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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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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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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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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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A Single Nucleotide Deletion in J Encoding GmELF3 Confers Long Juvenility and Is Associated with Adaption of Tropic Soybean

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Molecular Plant 2017年第4期10卷 656-658页

作者： Yanlei Yue Nianxi Liu bingjun jiang Mu Li Haijie Wang Ze jiang Huanting Pan Qiuju Xia Qibin Ma Tianfu Han Hai Nian State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural University Guangzhou 510642 China MOA Key Lab of Soybean Biology (Beijing) Institute of Crop ScienceThe Chinese Academy of Agricultural Sciences Beijing 100081 China Guangdong Provincial Key Laboratory of Plant Molecular Breeding South China Agricultural University Guangzhou 510642 China Institute of Crop Sciences Hainae Academy of Agricultural Sciences Haikou 571100 China BGl-Shenzhen Shenzhen 518083 China

Wild soybean is a typical short-day plant that begins flowering when the days are shorter than its critical photoperiod, Soybean was domesticated in the temperate region of East Asia at the relatively high latitude, and the breeding and release of soybean varieties have historically centered on mid- and high-latitude temperate regions. Low-latitude areas with tropical and sub- tropical climates were previously considered unsuitable for soy- bean production because most temperate soybean varieties ex- hibited precocious flowering and early maturity and suffered from low yields.

关键词： Single Nucleotide Deletion Encoding

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Genomic dissection of widely planted soybean cultivars leads to a new breeding strategy of crops in the post-genomic era

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The Crop Journal 2021年第5期9卷 1079-1087页

作者： Xinpeng Qi bingjun jiang Tingting Wu Shi Sun Caijie Wang Wenwen Song Cunxiang Wu Wensheng Hou Qijian Song Hon-Ming Lam Tianfu Han MARA Key Laboratory of Soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences The Chinese University of Hong KongShatinHong KongChina Soybean Genomics and Improvement Lab USDA-ARSBeltsvilleMD 20705USA

Soybeans specially the widely planted cultivars have been dramatically improved in agronomic performance and is well adapted to local planting environments after long-time domestication and *** the unique genomic features of popular cultivars will help to understand how soybean genomes have been modified through *** re-sequenced 134 soybean cultivars that were released and most widely planted over the last century in *** analyses established that these cultivars comprise two geographically distinct sub-populations:Northeast China (NE) versus the HuangHuai-Hai River Valley and South China (HS).A total of 309 selective regions were identified as being impacted by geographical *** HS sub-population exhibited higher genetic diversity and linkage disequilibrium decayed more rapidly compared to the NE *** study the association between phenotypic differences and geographical origins,we recorded the vegetative period under different growing conditions for two years,and found that clustering based on the phenotypic data was closely correlated with cultivar geographical *** iteratively calculating accumulated genetic diversity,we established a platform panel of cultivars and have proposed a novel breeding strategy named "Potalaization"for selecting and utilizing the platform cultivars that represent the most genetically diversity and the highest available agronomic performance as the "plateau"for accumulating elite loci and traits,breeding novel widely adapted cultivars,and upgrading breeding *** addition to providing new genomic information for the soybean research community,the "Potalaization"strategy that we devised will also be practical for integrating the conventional and molecular breeding programs of crops in the post-genomic era.

关键词： Soybean Widely planted cultivars Genomic re-sequencing Breeding strategy

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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

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Spatial differences in soybean bioactive components across China and their influence by weather factors

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The Crop Journal 2018年第6期6卷 659-668页

作者： Wenwen Song Ruping Yang Xiushi Yang Shi Sun Srinivasa Rao Mentreddy bingjun jiang Tingting Wu Shiyan Tian Enoch Sapey Cunxiang Wu Wensheng Hou Guixing Ren Tianfu Han MOA Key Laboratory of Soybean Biology Institute of Crop Sciences Chinese Academy of Agricultural Sciences Institute of Dryland Agriculture Gansu Academy of Agricultural Sciences Department of Biological and Environmental Sciences Alabama A&M University

Bioactive components are partially responsible for the nutritional and health benefits of soybeans. Four major bioactive components: isoflavones, oligosaccharides, phospholipids,and saponins, were quantified in 763 soybean samples collected from widely distributed regions across China from 2010 to 2013. A majority of the tested bioactive components showed generally declining trends from the north(high latitude) to the south(low latitude).A positive relationship between total oligosaccharides(TO) and altitude was observed. Total isoflavones(TI), phospholipids(TP) and TO were negatively correlated with cumulative temperature above or equal to 15 °C(AT15) and mean daily temperature(MDT), but positively correlated with diurnal temperature range(DTR) and hours of sunshine(HS).Total saponins(TS) were negatively correlated with MDT but positively correlated with rainfall(RF), whereas TO were negatively correlated with RF. Path-coefficient analysis showed that, besides genotype differences, temperature and HS during the reproductive period influenced TI and TP contents, while temperature and RF influenced TS and TO. The effects of weather factors on soybean bioactive components in diverse regions of China were characterized. These findings will be helpful in promoting soybean production for functional food purposes.

关键词： Soybean Geographic distribution Bioactive components Weather factors

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An improved initial rotor position estimation method using high-frequency pulsating voltage injection for PMSM

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Defence Technology（防务技术） 2024年第3期33卷 19-29页

作者： Yang jiang Ming Cheng School of Electrical Engineering Southeast UniversityNanjing 210096China

High frequency pulsating voltage injection method is a good candidate for detecting the initial rotor position of permanent magnet synchronous ***,traditional methods require a large number of filters,which leads to the deterioration of system stability and dynamic *** order to solve these problems,a new signal demodulation method is proposed in this *** proposed new method can directly obtain the amplitude of high-frequency current,thus eliminating the use of filters,improving system stability and dynamic performance and saving the work of adjusting filter *** addition,a new magnetic polarity detection method is proposed,which is robust to current measurement ***,experiments verify the effectiveness of the method.

关键词： Initial position detection Signal demodulation algorithm Magnetic polarity detection Filter elimination

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