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BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

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Journal of Integrative Plant Biology 2024年第9期66卷 1966-1982页

作者： Zhen Li Junhua Ye Qiaoling Yuan Mengchen Zhang Xingyu Wang Jing Wang Tianyi Wang hongge qian Xinghua Wei Yaolong Yang Lianguang Shang Yue Feng China National Center for Rice Improvement State Key Laboratory of Rice Biology and BreedingChina National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518124China National Nanfan Research Institute(Sanya) Chinese Academy of Agricultural SciencesSanya 572024China

Tiller angle is a key agricultural trait that establishes plant architecture,which in turn strongly affects grain yield by influencing planting density in *** shoot gravity response plays a crucial role in the regulation of tiller angle in rice,but the underlying molecular mechanism is largely ***,we report the identification of the BIG TILLER ANGLE2(BTA2),which regulates tiller angle by controlling the shoot gravity response in ***-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 ***2 interacted with AUXIN RESPONSE FACTOR7(ARF7)to modulate rice tiller angle through the gravity signaling *** BTA2 protein was highly conserved during *** 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 *** of BTA2 significantly increased grain yield in the elite rice cultivar Huanghuazhan under appropriate dense planting *** findings thus uncovered the BTA2-ARF7 module that regulates tiller angle by mediating the shoot gravity *** work offers a target for genetic manipulation of plant architecture and valuable information for crop improvement by producing the ideal plant type.

关键词： auxin domestication gravity response rice tiller angle

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BTA2 regulates tiller angle and the shoot gravity response through controlling auxin content and distribution in rice

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Journal of Integrative Plant Biology 2024年第09期 1966-1982页

作者： Zhen Li Junhua Ye Qiaoling Yuan Mengchen Zhang Xingyu Wang Jing Wang Tianyi Wang hongge qian Xinghua Wei Yaolong Yang Lianguang Shang Yue Feng China National Center for Rice Improvement State Key Laboratory of Rice Biology and Breeding China National Rice Research Institute Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences National Nanfan Research Institute (Sanya) Chinese Academy of Agricultural Sciences

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. BTA2interacted 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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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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A centromere map based on super pan-genome highlights the structure and function of rice centromeres

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Journal of Integrative Plant Biology 2024年第2期66卷 196-207页

作者： 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 Lianguang Shang State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China 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 SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya City 572024China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Rice(Oryza sativa)is a significant crop worldwide with a genome shaped by various evolutionary *** centromeres are crucial for chromosome segregation,and contain some unreported *** to the diverse and complex centromere region,a comprehensive understanding of rice centromere structure and function at the population level is *** constructed a high-quality centromere map based on the rice super pangenome consisting of a 251-accession panel comprising both cultivated and wild species of Asian and African *** showed that rice centromeres have diverse satellite repeat CentO,which vary across chromosomes and subpopulations,reflecting their distinct evolutionary *** 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 ***,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 *** 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 protein9 *** 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.

关键词： centromere super pan-genome CentoO satellite repeat rice

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基因组倒位变异参与塑造了水稻遗传和表型的多样性

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Science Bulletin 2024年第5期69卷 593-596页

作者：贺文闯贺慧英袁巧玲张海李笑霞王天依杨映雪杨龙波杨玉亭刘相培魏华张泓张斌郭明亮冷月施传琳吕阳陈武汪贤猛张志鹏于博汇张彬涛许强钱宏革周永锋王少奎钱前商连光 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 SciencesShenzhen 518120China School of Life Sciences Xiamen UniversityXiamen 361005China State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Provincial Key Laboratory of Plant Molecular BreedingSouth China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China Yazhouwan National Laboratory Sanya 572024China

Genomic structural variations affected widely gene function and morphological traits in *** inversions(INVs),as an important form of structural variation,can be large and extend to megabases in length[1],and form the genetic basis of local adaptation and ecotypic differentiation in sunflowers[2],Boechera stricta[3],monkeyflowers[4],mimetic butterflies[5]and ruffs[6],sex determination in nine-spined stickleback[7]and cancer and neurodevelopmental disease in human[8].At present,structural variants,and in particular,INVs,remain largely uncharacterized in plants despite their importance for local adaptation in a variety of species[1],with only a few studies exploring INVs polymorphisms at the population ***,it remains unclear whether adaptive INVs can directly shape the genetic basis for diverse phenotypes in plants,especially in domesticated crops.

