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| 1 | Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions显示文摘Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies(GWAS). Several rice populations have been re-sequenced in the past decade;however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding. | Xiuxiu Li Zhuo Chen Guomin Zhang Hongwei Lu Peng Qin Ming Qi Ying Yu Bingke Jiao Xianfeng Zhao Qiang Gao Hao Wang Yunyu Wu Juntao Ma Liyan Zhang Yongli Wang Lingwei Deng Shanguo Yao Zhukuang Cheng Diqiu Yu Lihuang Zhu Yongbiao Xue Chengcai Chu Aihong Li Shigui Li Chengzhi Liang | 2020 | Science China(Life Sciences)2020，63，11： | 8 |
| 2 | A nomogram to predict prognosis for gastric cancer with peritoneal dissemination显示文摘Objective: To identify independent prognostic factors to be included in a nomogram to predict the prognosis of gastric cancer patients with peritoneal dissemination.Methods: This is a retrospective study on 684 patients with a histological diagnosis of gastric cancer with peritoneal dissemination from the Sun Yat-sen University Cancer Center as the development set, and 62 gastric cancer patients from the Sixth Affiliated Hospital of Sun Yat-sen University as the validation group. Chi-square test and Cox regression analysis were used to compare the clinicopathological variables and the prognosis of gastric cancer patients with peritoneal dissemination. The Harrell's concordance index(C-index) and calibration curve were determined for comparisons of predictive ability of the nomogram.Results: Univariate and multivariate analyses showed that serum carcinoembryonic antigen(CEA) level(P=0.032), ascites grading(P=0.008), presence of extraperitoneal metastasis(P<0.001), seeding status(P=0.016) and performance status(P=0.009) were independent prognostic factors for gastric cancer patients with peritoneal dissemination in the development set. The nomogram model was constructed using these five factors. Internal validation showed that the C-index of the model was 0.641. For the external validation, the C-index of this model was 0.709.Conclusions: We developed and validated a nomogram to predict the prognosis for gastric cancer patients with peritoneal dissemination. This nomogram may play an important clinical role in guiding palliative therapy for these types of patients, although it may need more data for optimization. | Shi Chen Xijie Chen Runcong Nie Liying Ou Yang Aihong Liu Yuanfang Li Zhiwei Zhou Yingbo Chen Junsheng Peng | 2018 | Chinese Journal of Cancer Research2018，30，4： | 5 |
| 3 | CitGVD:a comprehensive database of citrus genomic variations显示文摘Citrus is one of the most important commercial fruit crops worldwide.With the vast genomic data currently available for citrus fruit,genetic relationships,and molecular markers can be assessed for the development of molecular breeding and genomic selection strategies.In this study,to permit the ease of access to these data,a web-based database,the citrus genomic variation database(CitGVD,http://gffzz1758061741e3440chnvu0f0c0ou6960q6.ffgz.tsg.suse.edu.cn/home)was developed as the first citrusspecific comprehensive database dedicated to genome-wide variations including single nucleotide polymorphisms(SNPs)and insertions/deletions(INDELs).The current version(V1.0.0)of CitGVD is an open-access resource centered on 1,493,258,964 high-quality genomic variations and 84 phenotypes of 346 organisms curated from in-house projects and public resources.CitGVD integrates closely related information on genomic variation annotations,related gene annotations,and details regarding the organisms,incorporating a variety of built-in tools for data accession and analysis.As an example,CitGWAS can be used for genome-wide association studies(GWASs)with SNPs and phenotypic data,while CitEVOL can be used for genetic structure analysis.These features make CitGVD a comprehensive web portal and bioinformatics platform for citrus-related studies.It also provides a model for analyzing genome-wide variations for a wide range of crop varieties. | Qiang Li Jingjing Qi Xiujuan Qin Wanfu Dou Tiangang Lei Anhua Hu Ruirui Jia Guojin Jiang Xiuping Zou Qin Long Lanzhen Xu Aihong Peng Lixiao Yao Shanchun Chen Yongrui He | 2020 | Horticulture Research2020，7，1： | 4 |
