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| 1 | A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding显示文摘一个高密度的单个核苷酸多型性(SNP ) 数组为遗传学者和分子的 breeders.With 是极其重要的 genomic 的巨大的数量的累积重新定序为精确 SNP 察觉的数据和可得到的技术,设计高密度、高质量的米饭 SNP 数组是可能的。这里,我们报导一个高密度的 riceSNP 数组和它的实用程序的开发。SNP 探针被屏蔽超过 10 设计从变化和一个数组说出 RiceSNP50 的 801 米饭的 re-sequencingdata 提取的 000 000 SNP loci 在 Illumina Infinium 站台上被生产。数组 contained51 478 个均匀地分布式的标记,其 68% 个在遗传因子的区域以内。有 parent/F1 relationshipswere 的几百米饭植物过去常为精确 SNP 打电话产生一个高质量的簇文件。应用程序测试证明这穿有的 highgenotyping 精确性,并且能被用于不同目的。例如,有好分辨率的精英米饭变化 wasclustered 的一个核心集合。染色体宽的协会研究(GWAS ) 分析正确地识别了描绘的 QTL.Further,这个数组成功地为变化确认和特点基因渗入被使用。作为一个精确 high-throughputgenotyping 工具, RiceSNP50 将在两功能的 genomics 学习和分子的 breeding.Key 词起一个重要作用: | Haodong Chen Weibo Xie Hang He Huihui Yu Wei Chen Jing Li Renbo Yu Yue Yao Wenhui Zhang Yuqing He Xiaoyan Tang Fasong Zhou Xing Wang Deng Qifa Zhang | 2014 | Molecular Plant2014，7，3： | 38 |
| 2 | Two gap-free reference genomes and a global view of the centromere architecture in rice显示文摘Rice(Oryza sativa),a major staple throughout the world and a model system for plant genomics and breeding,was the first crop genome sequenced almost two decades ago.However,reference genomes for all higher organisms to date contain gaps and missing sequences.Here,we report the assembly and analysis of gap-free reference genome sequences for two elite O.sativa xian/indica rice varieties,Zhenshan 97 and Minghui 63,which are being used as a model system for studying heterosis and yield.Gap-free reference genomes provide the opportunity for a global view of the structure and function of centromeres.We show that all rice centromeric regions share conserved centromere-specific satellite motifs with different copy numbers and structures.In addition,the similarity of CentO repeats in the same chromosome is higher than across chromosomes,supporting a model of local expansion and homogenization.Both genomes have over 395 non-TE genes located in centromere regions,of which∼41%are actively transcribed.Two large structural variants at the end of chromosome 11 affect the copy number of resistance genes between the two genomes.The availability of the two gap-free genomes lays a solid foundation for further understanding genome structure and function in plants and breeding climate-resilient varieties. | Jia-Ming Song Wen-Zhao Xie Shuo Wang Yi-Xiong Guo Dal-Hoe Koo Dave Kudrna Chenbo Gong Yicheng Huang Jia-Wu Feng Wenhui Zhang Yong Zhou Andrea Zuccolo Evan Long Seunghee Lee Jayson Talag Run Zhou Xi-Tong Zhu Daojun Yuan Joshua Udall Weibo Xie Rod AWing Qifa Zhang Jesse Poland Jianwei Zhang Ling-Ling Chen | 2021 | Molecular Plant2021，14，10： | 9 |
| 3 | Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F2 Population显示文摘Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an 'immortalized F2' population composed of 105 hybrids produced by intercrossing recombinant inbred lines(RILs) from a cross between Zhenshan 97 and Minghui 63,the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance(epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F_1 hybrid. | Dan Zhu Gang Zhou Caiguo Xu Qifa Zhang | 2016 | Journal of Genetics and Genomics2016，43，2： | 8 |
