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Super graph-based pan-genome: Bringing rice functional genomic study into a new dawn

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Molecular Plant 2022年第9期15卷 1409-1411页

Rice is one of the earliest domesticated crops that has been cultivated for thousands of years.Interestingly,unlike other crops that are predominantly domesticated by a singleto neventin one place,the domestication of rice is quite complicated;it independently occurred in Asia and Africa toform the Asian cultivated rice Oryza sativa and the African cultivated rice O.glaberrima,respectively.O.sativa was mainly domesticated from the Asian wild rice O.rufipogon in East/South Asia(Huang et al.,2012).Furthermore,O.sativa can be classified into two main types:Geng(O.sativa ssp.japonica)and Xian(O.sativa ssp.indica).Geng was domesticated as early as 9000 years ago,while Xian was domesticated lateralong with continuousgene flow from Geng(Choi etal.,2017).O.glaberrimawas domesticated from African wild rice O.barthi approximately 3500 years ago.O.barthii and O.rufipogon diverged approximately 600000 years ago.

关键词： cultivated crops japonica

Experimental study on failure characteristics of single-sided unloading rock under different intermediate principal stress conditions

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International Journal of Mining Science and Technology 2023年第3期33卷 275-287页

作者： Chongyan liu Guangming Zhao Wensong Xu Xiangrui Meng Zhixi Liu Xiang Cheng Gang Lin State Key Laboratory of Mining Response and Disaster Prevention and Control in Deep Coal Mines Anhui University of Science and TechnologyHuainan 232001China Key Laboratory of Safe and Effective Coal Mining Ministry of EducationAnhui University of Science and TechnologyHuainan 232001China Post-Doctoral Research Station Huaibei Mining Corporation LimitedHuaibei 235006China Laboratoire de Géologie Ecole Normale SupérieureParis 75005France

Investigation of unloading rock failure under differentσ_(2)facilitates the control mechanism of excavation surrounding rock.This study focused on single-sided unloading tests of granite specimens under true triaxial conditions.The strength and failure characteristics were studied with micro-camera and acoustic emission(AE)monitoring.Furthermore,the choice of test path and the effect ofσ_(2)on fracture of unloading rock were discussed.Results show that the increasedσ_(2)can strengthen the stability of single-sided unloading rock.After unloading,the rock’s free surface underwent five phases,namely,inoculation,particle ejection,buckling rupture,stable failure,and unstable rockburst phases.Moreover,atσ_(2)≤30 MPa,the b value shows the following variation tendency:rising,dropping,significant fluctuation,and dropping,with dispersed damages signal.Atσ_(2)≥40 MPa,the tendency shows:a rise,a decrease,a slight fluctuation,and final drop,with concentrated damages signal.After unloading,AE energy is mainly concentrated in the micro-energy range.With the increasedσ_(2),the micro-energy ratio rises.In contrast,low,medium and large energy ratios drop gradually.The increased tensile fractures and decreased shear fractures indicate that the failure mode of the unloading rock gradually changes from tensile-shear mode to tensile-split one.The fractional dimension of the rock fragments first increases and then decreases with an inflection point at 20 MPa.The distribution of SIF on the planes changes asσ_(2)increases,resulting in strengthening and then weakening of the rock bearing capacity.

关键词： Single-sided unloading Acoustic emission True triaxial Intermediate principal stress Stress intensity factor

Temperature driven antagonistic fate determination by two bHLH transcription factors:dormancy or germination

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Science China(Life Sciences) 2023年第5期66卷 1208-1209页

Dormancy or germination is an essential question that seed plants have to face.Under natural circumstances,seeds of plants usually maintain the status of dormancy until they meet the optimal condition to trigger the g... 详细信息

关键词： germination maintain determination

From one linear genome to a graph-based pan-genome: a new era for genomics

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Science China(Life Sciences) 2020年第12期63卷 1938-1941页

作者： Yucheng liu zhixi Tian State Key Laboratory of Plant Cell and Chromosome Engineering Center for Genome EditingInstitute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The seeds for genomics were sown with the development of DNA sequencing(Sanger et al., 1977), cultivated with each advance in molecular biology, and have since grown into one of the most important aspects of the life sciences. With the sequencing of the first draft human genome(Venter et al.,2001), the era of post-genomics began. Once one genome has been sequenced, it can be used as the reference for a certain species, and sequences from individuals can be mapped onto it to compare genetic variations among different lines.

关键词： Sanger genome genomics

Toward a “Green Revolution” for Soybean

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Molecular Plant 2020年第5期13卷 688-697页

作者： Shulin liu Min Zhang Feng Feng zhixi Tian State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovative Academy of Seed DesignChinese Academy of SciencesBeijing 100101China College of Advanced Agricultural Sciences University of Chinese Academy of SciencesBeijing 100049China

Soybean(Glycine max),as an economically important food and oilseedcrop,is a major source of plant proteins and oils.Although considerable progress has been made in increasing the yields of rice,wheat,and maize through the“Green Revolution”,little improvements have been made for soybean.With the increasing demand of soybean production and the rapid development of crop breeding technologies,time has come for this important crop to undergo a Green Revolution.Here,we briefly summarize the history of crop breeding and Green Revolution in other crops.We then discuss the possible directions and potential approaches toward achieving a Green Revolution for soybean.We provide our views and perspectives on how to breed new soybean varieties with improved yield.

