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Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo xianzhi xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Institute of Wetland Agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

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稻田甲烷产生与排放的影响因素及减排措施研究进展

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中国水稻科学 2024年第5期38卷 475-494页

作者：谢先芝刘奇华李新华李维平山东省农业科学院湿地农业与生态研究所济南250100 山东省公共资源交易中心济南250000

稻田甲烷(CH_(4))排放是农业生产中主要碳排放源之一。如何在保证丰产的前提下,有效降低水稻生产中CH_(4)的排放量成为现代农业科研工作者研究的焦点。围绕稻田CH_(4)的产生、排放与减排方式,本文综述了目前稻田CH_(4)产排的相关研究进... 详细信息

稻田甲烷(CH_(4))排放是农业生产中主要碳排放源之一。如何在保证丰产的前提下,有效降低水稻生产中CH_(4)的排放量成为现代农业科研工作者研究的焦点。围绕稻田CH_(4)的产生、排放与减排方式,本文综述了目前稻田CH_(4)产排的相关研究进展,阐述了稻田CH_(4)的产生、氧化过程、排放方式及其主要影响因素。稻田甲烷的产生排放与土壤理化性状(pH值、关键酶活性、含水量、温度、氧化还原程度、质地等)、水稻品种(根系形态活力与分泌物、通气组织、收获指数、株高等)、栽培技术(轮作模式、水肥调控、种植方式)、气候变化(气温、大气CO_(2)浓度、UV-B辐射)等因素密切相关。本文重点从选育高产低排新品种、研发稻田CH_(4)减排新物质、稻-渔低碳循环种养、土壤持续固碳减排、多种栽培调控方式耦合的新技术等方面入手,系统总结了稻田CH_(4)减排的技术措施,提出应根据不同稻区的生产特点,因地制宜,探索建立稻田CH_(4)减排高效综合技术体系。在此基础上,讨论了未来重点研究方向,以期为水稻丰产减排生产提供技术支撑,为顺利实现国家“双碳”目标提供有益参考。

关键词：稻田甲烷排放减排措施

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Priming for Saline-Alkaline Tolerance in Rice:Current Knowledge and Future Challenges

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Rice science 2023年第5期30卷 417-425页

作者： JIANG Changjie LIANG Zhengwei xie xianzhi Rice Research Institute Shandong Academy of Agricultural SciencesJinan 250100China Northeast Institute of Geography and Agroecology Chinese Academy of SciencesChangchun 130102China

Soil salinization and/or alkalization is a major constraint to crop production *** 60% of the cultivated land is affected by salt,over half of which is *** soils are characterized by high alkalinity and typically high salinity,which creates a complex saline-alkaline(SA) stress that affects plant *** cultivation has been accepted as an important strategy for effective utilization of SA land if water is available for ***,as a salt-sensitive plant,rice plants suffer severe SA-induced damage,which results in poor plant growth and grain *** approaches have been employed to improve rice productivity in SA *** them,the priming technique has emerged as a powerful method for enhancing SA tolerance in rice *** this review,we summarized how SA stress damages rice plants,and then presented how priming treatment can mitigate such damage.

关键词： saline-alkaline stress plant hormone abscisic acid reactive oxygen species antioxidant stress tolerance

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Introns in higher plant genes

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Chinese Science Bulletin 2002年第17期47卷 1409-1415页

作者： xianzhi xie Naihu Wu Chinese Acad Sci Inst Genet & Dev Biol Beijing 100080 Peoples R China

The intron is an important component of eu-karyotic gene. Extensive studies have been conducted to get a better understanding of its structure and function. This paper presents a brief review of the structure and function of introns in higher plant genes. It is shown that higher plant introns possess structural properties shared by all eukaryotic introns, however, they also exhibit a striking degree of diversity. The process of intron splicing in higher plant genes involves interaction between multiple cis -acting elements and trans-acting factors, such as 5’ splicing site, 3’ splicing site and many protein factors. The process of intron splicing is an important level at which gene expression is regulated. Especially alternative splicing of intron can regulate time and space of gene expression. In addition, some introns in higher plant genes also regulate gene expression by affecting the pattern of gene expression, enhancing the level of gene expression and driving the gene expression.