| 4 | Cloning and Expression Analysis of Citrus Genes Cs GH3.1 and Cs GH3.6Responding to Xanthomonas axonopodis pv. citri Infection显示文摘To study the functions of the early auxin-responsive genes Cs GH3.1 and Cs GH3.6 in citrus resistance against canker disease, we cloned Cs GH3.1and Cs GH3.6 in ‘Newhall' Navel Orange(Citrus sinensis Osbeck). They are 1 797 bp and 1 887 bp and encode 598 and 629 amino acids, respectively. In vitro mature leaves from susceptible ‘Newhall' and resistant Calamondin(C. madurensis) were inoculated by a Xanthomonas axonopodis pv. citri(Xac) bacterial suspension, and expression of Cs GH3.1 and Cs GH3.6 in the two varieties were analyzed using quantitative real-time PCR(q RT-PCR). ‘Newhall' leaves were treated with different hormones for 3 days, inoculated by Xac bacterial suspension, and then the symptoms in these leaves were investigated. We used q RT-PCR to analyze the effect of different hormones on Cs GH3.1 and Cs GH3.6 expression in ‘Newhall'leaves. The expression levels of both Cs GH3.1 and Cs GH3.6 were significantly induced by Xac in ‘Newhall' leaves, compared with levels in Calamondin leaves. 1-naphthy acetic acid(NAA) increased the hypertrophy of infection sites in ‘Newhall' leaves, while naphthyl-phthalamic acid(NPA)had no visible effect on lesion development. NAA hormone greatly improved expression of Cs GH3.1 in ‘Newhall', but not Cs GH3.6. These results indicate that the auxin primary-response gene Cs GH3.1 plays an important role in citrus susceptibility to Xac. | CHEN Min HE Yongrui XU Lanzhen PENG Aihong LEI Tiangang YAO Lixiao LI Qiang ZHOU Pengfei BAI Xiaojing DUAN Minjie JIANG Xueyou JIA Ruirui ZOU Xiuping CHEN Shanchun | 2016 | Horticultural Plant Journal2016，2，4： | 4 |
| 5 | Genome-wide analysis of NDR1/HIN1-like genes in pepper(Capsicum annuum L.)and functional characterization of CaNHL4 under biotic and abiotic stresses显示文摘Plant NDR1/HIN1-like(NHL)genes play an important role in triggering plant defenses in response to biotic stresses.In this study,we performed a genome-wide identification of the NHL genes in pepper(Capsicum annuum L.)and characterized the functional roles of these CaNHL genes in response to abiotic stresses and infection by different pathogens.Phylogenetic analysis revealed that CaNHLs can be classified into five distinct subgroups,with each group containing generic and specific motifs.Regulatory element analysis showed that the majority of the promoter regions of the identified CaNHLs contain jasmonic acid(JA)-responsive and salicylic acid(SA)-responsive elements,and transcriptomic analysis revealed that CaNHL genes are expressed in all the examined tissues of pepper.The CaNHL1,CaNHL4,CaNHL6,CaNHL10,CaNHL11,and CaNHL12 genes were significantly upregulated under abiotic stress as well as in response to different pathogens,such as TMV,Phytophthora capsici and Pseudomonas syringae.In addition,we found that CaNHL4 localizes to the plasma membrane.CaNHL4-silenced pepper plants display significantly increased susceptibility to TMV,Phytophthora capsici and Pseudomonas syringae,exhibiting reduced expression of JA-related and SA-related genes and reduced ROS production.However,transient overexpression of CaNHL4 in pepper increases the expression of JArelated and SA-related genes,enhances the accumulation of ROS,and inhibits the infection of these three pathogens.Collectively,for the first time,we identified the NHL genes in pepper and demonstrated that CaNHL4 is involved in the production of ROS and that it also regulates the expression of JA-related and SA-related genes in response to different pathogens,suggesting that members of the CaNHL family play an essential role in the disease resistance of pepper. | Changyun Liu Haoran Peng Xinyu Li Chaolong Liu Xing Lv Xuefeng Wei Aihong Zou Jian Zhang Guangjin Fan Guanhua Ma Lisong Ma Xianchao Sun | 2020 | Horticulture Research2020，7，1： | 2 |
