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| 1 | Toward a “Green Revolution” for Soybean显示文摘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. | Shulin Liu Min Zhang Feng Feng Zhixi Tian | 2020 | Molecular Plant2020，13，5： | 18 |
| 2 | Simultaneous changes in seed size, oil content and protein content driven by selection of SM/EEIhomologues during soybean domestication显示文摘Soybean accounts for more than half of the global production of oilseed and more than a quarter of the protein used globally for human food and animal feed.Soybean domestication involved parallel increases in seed size and oil content,and a concomitant decrease in protein content.However,science has not yet discovered whether these effects were due to selective pressure on a single gene or multiple genes.Here,re-sequencing data from>800 genotypes revealed a strong selection during soybean domestication on GmSWEETlOa.The selection of GmSWEETlOa conferred simultaneous increases in soybean-seed size and oil content as well as a reduction in the protein content.The result was validated using both near-isogenic lines carrying substitution of haplotype chromosomal segments and transgenic soybeans.Moreover,GmSWEETlOb was found to be functionally redundant with its homologue GmSWEETlOa and to be undergoing selection in current breeding,leading the the elite allele GrnSWEETlOb,a potential target for present-day soybean breeding.Both GmSWEETlOa and GmSWEETlOb were shown to transport sucrose and hexose,contributing to sugar allocation from seed coat to embryo,which consequently determines oil and protein contents and seed size in soybean.We conclude that past selection of optimal GmSWEETlOa alleles drove the initial domestication of multiple soybean-seed traits and that targeted selection of the elite allele GmSWEETlOb may further improve the yield and seed quality of modern soybean cultivars. | Shoudong Wang Shulin Liu Jie Wang Kengo Yokosho Bin Zhou Ya-Chi Yu Zhi Liu Wolf BFrommer Jian Feng Ma Li-Qing Chen Yuefeng Guan Huixia Shou Zhixi Tian | 2020 | National Science Review2020，7，11： | 17 |
| 3 | Development of gene-tagged molecular markers for starch synthesis-related genes in rice显示文摘Improving grain quality is an important goal in breeding new elite rice varieties,requiring effective tools for the identification of target genotypes.Molecular marker-aided selection(MAS),combined with conventional breeding approaches,enables us to pre-cisely identify the individual genotypes that are associated with different grain quality features,which can dramatically improve the breeding efficiency.However,to date,the number of molecular markers used in MAS for grain quality improvement is still somewhat limited.In this study,based on our previous study that rice grain quality is strongly associated with starch synthesis in the endosperm,we developed 51 gene-tagged molecular markers according to sequence variations in 18 starch synthesis-related genes from 16 typical rice cultivars.These markers can discriminate the different alleles among rice germplasms.These novel markers will provide effective tools in improving grain quality via the breeding new elite rice varieties. | TIAN ZhiXi YAN ChangJie QIAN Qian YAN Song XIE HuiLan WANG Fang XU JieFen LIU GuiFu WANG YongHong LIU QiaoQuan TANG ShuZhu LI JiaYang GU MingHong | 2010 | Chinese Science Bulletin2010，55，33： | 12 |
| 4 | De novo assembly of a Chinese soybean genome显示文摘Soybean was domesticated in China and has become one of the most important oilseed crops. Due to bottlenecks in their introduction and dissemination, soybeans from different geographic areas exhibit extensive genetic diversity. Asia is the largest soybean market; therefore, a high-quality soybean reference genome from this area is critical for soybean research and breeding.Here, we report the de novo assembly and sequence analysis of a Chinese soybean genome for 'Zhonghuang 13' by a combination of SMRT, Hi-C and optical mapping data. The assembled genome size is 1.025 Gb with a contig N50 of 3.46 Mb and a