关键词： intron pre-mRNA splicing expression and regulation of genes.

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拟南芥光敏色素B氨基酸位点突变对其结构与功能的影响

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植物学报 2024年第3期59卷 481-494页

作者：陈艳晓李亚萍周晋军解丽霞彭永彬孙伟和亚男蒋聪慧王增兰郑崇珂谢先芝山东师范大学生命科学学院济南250014 山东省农业科学院湿地农业与生态研究所济南250100 山东省农业科学院农作物种质资源研究所济南250100

生物体为适应外界不断变化的光环境,进化出不同的光受体,其中光敏色素是一类经典的植物感受红光和远红光的受体蛋白,其通过暗适应的Pr状态和光激活的Pfr状态之间的光转换来检测红光和远红光。植物光敏色素具有1个保守的N端感光区域和1个... 详细信息

生物体为适应外界不断变化的光环境,进化出不同的光受体,其中光敏色素是一类经典的植物感受红光和远红光的受体蛋白,其通过暗适应的Pr状态和光激活的Pfr状态之间的光转换来检测红光和远红光。植物光敏色素具有1个保守的N端感光区域和1个C端调节区域,其中N端部分包括NTE、PAS、GAF和PHY亚结构域, C端部分包括2个PAS结构域和1个组氨酸激酶相关结构域(HKRD)。为深入了解光敏色素的结构及功能,已获得许多光敏色素功能缺失或氨基酸位点突变体,并对其进行功能研究,发现N端结构域在光敏色素的光谱特性、光信号感知和光信号转导等方面均具有重要作用;而C端结构域是光敏色素的二聚化与核定位所必需。该文综述了拟南芥(Arabidopsis thaliana)中光敏色素B (phyB)各亚结构域中氨基酸位点突变对其功能的影响,以期深入理解phyB的结构及功能,为未来通过基因编辑手段进行作物农艺性状的遗传改良奠定基础。

关键词：光敏色素B 拟南芥结构域氨基酸位点突变功能

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OsSRK1,an Atypical S-Receptor-Like Kinase Positively Regulates Leaf Width and Salt Tolerance in Rice

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Rice science 2020年第2期27卷 133-142页

作者： ZHOU Jinjun JU Peina ZHANG Fang ZHENG Chongke BAI Bo LI Yaping WANG Haifeng CHEN Fan xie xianzhi Shandong Rice Research Institute Shandong Academy of Agricultural SciencesJinan 250100China Institute of Genetics and Development Biology the Chinese Academy of ScienceBeijing 100190China Shangdong Normal University Jinan 250014China

Receptor-like kinases(RLKs)are important for plant growth,development and defense *** S-receptor protein kinases(SRKs),which represent an RLK subfamily,control the selfincompatibility among Brassica ***,little information is available regarding SRK functions in *** identified a gene OsSRK1 encoding an atypical *** transcript of OsSRK1 was induced by abscisic acid(ABA),salt and polyethylene ***1 localized to the plasma membrane and *** width was increased in OsSRK1-overexpression(OsSRK1-OX)transgenic rice plants,likely because of an increase in cell number per ***,the expression levels of OsCYCA3-1 and OsCYCD2-1,which encode positive regulators of cell division,were up-regulated in leaf primordium of OsSRK1-OX rice plants relative to those in wild ***,the expression level of OsKRP1,which encodes cell cycle inhibitor,was down-regulated in the OsSRK1-OX ***,it is deduced that OsSRK1 regulates leaf width by promoting cell division in the leaf ***,OsSRK1-OX plants exhibited enhanced ABA sensitivity and salt tolerance compared with wild *** results suggest that OsSRK1 plays important roles in leaf development and salt responses in rice.

关键词： rice S-receptor-like protein kinase OsSRK1 salt tolerance leaf width cell division

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RNAi-mediated suppression of the abscisic acid catabolism gene Os ABA8ox1 increases abscisic acid content and tolerance to saline–alkaline stress in rice(Oryza sativa L.)