关键词：水稻遗传 flowers adaptation

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Identification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome∞

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Journal of Integrative Plant Biology 2023年第12期65卷 2541-2551页

作者： 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 Lianguang Shang Institute of Biotechnology Fujian Academy of Agricultural Sciences/Fujian Provincial Key Laboratory of Genetic Engineering for AgricultureFuzhou 350003China 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 SciencesShenzhen 518124China Xiamen Key Laboratory for Plant Genetics School of Life SciencesXiamen UniversityXiamen 361102China College of Bioscience and Biotechnology Hunan Agricultural UniversityChangsha 410128China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 311401China Yazhouwan National Laboratory Sanya City 572024China

Continuously increasing global temperatures present great challenges to food *** size,one of the critical components determining grain yield in rice(Oryza sativa L.),is a prime target for genetic ***,there is an immediate need for genetic improvement in rice to maintain grain yield under heat ***,quantitative trait loci(QTLs)endowing heat stress tolerance and grain size in rice are extremely ***,we identified a novel negative regulator with pleiotropic effects,Thermo‐Tolerance and grain Length 1(TTL1),from the super pan‐genomic and transcriptomic ***‐of‐function mutations in TTL1 enhanced heat tolerance,and caused an increase in grain size by coordinating cell expansion and ***1 was shown to function as a transcriptional regulator and localized to the nucleus and cell ***,haplotype analysis showed that hapL and hapS of TTL1 were obviously correlated with variations of thermotolerance and grain size in a core collection of *** 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 *** findings provide insights into TTL1 as a novel potential target for the development of high‐yield and thermotolerant rice varieties.

关键词： domestication grain size heat tolerance pan‐genome natural variation

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A complete assembly of the rice Nipponbare reference genome

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Molecular Plant 2023年第8期16卷 1232-1236页

作者： Lianguang Shang Wenchuang He Tianyi Wang Yingxue Yang qiang Xu Xianjia Zhao Longbo Yang Hong Zhang Xiaoxia Li Yang Lv Wu Chen Shuo Cao Xianmeng Wang Bin Zhang Xiangpei Liu Xiaoman Yu Huiying He Hua Wei Yue Leng Chuanlin Shi Mingliang Guo Zhipeng Zhang Bintao Zhang Qiaoling Yuan hongge qian Xinglan Cao Yan Cui qianqian Zhang Xiaofan Dai Congcong Liu Longbiao Guo Yongfeng Zhou Xiaoming Zheng Jue Ruan Zhukuan Cheng Weihua Pan qian qian 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 SciencesShenzhen 518120China Yazhouwan National Laboratory No.8 Huanjin RoadYazhou DistrictSanya CityHainan Province 572024China State Key Laboratory of Rice Biology China National Rice Research InstituteHangzhou 310006China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Key Laboratory of Plant Functional Genomics of the Ministry of Education Jiangsu Co-Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhou 225009China

Dear Editor,In 2005,the current commonly used rice reference genome(Oryza sativa *** ***)was initially released by the International Rice Genome Sequencing Project(International Rice Genome Sequencing Project,2005).Thereafter,the reference genome was further updated in 2013 with improved genome assembly(IRGSP-1.0)and gene annotations(MSU7,RAP-DB)(Kawahara et al.,2013;Sakai et al.,2013).In the past 10 years,this reference has been serving as one of the most important genetic resources for subsequent rice functional genomics *** several rice genomes had been assembled into gapless chromosomes with only 2–5 telomeres absent(Li et al.,2021;Song et al.,2021;Zhang et al.,2022),the IRGSP1.0 and its annotations still performed as the most widely used ***,limitations of sequencing technology and intricate genomic organization led to an under-representation of complex regions in this reference,leaving a total of 72 major gaps(including 19 telomeres),167 minor gaps,and 779 unknown bases(Kawahara et al.,2013),with an estimated length of3%of the genome unsolved.

关键词： Sakai bases assembly

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高速铁路铺设CRTS Ⅲ型板式无砟轨道地段的路基冻胀限值

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中南大学学报（自然科学版） 2024年第7期55卷 2712-2726页

作者：魏绍磊肖宏王宏阁王阳钱忠霞北京交通大学土木建筑工程学院北京100044 北京交通大学轨道工程北京市重点实验室北京100044 中国铁路设计集团有限公司天津300308

我国冻土地区高速铁路分布广泛,路基冻胀对高速铁路无砟轨道结构损伤影响较为突出,危害行车安全。但是目前尚未建立针对铺设CRTS Ⅲ型板式无砟轨道地段的路基冻胀控制限值。本文基于车辆-轨道耦合动力学理论和混凝土塑性损伤理论,考虑... 详细信息