| 6 | TSC1 enables plastid development under dark conditions, contributing to rice adaptation to transplantation shock显示文摘Since its domestication from wild rice thousands of years ago, rice has been cultivated largely through transplantation. During transplantation from the nursery to the paddy field, rice seedlings experience transplantation shock which affects their physiology and production.However, the mechanisms underlying transplantation shock and rice adaptation to this shock are largely unknown. Here,we isolated a transplant-sensitive chloroplast-deficient(tsc_1)rice mutant that produces albino leaves after transplantation.Blocking light from reaching the juvenile leaves and leaf primordia caused chloroplast deficiencies in transplanted tsc_1 seedlings. TSC_1 encodes a noncanonical adenosine triphosphate-binding cassette(ABC) transporter homologous to At NAP_(14) and is of cyanobacterial origin. We demonstrate that TSC_1 controls plastid development in rice under dark conditions, and functions independently of light signaling.However, light rescued the tsc_1 mutant phenotype in a spectrum-independent manner. TSC_1 was upregulated following transplantation, and modulated the iron and copper levels, thereby regulating prolamellar body formation during the early P_4 stage of leaf development. Therefore, TSC_1 is indispensable for plastid development in the absence of light,and contributes to adaptation to transplantation shock.Our study provides insight into the regulation of plastid development and establishes a framework for improving recovery from transplantation shock in rice. | Xiaoliang Shi Sunlu Chen Yu Peng Yufeng Wang Jiugeng Chen Zhanghua Hu Baohe Wang Aihong Li Daiyin Chao Yuhong Li Sheng Teng | 2018 | Journal of Integrative Plant Biology2018，60，2： | 2 |
| 7 | The prevalence of dementia in urban and rural areas of China显示文摘 | Jianping Jia Fen Wang Cuibai Wei Aihong Zhou Xiangfei Jia Fang Li Muni Tang Lan Chu Youlong Zhou Chunkui Zhou Yong Cui Qi Wang Weishan Wang Peng Yin Nan Hu Xiumei Zuo Haiqing Song Wei Qin Liyong Wu Dan Li Longfei Jia Juexian Song Ying Han Yi Xing Peijie Y | 2013 | Alzheimer’s & Dementia: The Journal of the Alzheimer’s Association2013，，： | 2 |
| 8 | Enantioseparation by HPLC Using an Inorganic Chiral Mesoporous Silica with Highly-ordered Structure显示文摘Highly-ordered inorganic chiral mesoporous silica(HOCMS)has attracted substantial interest in recent decades.High performance liquid chromatography(HPLC)is the most important approach for the separation of enantiomers and herein reported an HPLC chiral stationary phase composed of HOCMS.The column was fabricated by conventional high pressure slurry packing.Eighteen racemates,including alcohols,ketones,amines,aldehydes and organic acids,were resolved on the column.Good chiral separations of hydrobenzoin,metoprolol,propranolol hydrochloride,4-methyl-2-pentanol,omeprazole,2,2′-furoin and ketoprofen were obtained.The relative standard devi-ations for five replicate separations of racemates were 0.1%–0.16%for retention time and 1.73%–2.64%for peak areas.The results suggest that HOCMS is a promising candidate for preparation of chiral stationary phases for HPLC. | PENG Bo FU Shiguo LI Yanxia ZHANG Junhui XIE Shengming LI Li LYU Yun DU AN Aihong CHEN Xuexian YUAN Liming | 2019 | Chemical Research in Chinese Universities2019，35，6： | 1 |
| 9 | Estimating soil organic carbon using VIS/NIR spectroscopy with SVMR and SPA methods显示文摘 | Peng Xiaoting Shi Tiezhu Song Aihong | 2014 | Remote Sensing2014，6，4： | 1 |
| 10 | Estimating soil organic carbon using Vis/NIR spectroscopy with SVMR and SPA methods显示文摘 | Peng Xiaoting Shi Tiezhu Song Aihong | 2014 | Remote Sensing2014，6，4： | 1 |
| 11 | Effi- cient auto-excision of a selectable marker gene from transgenic citrus by combining the Cre/loxP system and ipt selection 显示文摘 | Zou Xiuping Peng Aihong Xu Lanzhen | 2013 | Plant Cell Rep2013，32，10： | 1 |