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The Crop Journal 2022年第2期10卷 354-367页

作者： Xiaolong Liu xianzhi xie Chongke Zheng Lixing Wei Xiaowei Li Yangyang Jin Guohui Zhang Chang-Jie Jiang Zhengwei Liang Northeast Institute of Geography and Agroecology Chinese Academy of SciencesChangchun 130102JilinChina Shandong Rice Research Institute Shandong Academy of Agricultural SciencesJinan 250100ShandongChina College of Life Science and Resources and Environment Yichun UniversityYichun 336000JiangxiChina Da’an Sodic Land Experiment Station Da’an 131317JilinChina Dongying Academy of Agricultural Sciences Dongying 257091ShandongChina College of Life Sciences Engineering Research Center of the Chinese Ministry of Education for Bioreactor and Pharmaceutical DevelopmentJilin Agricultural UniversityChangchun 130118JilinChina Institute of Agrobiological Sciences NAROKannondai 2-1-2Tsukuba 305-8602Japan

Saline–alkaline(SA) stress is characterized by high salinity and high alkalinity(high p H), which severely inhibit plant growth and cause huge losses in crop yields worldwide. Here we show that a moderate elevation of endogenous abscisic acid(ABA) levels by RNAi-mediated suppression of Os ABA8 ox1(Os ABA8 ox1-kd), a key ABA catabolic gene, significantly increased tolerance to SA stress in rice plants. We produced Os ABA8 ox1-kd lines in two different japonica cultivars, Dongdao 4 and Nipponbare. Compared with nontransgenic control plants(WT), the Os ABA8 ox1-kd seedlings accumulated 25.9%–55.7% higher levels of endogenous ABA and exhibited reduced plasmalemma injury, ROS accumulation and Na;/K;ratio, and higher survival rates, under hydroponic alkaline conditions simulated by 10, 15, and 20 mmol L-1 of Na;CO;. In pot trials using SA field soils of different alkali levels(p H 7.59, 8.86, and 9.29), Os ABA8 ox1–kd plants showed markedly higher seedling survival rates and more vigorous plant growth, resulting in significantly higher yield components including panicle number(85.7%–128.6%), spikelets per panicle(36.9%–61.9%), branches(153.9%–236.7%), 1000–kernel weight(20.0%–28.6%), and percentage of filled spikelets(96.6%–1340.8%) at harvest time. Under severe SA soil conditions(p H = 9.29, EC = 834.4 μS cm-1),Os ABA8 ox1-kd lines showed an 194.5%–1090.8% increase in grain yield per plant relative to WT *** results suggest that suppression of Os ABA8 ox1 to increase endogenous ABA levels provides a new molecular approach for improving rice yield in SA paddies.

关键词： Rice(Oryza sativa L.) Saline–alkaline stress Abscisic acid(ABA) OsABA8ox1-kd Endogenous ABA levels

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Overexpression of OsPIL15, a phytochrome-interacting factor-like protein gene, represses etiolated seedling growth in rice

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Journal of Integrative Plant Biology 2014年第4期56卷 373-387页

作者： Jinjun Zhou Qianqian Liu Fang Zhang Yingying Wang Shiyong Zhang Huimin Cheng Lihua Yan Li Li Fan Chen xianzhi xie Shandong Rice Research Institute Shandong Academy of Agricultural Sciences Shandong Provincial Key Laboratory of Crop Genetic Improvement Ecology and Physiology College of Life Sciences Shandong Normal University Institute of Genetics and Developmental Biology the Chinese Academy of Sciences