scaffold N50 of 51.87 Mb. Comparisons between this genome and the previously reported reference genome(cv. Williams82) uncovered more than 250,000 structure variations. A total of 52,051 protein coding genes and 36,429 transposable elements were annotated for this genome, and a gene co-expression network including 39,967 genes was also established. This high quality Chinese soybean genome and its sequence analysis will provide valuable information for soybean improvement in the future. | Yanting Shen Jing Liu Haiying Geng Jixiang Zhang Yucheng Liu Haikuan Zhang Shilai Xing Jianchang Du Shisong Ma Zhixi Tian | 2018 | Science China(Life Sciences)2018，61，8： | 11 |
| 5 | An efficient methodology for utilization of K-feldspar and phosphogypsum with reduced energy consumption and CO2 emissions显示文摘The issues of reducing CO_2 emissions, sustainably utilizing natural mineral resources, and dealing with industrial waste offer challenges for sustainable development in energy and the environment. We propose an efficient methodology via the co-reaction of K-feldspar and phosphogypsum for the extraction of soluble potassium salts and recovery of SO_2 with reduced CO_2 emission and energy consumption. The results of characterization and reactivity evaluation indicated that the partial melting of K-feldspar and phosphogypsum in the hightemperature co-reaction significantly facilitated the reduction of phosphogypsum to SO_2 and the exchange of K^+(K-feldspar) with Ca^(2+)(CaSO_4 in phosphogypsum). The reaction parameters were systematically investigated with the highest sulfur recovery ratio of ~ 60% and K extraction ratio of ~ 87.7%. This novel methodology possesses an energy consumption reduction of ~ 28% and CO_2 emission reduction of ~ 55% comparing with the present typical commercial technologies for utilization of K-feldspar and the treatment of phosphogypsum. | Zhixi Gan Zheng Cui Hairong Yue Siyang Tang Changjun Liu Chun Li Bin Liang Heping Xie | 2016 | Chinese Journal of Chemical Engineering2016，24，11： | 11 |
| 6 | Recently duplicated sesterterpene(C25) gene clusters in Arabidopsis thaliana modulate root microbiota显示文摘Land plants co-speciate with a diversity of continually expanding plant specialized metabolites(PSMs) and root microbial communities(microbiota).Homeostatic interactions between plants and root microbiota are essential for plant survival in natural environments.A growing appreciation of microbiota for plant health is fuelling rapid advances in genetic mechanisms of controlling microbiota by host plants.PSMs have long been proposed to mediate plant and single microbe interactions.However,the effects of PSMs,especially those evolutionarily new PSMs,on root microbiota at community level remain to be elucidated.Here,we discovered sesterterpenes in Arabidopsis thaliana,produced by recently duplicated prenyltransferase-terpene synthase(PT-TPS) gene clusters,with neo-functionalization.A single-residue substitution played a critical role in the acquisition of sesterterpene synthase(sesterTPS) activity in Brassicaceae plants.Moreover,we found that the absence of two root-specific sesterterpenoids,with similar chemical structure,significantly affected root microbiota assembly in similar patterns.Our results not only demonstrate the sensitivity of plant microbiota to PSMs but also establish a complete framework of host plants to control root microbiota composition through evolutionarily dynamic PSMs. | Qingwen Chen Ting Jiang Yong-Xin Liu Haili Liu Tao Zhao Zhixi Liu Xiangchao Gan Asis Hallab Xuemei Wang Juan He Yihua Ma Fengxia Zhang Tao Jin M. Eric Schranz Yong Wang Yang Bai Guodong Wang | 2019 | Science China(Life Sciences)2019，62，7： | 11 |
