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A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

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The Crop Journal 2024年第1期12卷 142-153页

作者： Anqi Zhang Tangchao Kong Baiquan Sun Shizheng Qiu Jiahe Guo Shuyong Ruan Yu Guo Jirui Guo Zhishuai Zhang Yue Liu Zheng Hu Tao Jiang Yadong Liu Shuqi Cao Shi Sun Tingting Wu Huilong Hong Bingjun Jiang Maoxiang Yang Xiangyu Yao Yang Hu Bo Liu tianfu han Yadong Wang Center for Bioinformatics School of Computer Science and TechnologyHarbin Institute of TechnologyHarbin 150001HeilongjiangChina Ministry of Agriculture Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary ***,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into ***,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong *** employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly *** assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference *** annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are ***13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier ***,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic *** summary,we deliver the first complete Chinese soybean cultivar T2T *** comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

关键词： Soybean Telomere-to-Telomere assembly Zhonghuang 13 Structure variations

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大豆B类花器官特征基因的生物信息学分析

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大豆科学 2024年第2期43卷 129-138页

作者：王曦昕蒋炳军袁珊武婷婷孙石张亮生韩天富东北农业大学农学院黑龙江哈尔滨150030 中国农业科学院作物科学研究所北京100081 浙江大学农业与生物技术学院浙江杭州310058

大豆花器官较小且闭花授粉,导致人工杂交效率低,品种遗传基础狭窄。MADS-box基因家族成员APETALA3(AP3)和PISTILLATA(PI)作为花发育ABCDE模型中的B类基因,共同控制花瓣与雄蕊的形成,在花器官形态建成中发挥重要作用。为明确大豆中B类基... 详细信息

大豆花器官较小且闭花授粉,导致人工杂交效率低,品种遗传基础狭窄。MADS-box基因家族成员APETALA3(AP3)和PISTILLATA(PI)作为花发育ABCDE模型中的B类基因,共同控制花瓣与雄蕊的形成,在花器官形态建成中发挥重要作用。为明确大豆中B类基因的进化模式,并探究其在不同大豆品种中的遗传变异,本研究通过生物信息学手段对大豆B类基因进行了基因结构、系统进化、保守基序、共线性、单倍型分析及物理性质预测等研究。结果显示:大豆基因组中11个B类基因,分别属于3个亚组,其中GmAP304(Glyma.04G027200)、GmAP306(Glyma.06G027200)、GmAP303(Glyma.03G111500)、GmAP316(Glyma.16G105600)和GmAP312(Glyma.12G118100)属于paleoAP3亚组,GmTM601(Glyma.01G169600)和GmTM611(Glyma.11G073700)属于TM6亚组,GmPI13(Glyma.13G034100)、GmPI14(Glyma.14G155100)、GmPI04(Glyma.04G245500)和GmPI06(Glyma.06G117600)属于PI亚组,且各亚组B类基因结构相对保守;大豆B类基因编码的蛋白中共有10个motif,其中motif 1、motif 4和motif 5与MADS结构域重叠。表达量数据分析显示,GmAP304、GmAP306、GmPI04、GmPI06、GmPI13、GmPI14、GmTM601和GmTM611在大豆花中有较高表达。结合单倍型分析发现,GmAP304、GmAP312、GmPI06、GmPI13和GmPI14在栽培大豆中只包含1种单倍型,比其它大豆B类基因更加保守,可能在控制花器官形成中行使更为重要的功能。本研究结果有助于完善大豆花器官发育模型,进一步阐明B类基因的功能,为大豆花器官的改造提供分子靶点,对提高大豆育种效率、拓宽品种遗传基础具有重要意义。

关键词：大豆 APETALA3 PISTILLATA MADS-box 花器官特征基因

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Optimization of Gas Production from Hydrate-Bearing Sediments with Fluctuation Characteristics

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Journal of Ocean University of China 2024年第3期23卷 618-632页

作者： LI Yaobin XU tianfu XIN Xin YU han YUAN Yilong ZHU Huixing Key Laboratory of Groundwater Resources and Environment Ministry of EducationJilin UniversityChangchun 130021China Jilin Provincial Key Laboratory of Water Resources and Environment Jilin UniversityChangchun 130021China