Phytochrome-interacting factors （PIFs） regulate an array of developmental responses ranging from seed germi- nation to vegetational architecture in Arabidopsis. However, information regarding the functions of the PIF family in monocots has not been widely reported. Here, we investigate the roles of OsPIL15, a member of the rice （Oryza sativa L. cv. Nipponbare） PIF family, in regulating seedling growth. OsPIL15 encodes a basic helix-loop-helix factor localized in the nucleus. OsPIL15-OX seedlings exhibit an exaggerated shorter above- ground part and undeveloped root system relative to wild-type seedlings, suggesting that OsPIL15 represses seedling growth in the dark. Microarray analysis combined with gene ontology analysis revealed that OsPIL15 represses a set of genes involved in auxin pathways and cell wall organization or biogenesis. Given the important roles of the auxin pathway and cell wall properties in controlling plant growth, we speculate that OsPIL15 represses seedling growth likely by regulating the auxin pathway and suppressing cell wall organization in etiolated rice seedlings. Additionally, exposure to red light or far-red light relieved growth retardation and promoted seedling elongation in the OsPIL15-OX lines, despite higher levels of OsPIL15 transcripts under red light and far-red light than in the dark. These results suggest that light regulation of OsPIL15 expres- sion is probably involved in photomorphogenesis in rice.

关键词： Auxin cell wall etiolated seedling rice photomorpho-genesis phytochrome-interacting factor

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表型组学在水稻研究中的应用

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中国水稻科学 2020年第4期34卷 300-306页

作者：彭永彬谢先芝山东省水稻研究所济南250100

水稻作为重要粮食作物,其重要农艺性状的功能基因组研究是植物生物学研究的热点。植物基因型、表型和环境三者构成了遗传学研究的铁三角。随着高通量测序技术的快速发展,基因型的研究更加简单快速。然而表型研究严重滞后于基因型研究。... 详细信息

水稻作为重要粮食作物,其重要农艺性状的功能基因组研究是植物生物学研究的热点。植物基因型、表型和环境三者构成了遗传学研究的铁三角。随着高通量测序技术的快速发展,基因型的研究更加简单快速。然而表型研究严重滞后于基因型研究。目前传统的表型信息的获取存在所需劳动量巨大、成本高,所获取表型数据受人工主观因素影响大等诸多难题。高通量表型组学可无损、高通量、精准获取表型信息,对解决以上难题具有关键作用。本文对表型组学在水稻中的研究应用情况进行整理,为今后水稻基因组学和表型组学等多学科相结合的现代研究手段提供理论支撑。

关键词：水稻表型组学农艺性状基因组学

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Transcriptome analysis reveals immune-related genes in tissues of Vibrio anguillarum-infected turbot Scophthalmus maximus

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Journal of Oceanology and Limnology 2024年第1期42卷 332-344页

作者： Yuting SONG Maqsood Ahmed SOOMRO xianzhi DONG Guobin HU College of Marine Life Sciences Ocean University of ChinaQingdao 266003China Institute of Evolution&Marine Biodiversity Ocean University of ChinaQingdao 266003China Institute of Biophysis Chinese Academy of SciencesBeijing 100101China

Turbot Scophthalmus maximus is an important mariculture fish species with high economic ***,the bacterial diseases caused by Vibrio anguillarum infection bring huge economic losses to the turbot aquaculture *** understand the immune response of the turbot against *** infection and to explore novel immune-related genes,the transcriptome analysis of turbot spleen and gills were conducted after *** *** expressed genes(DEGs)were identified in spleen and gill of the turbot amounted to 17261 and 16436,respectively.A large number of immunerelated DEGs were enriched in cytokine-cytokine receptor interaction signaling pathway,and the others by the kyoto encyclopedia of genes and genomes(KEGG)*** gene ontology(GO)classification analysis revealed that *** infection had the greatest effect on biological processes and cellular *** immune-related DEGs were identified in the spleen(cstl.1,egfl6,lamb21,v2rx4,calcr,and gpr78a)and gills(ghra,sh3gl2a,cst12,inhbaa,cxcl8,and il-1b)by heat *** proteinprotein interaction(PPI)networks were constructed to analyze the immune *** results demonstrate that the maturation and antigen processing of major histocompatibility complex(MHC)class II molecule,and calcitonin-or adrenomedullin-regulated physiological activity were important events in the immunity of turbot against *** *** the gills,the protein interactions in TGF-βsignaling pathway,production of inflammatory factors,and endocytosis regulation were most *** research laid a foundation for discovering novel immune-related genes and enriching the knowledge of immune mechanisms of turbot against *** infection.

关键词： Scophthalmus maximus Vibrio anguillarum transcriptome differentially expressed genes immune mechanism

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