| 7 | Update soybean Zhonghuang 13 genome to a golden reference显示文摘Dear Editor,Soybean is one of the most important crops worldwide.A high-quality reference genome will facilitate its functional analysis and molecular breeding (Wang and Tian,2015).Previously,we de novo assembled a high-quality Chinese soybean genome Gmax_ZH13 (Shen et al.,2018,Yang and Huang,2018).However,due to technical limitations at the time when we generated Gmax_ZH13,a large number of small contigs were not anchored onto chromosomes.Therefore,we here build a new golden reference genome for Zhonghuang 13 consisting of 20 nearly complete chromosomes by adding more single-molecule real time (SMRT) sequencing reads.Furthermore,we add large RNA-seq and smRNA-seq datasets for improving the annotation of its protein coding genes. | Yanting Shen Huilong Du Yucheng Liu Lingbin Ni Zheng Wang Chengzhi Liang Zhixi Tian | 2019 | Science China(Life Sciences)2019，62，9： | 6 |
| 8 | FED:a web tool for foreign element detection of genome-edited organism显示文摘Dear Editor,Genome editing,especially the newly developed CRISPR technology,is now widely implemented for diverse medical and agricultural applications(Puchta,2018).However,for genome editing,the DNA cassettes encoding the editing components are usually assembled and delivered into the cells of organisms(Cong et al.,2013). | Qing Liu Xiaozhen Jiao Xiangbing Meng Chun Wang Cao Xu Zhixi Tian Chuanxiao Xie Genying Li Jiayang Li Hong Yu Kejian Wang | 2021 | Science China(Life Sciences)2021，64，1： | 6 |
| 9 | From one linear genome to a graph-based pan-genome: a new era for genomics显示文摘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. | Yucheng Liu Zhixi Tian | 2020 | Science China(Life Sciences)2020，63，12： | 3 |
| 10 | Impact of immunization programs on 11 childhood vaccine-preventable diseases in China: 1950–2018显示文摘To evaluate the achievements of China’s immunization program between 1950 and 2018,we chose 11 vaccine-preventable diseases(VPDs)as representative notifiable diseases and used annual surveillance data obtained between 1950 and 2018 to derive disease incidence and mortality trends.Quasi-Poisson and polynomial regression models were used to estimate the impacts of specific vaccine programs,and life-table methods were used to calculate the loss of life expectancy,years of life lost,and loss of working years.The total notification number for the 11 VPDs was 211,866,000 from 1950 to 2018.The greatest number occurred in 1959,with a total incidence of 1,723 per million persons.From 1978 to 2018,a substantial decline was observed in the incidence of major infectious diseases.The incidence of pertussis fell 98%from 126.35 to 1.58 per million,and the incidences of measles,meningococcal meningitis,and Japanese encephalitis fell 99%,99%,and 98%,respectively.The regression models showed that most of the 11 diseases exhibited dramatic declines in morbidity after their integration into the Expanded Program on Immunization(EPI),while varicella and paratyphoid fever,which were not integrated into the EPI,showed increased morbidity.From 1978 to 2018,the total life expectancy for the 11 VPDs increased by 0.79 years,and similar results were obtained for different age groups.China has had great success in controlling VPDs in recent decades,and improving vaccination coverage is a key aspect of controlling VPDs in China. | Jinhua Pan Yesheng Wang Lingsheng Cao Ying Wang Qi Zhao Shenglan Tang Wenfeng Gong Lei Guo Zhixi Liu Zexuan Wen Bo Zheng Weibing Wang | 2021 | The Innovation2021，2，2： | 2 |
| 11 | QNE1 is a key flowering regulator determining the length of the vegetative period in soybean cultivars显示文摘The soybean E1 gene is a major regulator that plays an important role in flowering time and maturity.However,it remains unclear how cultivars carrying the dominant E1 allele adapt to the higher latitudinal areas of northern China.We mapped the novel quantitative trait locus QNE1(QTL near E1) for flowering time to the region proximal to E1 on chromosome 6 in two mapping populations.Positional cloning revealed Glyma.06G204300,encoding a TCP-type transcription factor,as a strong candidate gene for QNE1.Association analysis further confirmed that functional single nucleotide polymorphisms(SNPs) at nucleotides 686 and 1,063 in the coding region of Glyma.06G204300 were significantly associated with flowering time.The protein encoded by the