghui 8015(ZH8015)using Pac Bio HiFi,Hi-C,and ONT(Oxford Nanopore Technologies)ultra-long sequencing technologies,annotating 43037 gene ***,utilizing this genome along with transcriptomic and metabolomic techniques,we explored ZH8015's response to brown planthopper(BPH)*** transcriptomic sampling indicated significant changes in gene expression levels around 48 h after BPH *** analysis revealed particularly significant alterations in genes related to reactive oxygen species scavenging and cell wall *** results demonstrated marked increases in levels of several monosaccharides,which are components of the cell wall and dramatic changes in flavonoid *** association analysis identified differentially expressed genes associated with key metabolites,shedding light on ZH8015's response to BPH *** summary,this study constructed a reliable genome sequence resource for ZH8015,and the preliminary multi-omics results will guide future insect-resistant breeding research.

关键词： brown planthopper gapless genome genome assembly multi-omics Nilaparvata lugens rice

Carotenoid isomerase regulates rice tillering and grain productivity by its biosynthesis pathway

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Journal of Integrative Plant Biology 2024年第2期66卷 172-175页

作者： Chaoqing Ding Zhengji Shao Yuping Yan Guangheng Zhang Dali Zeng Li Zhu Jiang Hu Zhenyu Gao Guojun Dong Qian Qian Deyong Ren state key laboratory of rice Biology and Breeding ChinaNational Rice Research InstituteHangzhou 310006China

Tillers are unique inflorescence-like branches in grasses,and their number determines the panicle number,plant architecture,and yield(Shang et al.,2021).Tiller formation mainly undergoes axillary meristem(AM)initiation and tiller bud outgrowth(Wang et al.,2018;Yan et al.,2023).The rice(Oryza sativa)KNOX gene OSH1 is expressed in AMs,and an osh1 mutant produces fewer tillers(Tanaka et al.,2015).

关键词： sativa Oryza panicle