关键词： soybean yield Green Revolution

Oil crops: From the classical traits to genetic improvement

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Journal of Integrative Plant Biology 2021年第6期63卷 979-980页

作者： Zhicheng Dong zhixi Tian Baohui liu Guangzhou Key Laboratory of Crop Gene Editing Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhou 510405China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignThe Chinese Academy of SciencesBeijing 100101China

Soybean, oilseed rape, peanut, and so on, are importantresources of vegetable oil for human beings. Cultivation and production of these oil crops are expected to increase due to continuous population growth, which pos... 详细信息

关键词： crops Cultivation resources

Precise Positioning Method for Seafloor Geodetic Stations Based on the Temporal Variation of Sound Speed Structure

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Journal of Geodesy and Geoinformation Science 2023年第2期6卷 81-92页

作者： Shuang ZHAO Zhenjie WANG zhixi NIE Kaifei HE Huimin liu Zhen SUN Chinese Academy of Surveying and Mapping Beijing 100036China College of Oceanography and Space Informatics China University of Petroleum(East China)Qingdao 266580China Qingdao Institute of Marine Geology China Geological SurveyQingdao 266237China

At present,GNSS-Acoustic(GNSS-A)combined technology is widely used in positioning for seafloor geodetic stations.Based on Sound Velocity Profiles(SVPs)data,the equal gradient acoustic ray-tracing method is applied in high-precision position inversion.However,because of the discreteness of the SVPs used in the forementioned method,it ignores the continuous variation of sound velocity structure in time domain,which worsens the positioning accuracy.In this study,the time-domain variation of Sound Speed Structure(SSS)has been considered,and the cubic B-spline function is applied to characterize the perturbed sound velocity.Based on the ray-tracing theory,an inversion model of“stepwise iteration&progressive corrections”for both positioning and sound speed information is proposed,which conducts the gradual correction of seafloor geodetic station coordinates and disturbed sound velocity.The practical data was used to test the effectiveness of our method.The results show that the Root Mean Square(RMS)errors of the residual values of the traditional methods without sound velocity correction,based on quadratic polynomial correction and based on cubic B-spline function correction are 1.43 ms,0.44 ms and 0.21 ms,respectively.The inversion model with sound velocity correction can effectively eliminate the systematic error caused by the change of SSS,and significantly improve the positioning accuracy of the seafloor geodetic stations.

关键词： GNSS-Acoustic sound speed structure temporal variation seafloor positioning

GenoBaits Soy40K:a highly flexible and low-cost SNP array for soybean studies

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Science China(Life Sciences) 2022年第9期65卷 1898-1901页

作者： Yucheng liu Shulin liu Zhifang Zhang Lingbin Ni Xingming Chen Yunxia Ge Guoan Zhou zhixi Tian State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China MolBreeding Biotechnology Co. Ltd.Shijiazhuang 050035China University of Chinese Academy of Sciences Beijing 100039China

Dear Editor,Soybean(Glycine max[L.]Merr.)provides more than half of the oilseeds and more than a quarter of protein worldwide.It is estimated that the production of soybean has to be doubled by 2050 to meet the needs of the rapidly increasing consumption of soybean seeds along with a continuously increasing population(Ray et al.,2013).As such,development of a genotyping platform with high throughput,high efficiency and high precision but low-cost is urgently needed to accelerate soybean functional study and molecular design breeding.

关键词： soybean cost doubled

SoyOmics:A deeply integrated database on soybean multi-omics

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Molecular Plant 2023年第5期16卷 794-797页

作者： Yucheng liu Yang Zhang Xiaonan liu Yanting Shen Dongmei Tian Xiaoyue Yang Shulin liu Lingbin Ni Zhang Zhang Shuhui Song zhixi Tian State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China National Genomics Data Center&CAS Key Laboratory of Genome Sciences and Information Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China China National Center for Bioinformation Beijing 100101China University of Chinese Academy of Sciences Beijing 100039China

Dear Editor,As one of the most important crops to supply the majority of plant oil and protein for the whole world,soybean is facing an increasing global demand.The reference genome of accession"Williams82"opened the gate of genomics research in soybean(Schmutz et al.,2010).After that,vast multi-omics data were generated,thereby providing valuable resources for functional study and molecular breeding.Parts of these data have been collected in different soybean databases(see details in Supplemental Table 1),such as Soybase(Grant et al.,2010)and SoyKB(Joshi et al.,2012),which made valuable efforts to facilitate the wide utility of these data.Nevertheless,these existing databases poorly tackled multi-omics data integration and interactivity for soybean,provoking tremendous challenges for researchers to deal with these big omics data,particularly considering the unprecedented rate of data growth(Yang et al.,2021).Thus,constructing an integrated multi-omics database for soybean that provides a one-stop solution for big data mining with friendly interactivity is highly desired.

关键词： database details thereby