candidate gene is localized primarily to the nucleus.Furthermore,soybean and Brassica napus plants overexpressing Glyma.06G204300 exhibited early flowering.We conclude that despite their similar effects on flowering time,QNE1 and E4 may control flowering time through different regulatory mechanisms,based on expression studies and weighted gene co-expression network analysis of flowering time-related genes.Deciphering the molecular basis of QNE1 control of flowering time enriches our knowledge of flowering gene networks in soybean and will facilitate breeding soybean cultivars with broader latitudinal adaptation. | Zhengjun Xia Hong Zhai Yanfeng Zhang Yaying Wang Lu Wang Kun Xu Hongyan Wu Jinglong Zhu Shuang Jiao Zhao Wan Xiaobin Zhu Yi Gao Yingxiang Liu Rong Fan Shihao Wu Xin Chen Jinyu Liu Jiayin Yang Qijian Song Zhixi Tian | 2022 | Science China(Life Sciences)2022，65，12： | 1 |
| 12 | GenoBaits Soy40K:a highly flexible and low-cost SNP array for soybean studies显示文摘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. | Yucheng Liu Shulin Liu Zhifang Zhang Lingbin Ni Xingming Chen Yunxia Ge Guoan Zhou Zhixi Tian | 2022 | Science China(Life Sciences)2022，65，9： | 1 |
| 13 | Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities显示文摘 | Zhixi Tian Qian Qian Qiaoquan Liu | 2009 | Proc Natl Acad Sei USA2009，106，21： | 1 |
| 14 | Construction of DNA Fingerprint Using SSR Marker for Hybrid Rice Cultivars Approved by Hunan Province显示文摘[Objective] This study aimed to construct DNA fingerprint for hybrid rice cultivars those have been approved by Hunan Province. [Method] The primers which produced polymorphic and bright DNA bands were selected to construct the DNA molecular fingerprint map for 77 major hybrid rice cultivars approved by Hunan Province. [Result] A total of 48 SSR primers were selected. Every cultivar had its unique fingerprint map so that the obtained data could identify different hybrid rice cultivars. [Conclusion] This study made great contributions to the perfection of hybrid rice germplasm identification. | Qingcai ZHAN Zifa XIAO Keyong ZHU Zhixi LIU Zhaohua LI Shuzhen ZENG | 2012 | Agricultural Biotechnology2012，1，4： | 1 |
| 15 | Precise Positioning Method for Seafloor Geodetic Stations Based on the Temporal Variation of Sound Speed Structure显示文摘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. | Shuang ZHAO Zhenjie WANG Zhixi NIE Kaifei HE Huimin LIU Zhen SUN | 2023 | Journal of Geodesy and Geoinformation Science2023，6，2： | 1 |
| 16 | Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities显示文摘 | Tian Zhixi Qian Qian Liu Qiaoquan | 2009 | Proc Natl Acad Sci USA2009，106，21： | 1 |
| 17 | InP-Based Passive Ring-Resonator-Coupled Lasers显示文摘 | BIAN Zhixi Liu Bin SHAKOURI Ali | 2003 | IEEE Journal of Quan- tum Electronics2003，，7： | 1 |
| 18 | Super graph-based pan-genome: Bringing rice functional genomic study into a new dawn显示文摘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. | Yucheng Liu Zhixi Tian | 2022 | Molecular Plant2022，15，9： | 0 |
| 19 | Impact of the national hepatitis B immunization program in China:a modeling study显示文摘Background:Elimination of hepatitis B virus(HBV)is a striking challenge for countries with high or moderate disease burden.Therefore,using China as a practical case to share experiences for similar countries may accelerate the achievement of the WHO 2030 target of 90%reduction in HBV-related incidence.We aim to evaluate the impact of national HBV immunization strategies in China;and the feasibility to achieve WHO 2030 targets under diferent scenarios.Methods:We constructed an expanded Susceptible-Exposed-Infectious-Recovered(SEIR)model and decision treeMarkov model to estimate the epidemic of HBV in China,assess the feasibility of 2030 Elimination Goals through the projections and conduct the economic analysis.Least square method was used to calibrate the expanded SEIR model by yearly data of laboratory-confrmed HBV cases from 1990 to 2018.Two models were separately used to evaluate the impact and cost-efectiveness of HBV vaccine by comparing