As an important source of low-carbon,clean fossil energy,natural gas hydrate plays an important role in improving the global energy consumption *** the hydrate industry in the South China Sea is important to achieving‘carbon peak and carbon neutrality’goals as soon as ***-water areas subjected to the action of long-term stress and tectonic movement have developed complex and volatile terrains,and as such,the morphologies of hydrate-bearing sediments(HBSs)fluctuate *** key to numerically simulating HBS morphologies is the establishment of the conceptual model,which represents the objective and real description of the actual geological ***,current numerical simulation models have characterized HBSs into horizontal strata without considering the fluctuation *** representing the HBS as a horizontal element reduces simulation ***,the commonly used horizontal HBS model and a model considering the HBS’s fluctuation characteristics with the data of the SH2 site in the Shenhu Sea area were first constructed in this ***,their production behaviors were compared,and the huge impact of the fluctuation characteristics on HBS production was *** this basis,the key parameters affecting the depressurization production of the fluctuating HBSs were studied and *** research results show that the fluctuation characteristics have an obvious influence on the hydrate production of HBSs by affecting their temperatures and pressure distributions,as well as the transmission of the pressure drop and methane gas ***,the results show that the gas productivity of fluctuating HBSs was about 5%less than that of horizontal *** optimizing the depressurization amplitude,well length,and layout location of vertical wells,the productivity of fluctuating HBSs increased by about 56.6%.

关键词： natural gas hydrate numerical simulation fluctuation characteristics depressurization production production well optimization

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GmNMHC5 may promote nodulation via interaction with GmGAI in soybean

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The Crop Journal 2022年第1期10卷 273-279页

作者： Wenting Wang Zhili Wang Wensheng Hou Li Chen Bingjun Jiang Wenya Ma Lijuan Bai Wenwen Song Cailong Xu tianfu han Yongjun Feng Cunxiang Wu School of Life Science Beijing Institute of TechnologyBeijing 100081China MARA Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Soybean(Glycine max[L.]Merr.)is a food and oil crop whose growth and yield are influenced by root and nodule *** the present study,Gm NMHC5 was found to promote the formation of nodules in overexpressing *** contrast,the number of nodules in Gmnmhc5 edited with CRISPR/Cas9 decreased *** 35 S:Gm NMHC5 mutants,expression levels of genes involved in nodulation were significantly *** in vitro and in vivo biochemical analyses showed that Gm NMHC5 directly interacted with Gm GAI(a DELLA protein),and the content of gibberellin 3(GA_(3))in overexpressing mutants was lower than that in the wild *** results revealed that Gm NMHC5 participates in the classical GA signaling pathway,and may regulate the content of GA_3 to match the optimal concentration required for nodule formation,thereby promoting nodulation by directly interacting with Gm GAI.A model illustrating the mechanism by which Gm NMHC5 promotes soybean nodulation is presented.

关键词： Glycine max GmNMHC5 GmGAI Nodulation GA pathway

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History, current status, and prospects of soybean production and research in sub-Saharan Africa

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The Crop Journal 2018年第3期6卷 226-235页

作者： Dalia Mohamedkheir Khojely Seifeldin Elrayah Ibrahim Enoch Sapey tianfu han MOA Key Lab of Soybean Biology (Beijing) Institute of Crop SciencesChinese Academy of Agricultural Sciences Gezira Research Station Agricultural Research Corporation (ARC) Oil Palm Breeding and Genetics CSIR-Oil Palm Research Institute

Soybean(Glycine max(L.) Merr.) is a non-native and non-staple crop in sub-Saharan Africa(SSA) with potential to be a commercial crop owing to its wide range of uses as food, feed,and industrial raw material. Soybean was first introduced to SSA by Chinese traders in the19 th century and was cultivated as an economic crop as early as 1903 in South Africa. In the past four decades, soybean cultivation area and production in SSA has increased exponentially, from about 20,000 ha and 13,000 t in the early 1970 s to 1,500,000 ha and2,300,000 t in 2016. Soybean yield has been stagnant in SSA for decades at about 1.1 t ha^(-1),much lower than the world average, representing one of the most challenging issues in the soybean industry in SSA. The low soybean yield in SSA can be attributed to the use of poorperforming varieties and to the limited application of fertilizers and rhizobial inoculants in soils with no history of soybean production. South Africa, Nigeria, Zambia, and Uganda are the leading soybean producers in SSA. Soybean research in SSA is conducted by international and national research institutions, including IITA, national soybean improvement programs, universities, and the private sector. Between 1970 and 2011, 195 soybean varieties were released by IITA, private breeders, and national soybean improvement programs in SSA. This paper reviews the history and current state of soybean production and of the utilization and adoption of tropical varieties in SSA, addresses the major soybean yield-limiting factors across the region, and discusses the potential of the soybean industry in SSA. It also highlights soybean improvement efforts and lessons learned from previous soybean improvement efforts and the current progress of some national soybean improvement programs in SSA. Opportunities for scaling up tropical soybean as a major crop across SSA countries are promising.