| 12 | CsBZIP40 confers resistance against citrus bacterial canker by repressing CsWRKY43-CsPrx53/CsSOD13 cascade mediated ROS scavenging显示文摘As the bacterial etiologic agent causing citrus bacterial canker(CBC),Xanthomonas citri subsp.citri(Xcc)seriously impacts citrus plantation and fruit production globally.In an earlier study,we demonstrated that CsBZIP40 can positively impact CBC resistance in the sweet orange(Citrus sinensis).However,the mechanistic basis for the protective benefits conferred by CsBZIP40 is yet to be delineated.Here,we show that CsBZIP40 positively regulates CBC resistance and reactive oxygen species(ROS)homeostasis in transgenic sweet orange overexpressing CsBZIP40.CsBZIP40 directly binds to the TGA-box of the CsWRKY43 promoter to repress its transcriptional activity.CsWRKY43 overexpression induces CBC susceptibility in transgenic sweet oranges.In contrast,its inhibition produces strong resistance to CBC.CsWRKY43 directly binds to the W-boxes of the CsPrx53 and CsSOD13 promoters to positively regulate the activities of these antioxidant enzymes,resulting in the negative regulation of ROS homeostasis and CBC resistance in sweet orange plants.CsPrx53/CsSOD13 knockdown enhances ROS accumulation and CBC resistance.Overall,our results outline a regulatory pathway through which CsBZIP40 transcriptionally represses CsWRKY43-CsPrx53/CsSOD13 cascade-mediated ROS scavenging in a manner conducive to CBC resistance.These mechanisms underscore the potential importance of CsBZIP40,CsWRKY43,CsPrx53,and CsSOD13,providing promising strategies for the prevention of CBC. | Qiang Li Xiujuan Qin Miao Zhang Qiyuan Yu Ruirui Jia Jie Fan Xin Huang Jia Fu Chenxi Zhang Baohang Xian Wen Yang Qin Long Aihong Peng Lixiao Yao Shanchun Chen Yongrui He | 2023 | Horticulture Research2023，10，8： | 0 |
| 13 | Production of marker-free transgenic plants from mature tissues of navel orange using a Cre/loxP site-recombination system显示文摘Genetic transformation with mature material as the explants could shorten the transgenic period and avoid seed dependence compared with genetic transformation using the epicotyl seedling stem segments as the receptor. Here, we constructed an Agrobacterium tumefaciensmediated transformation for generation of marker-free transgenic plants from navel orange(Citrus sinensis Osbeck) mature stems using a CreloxP recombination system. To efficiently recover the regenerated buds from mature tissues, five recovery methods were compared: in vitro micrografting of 0.1-0.5(1-2 weeks), > 0.5 cm(3-4 weeks) and > 1 cm long lignified bud and in vitro micrografting of explants with a bud and rooting regenerated bud. The data showed that in vitro micrografting of > 1 cm long regenerated bud with expanded leaves after one month of continuous culture for lignification was the optimal solution for plant recovery from mature tissues. Transgenic plants without selectable marker genes were created from navel orange(Citrus sinensis Osbeck) tissue using a transformation vector PLI-35SPR1aCB containing a Cre/loxP system recombination together with genes encoding the selectable marker isopentenyl transferase(IPT) and an anti-bacterial peptide(PR1aCB).Using IPT positive selection, the transformation efficiency determined by PCR was 0.9%, and in total, 20 transgenic plants were obtained.Southern blotting confirmed further their transgenicity. PCR and sequencing analysis demonstrated that both the Cre and IPT genes had been successfully removed from the transgenic plants(deletion efficiency 100%). Over all, using Cre/loxP system recombination together with the IPT positive selection, marker-free transgenic plants can be recovered efficiently from mature tissues of navel orange(Citrus sinensis Osbeck), which provides a potential method for production of transgenic plants from citrus mature tissue. | Yongrui He Lanzhen Xu Aihong Peng Tiangang Lei Qiang Li Lixiao Yao Guojin Jiang Shanchun Chen Zhengguo Li Xiuping Zou | 2023 | Horticultural Plant Journal2023，9，3： | 0 |
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