| 4 | From Green Super Rice to green agriculture:Reaping the promise of functional genomics research显示文摘Producing sufficient food with finite resources to feed the growing global population while having a smaller impact on the environment has always been a great challenge.Here,we review the concept and practices of Green Super Rice(GSR)that have led to a paradigm shift in goals for crop genetic improvement and models of food production for promoting sustainable agriculture.The momentous achievements and global deliveries of GSR have been fueled by the integration of abundant genetic resources,functional gene discoveries,and innovative breeding techniques with precise gene and whole-genome selection and efficient agronomic management to promote resource-saving,environmentally friendly crop production systems.We also provide perspectives on new horizons in genomic breeding technologies geared toward delivering green and nutritious crop varieties to further enhance the development of green agricul-ture and better nourish the world population. | Sibin Yu Jauhar Ali Shaochuan Zhou Guangjun Ren Huaan Xie Jianlong Xu Xinqiao Yu Fasong Zhou Shaobing Peng Liangyong Ma Dingyang Yuan Zefu Li Dazhou Chen Ruifeng Zheng Zhigang Zhao Chengcai Chu Aiqing You Yu Wei Susong Zhu Qiongyao Gu Guangcun He Shigui Li Guifu Liu Changhua Liu Chaopu Zhang Jinghua Xiao Lijun Luo Zhikang Li Qifa Zhang | 2022 | Molecular Plant2022，15，1： | 6 |
| 5 | Integrated genomic analysis identifies deregulated JAK/STAT-MYC-biosynthesis axis in aggressive NK-cell leukemia显示文摘好攻击的 NK 房间白血病(ANKL ) 是在从亚洲的人之中是更流行的 NK 房间瘤的一种稀罕形式并且中央并且南美洲。病人们通常在天以内死到月,甚至在收到迅速的治疗学的管理以后。这里,我们由集成整个染色体执行了 ANKL 的第一全面研究, transcriptome 并且定序指向,象功能的试金一样的 cytokine 数组。在 JAK-STAT 小径的变化在 48% 被识别(14/29 ) ANKL 病人,当细胞外的 STAT3 激发器 IL10 被 56 褶层的一般水准提高时(P < 0.0001 ) 在检查的所有病人的血浆。另外的经常变异的基因包括的 TP53 (34%) , TET2 (28%) , CREBBP (21%) 和 MLL2 (21%) 。耐心的 NK 白血病房间在多重新陈代谢的小径显示出 STAT3 phosphorylation, MYC 表示和 transcriptional 活动的突出的激活。机能上地, STAT3 激活和 MYC 表示为 ANKL 房间的增长和幸存是批评的。发信号的 STAT 调整了发信号的 MYC 抄写节目,和两 STAT, MYC 抄写被要求维持核苷酸合成和 glycolysis 的激活。一起, JAK-STAT 小径在 ANKL 为 genomic 改变和 IL10 刺激代表一个主要目标。这最新发现的 JAK/STAT-MYC-biosynthesis 轴可以在对待白血病的这种子类型为新奇治疗学的策略的发展提供机会。 | Liang Huang Dan Liu Na Wang Shaoping Ling Yuting Tang Jun Wu Lingtong Hao Hui Luo Xuelian Hu Lingshuang Sheng Lijun Zhu Di Wang Yi Luo Zhen Shang Min Xiao Xia Mao Kuangguo Zhou Lihua Cao Lili Dong Xinchang Zheng Pinpin Sui Jianlin He Shanlan Mo Jin Yan Qilin Ao Lugui Qiu Hongsheng Zhou Qifa Liu Hongyu Zhang Jianyong Li Jie Jin Li Fu Weili Zhao Jieping Chen Xin Du Guoliang Qing Hudan Liu Xin Liu Gang Huang Ding Ma Jianfeng Zhou Qian-fei Wang | 2018 | Cell Research2018，28，2： | 5 |
| 6 | Suppression of starch synthase I(SSI) by RNA interference alters starch biosynthesis and amylopectin chain distribution in rice plants subjected to high temperature显示文摘Based on known cDNAs of rice starch synthase isoforms,we constructed dsRNA interference vectors for starch synthase I(SSI)to produce transgenic plants containing starch with a moderately high amylose content.We investigated the effect of SSI suppression on grain quality traits,starch biosynthesis,and amylopectin chain distribution in rice plants exposed to two different temperature regimes.The activities and transcripts of BEs,DBEs,and other SS isoforms were further investigated to clarify the effect of SSI suppression on these key enzymes and their specific isoforms under different temperature treatments.Suppression of SSI by RNAi altered grain starch component and amylopectin chain distribution,but it exerted only a slight effect on total starch content(%)and accumulation amount(mg kernel?1)and on starch granule morphology and particle size distribution.Under normal