关键词： Soybean Sub-Saharan Africa(SSA) History Current status Prospects

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Physiological and molecular studies of staygreen caused by pod removal and seed injury in soybean

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The Crop Journal 2016年第6期4卷 435-443页

作者： Xinxin Zhang Min Wang Tingting Wu Cunxiang Wu Bingjun Jiang Changhong Guo tianfu han Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang College of Life Science and TechnologyHarbin Normal University MOA Key Laboratory of Soybean Biology (Beijing) Institute of Crop Sciencethe Chinese Academy of Agricultural Sciences

Leaves provide substances and signals for pod and seed development in ***,the regulatory feedbacks of pod and seed to leaf development remain *** investigated the effects of pod and seed on leaf senescence by conducting pod removal and seed injury *** removal and seed injury delayed leaf senescence and caused the staygreen phenotype of *** were dosage effects of pod number on the extent of staygreen in depodded *** concentrations of chlorophyll(SPAD value,an index of relative chlorophyll content),soluble protein,and soluble sugar in the leaves of depodded plants were higher than those of intact *** seed development,the content of IAA decreased,while that of ABA *** trend was more pronounced in intact than in depodded and seed-injured *** GA3/ABA ratio decreased gradually in all *** content of GA3 was relatively stable and was higher in intact than in depodded *** expression levels of four senescence-related genes,Gm SARK,Gm SGR1,Gm CYN1,and Gm NAC,declined in depodded or seed-injured treatments and were positively correlated with the number of leaves retained on *** FT2 a,the major flowering-promoting gene,was expressed at a higher level while E1,a key flowering inhibitory gene,was expressed at a lower level in depodded than in intact *** propose that the pod or seed can regulate leaf *** the seed is aborted owing to disease infection or pest attack,the leaves stay green because of the absence of the seed signals for senescence.

关键词： Soybean Seed injury Staygreen Source–sink relationship

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A new distinct geminivirus causes soybean stay-green disease

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Molecular Plant 2022年第6期15卷 927-930页

作者： Ruixiang Cheng Ruoxin Mei Rong Yan Hongyu Chen Dan Miao Lina Cai Jiayi Fan Gairu Li Ran Xu Weiguo Lu Yu Gao Wenwu Ye Shuo Su tianfu han Junyi Gai Yuanchao Wang Xiaorong Tao Yi Xu Department of Plant Pathology Nanjing Agricultural UniversityNanjing 210095China The Key Laboratory of Bio-interaction and Crop Health Nanjing Agricultural UniversityNanjing 210095China Key Laboratory of Soybean Disease and Pest Control(Ministry of Agriculture and Rural Affairs) Nanjing Agricultural UniversityNanjing 210095China Engineering Laboratory of Animal Immunity of Jiangsu Province College of Veterinary MedicineAcademy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China Crop Research Institute Shandong Academy of Agricultural SciencesJinanShandong 250100China Henan Academy of Crop Molecular Breeding ZhengzhouHenan 450002China College of Plant Protection Jilin Agricultural UniversityChangchunJilin 130018China MOA Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Soybean Research Institute Nanjing Agricultural UniversityNanjing 210095China

Dear Editor,Plant viruses make up almost half of the plant disease-causing pathogens,affecting crop yields and the global economy(Savary et al.,2019).Soybean(Glycine max)is one of the most valuable legume crops in the world,supplying 25%of the global edible oil and two-thirds of the global concentrated protein for livestock ***,the outbreak of soybean stay-green syndrome with delayed leaf senescence(stay-green),flat pods,and increased number of abnormal seeds has swept the soybean production in the Huang-Huai-Hai region of China,resulting in huge yield losses(Xu et al.,2019).This disease has become an epidemic and prominent problem in soybean production and is still expanding its geography,including North America,posing a serious threat to soybean production(Harbach et al.,2016;Zhang et al.,2016;Li et al.,2019).However,the cause of soybean stay-green syndrome remains obscure.

关键词： soybean crops expanding

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Soybean hairy roots produced in vitro by Agrobacterium rhizogenes-mediated transformation

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The Crop Journal 2018年第2期6卷 162-171页

作者： Li Chen Yupeng Cai Xiujie Liu Chen Guo Shi Sun Cunxiang Wu Bingjun Jiang tianfu han Wensheng Hou National Center for Transgenic Research in Plants Institute of Crop Science Chinese Academy of Agricultural Sciences Ministry of Agriculture Key Laboratory of Soybean Biology (Beijing) Institute of Crop Science Chinese Academy of Agricultural Sciences

Soybean is one of the world's most important oil and protein crops. Efficient transformation is a key factor for the improvement of soybean by genetic modification. We describe an optimized protocol for the Agrobacterium rhizogenes-mediated transformation of soybean and the induction of hairy root development in vitro. Cotyledons with 0.5-cm hypocotyls were cut from 5-day-old seedlings and used as explants. After infection and co-cultivation,hairy roots were produced in induction culture medium after 10–12 days. Using this method, 90%–99% of the infected explants of five different cultivars produced hairy roots within one month. Observations using reporter constructs showed that 30%–60% of the hairy roots induced were transformed. Based on high transformation efficiency and short transformation period, this method represents an efficient and rapid platform for study of soybean gene function.