prevalence of chronic HBV infections,qualityadjusted life-years(QALYs),incremental cost efectiveness ratio and beneft–cost ratio(BCR)under various intervention options,providing a basis for exploring new containment strategies.Results:Between 1990 and 2020,the number of chronic HBV infections decreased by 33.9%.The current status quo would lead to 55.73 million infections(3.95%prevalence)in 2030,compared to 90.63 million(6.42%prevalence)of the“Without the NIP”scenario(NIP:National Immunization Program),114.78 million(8.13%prevalence)without any interventions.The prevention of mother to child transmission(PMTCT)strategy showed a net beneft as 12,283.50 dollars per person,with BCR as 12.66,which is higher than that of universal vaccination at 9.49.Compared with no screening and no vaccination,the PMTCT strategy could save 7726.03 dollars for each QALY increase.Conclusions:Our fndings proved the HBV vaccination has demonstrated a substantial positive impact on controlling the epidemic of HBV in terms of efectiveness and economy after about 30 years of implementation of the national hepatitis B immunization program which also provided containment experience for high or medium burden countries.As for China,the next step should focus on exploring strategies to improve diagnosis and treatment coverage to reduce the burden of HBV-related deaths and ultimately eliminate HBV. | Zhixi Liu Mengying Li David W.Hutton Abram L.Wagner Ye Yao Wenlong Zhu Lingsheng Cao Shenglan Tang Jinhua Pan Yesheng Wang Qi Zhao Hong Ren Ying Wang Weibing Wang | 2022 | Infectious Diseases of Poverty2022，11，5： | 0 |
| 20 | Vaccination as an alternative to non-drug interventions to prevent local resurgence of COVID-19显示文摘Background:While a COVID-19 vaccine protects people from serious illness and death,it remains a concern when and how to lift the high-cost and strict non-pharmaceutical interventions(NPIs).This study examined the joint efect of vaccine coverage and NPIs on the control of local and sporadic resurgence of COVID-19 cases.Methods:Between July 2021 and January 2022,we collected the large-scale testing information and case number of imported COVID-19 patients from the website of the National Health Commission of China.A compartment model was developed to identify the level of vaccine coverage that would allow safe relaxation of NPIs,and vaccination strategies that can best achieve this level of coverage.We applied Monte Carlo simulation 50000 times to remove random fuctuation efects and obtain ftted/predicted epidemic curve based on various parameters with 95% confdence interval at each time point.Results:We found that a vaccination coverage of 50.4% was needed for the safe relaxation of NPIs,if the vaccine efectiveness was 79.3%.The total number of incidence cases under the key groups frstly strategy was 10^(3) times higher than that of accelerated vaccination strategy.It needed 35 months to fully relax NPIs if the key groups frstly strategy was implemented,and 27 months were needed with the accelerated vaccination strategy.If combined the two strategies,only 8 months are needed to achieve the vaccine coverage threshold for the fully relaxation of NPIs.Sensitivity analyses results shown that the higher the transmission rate of the virus and the lower annual vaccine supply,the more difcult the epidemic could be under control.When the transmission rate increased 25% or the vaccination efectiveness rate decreased 20%,33 months were needed to reduce the number of total incidence cases below 1000.Conclusions:As vaccine coverage improves,the NPIs can be gradually relaxed.Until that threshold is reached,however,strict NPIs are still needed to control the epidemic.The more transmissible SARS-CoV-2 variant led to higher resurgence probability,which indicates the importance of accelerated vaccination and achieving the vaccine coverage earlier. | Jinhua Pan Wenlong Zhu Jie Tian Zhixi Liu Ao Xu Ye Yao Weibing Wang | 2022 | Infectious Diseases of Poverty2022，11，2： | 0 |
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