我国冻土地区高速铁路分布广泛,路基冻胀对高速铁路无砟轨道结构损伤影响较为突出,危害行车安全。但是目前尚未建立针对铺设CRTS Ⅲ型板式无砟轨道地段的路基冻胀控制限值。本文基于车辆-轨道耦合动力学理论和混凝土塑性损伤理论,考虑混凝土结构损伤和车轨相互作用,建立车辆-无砟轨道-冻胀路基静动力分析模型,分析路基冻胀对CRTS Ⅲ型板式无砟轨道结构的损伤和车辆动力性能指标的影响。综合静、动力控制指标,提出一种针对冻胀变形的分级控制限值;分别考虑轨道结构层间离缝和结构损伤、钢轨垂向动位移、乘车舒适性和行车安全性等多项控制指标,将路基冻胀限值划分为5个区域。研究结果表明:路基冻胀作用于轨道板中部时损伤和离缝量出现极值;结构损伤和车辆动力学响应均随波长减小和波峰增大而呈增大趋势,且均对波长的影响更为敏感。可以根据不同分区的冻胀限值保障车辆运营安全,为冻土区无砟轨道养护维修提供参考。

关键词：高速铁路路基冻胀限值 CRTSⅢ型板式无砟轨道车辆-轨道耦合动力学混凝土塑性损伤

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江苏省常州市武进区昆虫多样性及区系特征分析

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内蒙古林业调查设计 2022年第1期45卷 52-57,85页

作者：王倩钱宏革苏日娜白晓拴内蒙古师范大学生命科学与技术学院内蒙古呼和浩特010022 湖南农业大学生物科学技术学院湖南长沙410125

2018年7月28日至8月22日,2019年4月18~24日在江苏省常州市武进区选取42条样线进行了昆虫调查。经统计,在科级、属级、种级水平上,半翅目昆虫的数目(21科52属57种)都是最多的,鞘翅目昆虫(19科43属49种)次之,而蜚蠊目和革翅目昆虫(1科1属1... 详细信息

2018年7月28日至8月22日,2019年4月18~24日在江苏省常州市武进区选取42条样线进行了昆虫调查。经统计,在科级、属级、种级水平上,半翅目昆虫的数目(21科52属57种)都是最多的,鞘翅目昆虫(19科43属49种)次之,而蜚蠊目和革翅目昆虫(1科1属1种)最少。物种多样性指数分析表明,武进区半翅目昆虫的多样性指数(4.0132)和均匀度指数(0.9926)最高,优势度指数(0.0248)最低;鞘翅目昆虫的丰富度指数(8.4555)最高。武进区不同生境中昆虫多样性指数和丰富度指数均表现为草地灌木>森林>水域>耕地>居民地;优势度指数表现为居民地>耕地>水域>森林>草地灌木;均匀度指数表现为森林>草地灌木>水域>耕地>居民地。武进区昆虫在世界动物地理分布中具有典型的东洋界分布类型,与古北界关系密切;在中国动物地理分布中,武进区昆虫分布组成以全国、华中区、华中区—华南区、华中区—华南区—西南区、华中区—华南区—西南区—华北区5种分布型为主。

关键词：昆虫多样性群落生境类型区系特征江苏

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褐背施蝗Schmidtiacris schmidti雄成虫染色体核型分析

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植物保护学报 2021年第1期48卷 239-240页

作者：钱宏革林晨王宁王树森温苏雅勒图李媛媛内蒙古师范大学生命科学与技术学院呼和浩特010022 中国农业科学院草原研究所呼和浩特010010 内蒙古农业大学沙漠治理学院呼和浩特010018 乌拉特后旗林业局内蒙古巴彦诺尔015500 内蒙古民族大学农学院通辽028000

蝗灾一直是世界性的难题,几乎所有国家都曾经或正在遭受蝗灾为害(于红妍和石旺鹏,2020)。随着监测和防控技术的发展以及人们环保意识的进一步加强和绿色治理技术的广泛应用,蝗灾将被可持续控制(赵紫华等,2020)。作为生物遗传物质的载体... 详细信息

蝗灾一直是世界性的难题,几乎所有国家都曾经或正在遭受蝗灾为害(于红妍和石旺鹏,2020)。随着监测和防控技术的发展以及人们环保意识的进一步加强和绿色治理技术的广泛应用,蝗灾将被可持续控制(赵紫华等,2020)。作为生物遗传物质的载体,染色体在各个物种细胞内的数量是一定的,但对于不同物种来说,其染色体数目、相对长度、着丝粒位置会有所不同。对染色体特征进行研究和分析,可以为昆虫近缘种的鉴别、物种演化及亲缘关系分析提供参考和依据。

关键词：亲缘关系分析防控技术染色体核型分析可持续控制蝗灾物种演化相对长度绿色治理

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