关键词： Agrobacterium rhizogenes Hairy root Protocol Soybean Transformation

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铜绿假单胞菌在液滴界面的二维和三维运动特征

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微生物学报 2022年第8期62卷 3124-3136页

作者：朱晓艳韩苗韩天富韩峥王钢郑州大学物理学院河南郑州450001 中国农业大学土地科学与技术学院北京100193 中国农业科学院农业资源与农业区划研究所北京100081

【目的】环境中无处不在的气-液界面能够影响细菌的运动和养分的传输扩散,进而调控微生物的种群互作和群落结构。因此,系统地认知微生物在微观界面的运动特征对于理解和解析微生物多样性的产生、维持机制以及生态功能至关重要。【方法... 详细信息

【目的】环境中无处不在的气-液界面能够影响细菌的运动和养分的传输扩散,进而调控微生物的种群互作和群落结构。因此,系统地认知微生物在微观界面的运动特征对于理解和解析微生物多样性的产生、维持机制以及生态功能至关重要。【方法】本文基于微流体显微系统(超高速荧光显微镜和数字全息显微镜),以具备主动运动能力的模式菌株铜绿假单胞菌(Pseudomonas aeruginosa PAO1)为研究对象,观测并解析了细菌细胞在气-液界面的二维运动特征和气-液-固界面的二维与三维运动特征。【结果】PAO1既能在气-液界面处执行近似直线轨迹的运动,也能在气-液界面下方执行顺时针或逆时针旋转的圆周运动(最小曲率半径Rmin=3μm)。在气-液-固界面处,6.45%的不运动细胞聚集于气-液-固界面边缘处,并在该处完成不可逆附着;同时,游动细胞由于受到液滴内部毛细管流和马兰戈尼(Marangoni)涡流运动的综合作用,直线游动至距界面约40μm内的区域后,其运动轨迹转变为垂直界面方向返回或以近似界面平行方向运动并附着,这些行为显著调节了PAO1的空间分布,促使了其朝向气-液-固界面的迁移,表明个体PAO1的鞭毛在此处的主动游动作用较弱。【结论】PAO1在气-液界面处能够执行与固-液界面类似的运动轨迹,且能够在各种作用力下朝向气-液-固界面运动并附着。

关键词：气-液界面气-液-固界面数字全息显微镜铜绿假单胞菌细菌运动性

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Feeding of Riptortus pedestris on soybean plants, the primary cause of soybean staygreen syndrome in the Huang-Huai-Hai river basin

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The Crop Journal 2019年第3期7卷 360-367页

作者： Kai Li Xinxin Zhang Jianqiu Guo hannah Penn Tingting Wu Lin Li Hong Jiang Lidan Chang Cunxiang Wu tianfu han Soybean Research Institute Nanjing Agricultural UniversityNanjing 210095JiangsuChina MOA Key Laboratory of Soybean Biology (Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Luoyang Academy of Agriculture and Forestry Sciences Luoyang 471022HenanChina Department of Entomology Louisiana State UniversityLA 70803USA

Staygreen syndrome or Zhengqing in soybean has recently become a major issue for Chinese growers in the Huang-Huai-Hai river *** previous studies revealed that staygreen can be induced when pods/seeds are damaged, it is unknown whether virus infection or insect infestation causes *** determine whether viral infection causes staygreen, a survey of soybean staygreen incidence in the Huang-Huai-Hai river basin was conducted in 2016 and *** samples were collected and analyzed using DAS-ELISA for Soybean mosaic virus, Watermelon mosaic virus, Bean pod mottle virus, Cucumber mosaic virus, and Bean common mosaic *** survey showed that the severity of soybean staygreen syndrome was most prevalent in Beijing, Henan, Shaanxi, and some parts of Shandong provinces, with yield losses from 0 to nearly 100%, but only a small fraction of samples were positive for the tested viruses.A field cage experiment and an insecticide treatment field trial were conducted to determine the contribution of the bean bug, Riptortus pedestris, to staygreen *** field cage experiment showed that *** treatment resulted in shorter plants, more empty pods, increased numbers of abnormal seeds, and decreased *** field experiment showed that there were fewer *** and less soybean staygreen incidence in fields treated with insecticide than in untreated control ***, these results suggest that *** infestation rather than virus infection induces staygreen syndrome and that growers in this region can mitigate staygreen syndrome via bean bug control.

关键词： Soybean Staygreen syndrome Zhengqing DAS-ELISA Viral infection Bean bug (R. pedestris)

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