temperature(NT),insignificant differences in kernel weight,chalky kernel proportion,chalky degree,and starch granule morphology between SSI-RNAi line and its wild type(WT)were observed.However,amylose content(AC)level and granule-bound starch synthase(GBSS)activity in rice endosperms were markedly increased by SSI-RNAi suppression.The chalky kernel proportion and chalky degree of SSIRNAi lines were significantly higher than those of WT under high temperature(HT)exposure at filling stage.Inhibition of SSI by RNAi affected amylopectin chain distribution and raised starch gelatinization temperature(GT)in two ways:directly from the SSI deficiency itself and indirectly by reducing BEIIb amounts in an SSI-deficient background.The deficiency of SSI expression led to an alteration in the susceptibility of grain chalkiness occurrence and starch gelatinization temperature to HT exposure,owing to a pleiotropic effect of SSI deficiency on the expression of other genes associated with starch biosynthesis. | Qian Zhao Xiaoxia Du Zhanyu Han Yu Ye Gang Pan Muhammad-Asad-Ullah Asad Qifa Zhou Fangmin Cheng | 2019 | The Crop Journal2019，7，5： | 2 |
| 7 | Real-time whole-brain imaging of hemodynamics and oxygenation at micro-vessel resolution with ultrafast wide-field photoacoustic microscopy显示文摘High-speed high-resolution imaging of the whole-brain hemodynamics is critically important to facilitating neurovascular research.High imaging speed and image quality are crucial to visualizing real-time hemodynamics in complex brain vascular networks,and tracking fast pathophysiological activities at the microvessel level,which will enable advances in current queries in neurovascular and brain metabolism research,including stroke,dementia,and acute brain injury.Further,real-time imaging of oxygen saturation of hemoglobin(sO_(2))can capture fast-paced oxygen delivery dynamics,which is needed to solve pertinent questions in these fields and beyond.Here,we present a novel ultrafast functional photoacoustic microscopy(UFF-PAM)to image the whole-brain hemodynamics and oxygenation.UFF-PAM takes advantage of several key engineering innovations,including stimulated Raman scattering(SRS)based dual-wavelength laser excitation,water-immersible 12-facet-polygon scanner,high-sensitivity ultrasound transducer,and deep-learning-based image upsampling.A volumetric imaging rate of 2 Hz has been achieved over a field of view(FOV)of 11×7.5×1.5 mm^(3) with a high spatial resolution of~10 μm.Using the UFF-PAM system,we have demonstrated proof-of-concept studies on the mouse brains in response to systemic hypoxia,sodium nitroprusside,and stroke.We observed the mouse brain's fast morphological and functional changes over the entire cortex,including vasoconstriction,vasodilation,and deoxygenation.More interestingly,for the first time,with the whole-brain FOV and micro-vessel resolution,we captured the vasoconstriction and hypoxia simultaneously in the spreading depolarization(SD)wave.We expect the new imaging technology will provide a great potential for fundamental brain research under various pathological and physiological conditions. | Xiaoyi Zhu Qiang Huangl Anthony Dispirito Tri Vu Qiangzhou Rong Xiaorui Peng Huaxin Sheng Xiling Shen Qifa Zhou Laiming Jiang Ulrike Hoffmann Junjie Yao | 2022 | Light(Science & Applications)2022，11，6： | 2 |
| 8 | Band selection for analysing wheat water status under field condition susing relative depth indices ( RDI ) 显示文摘 | ZHAO CHUNJIANG ZHOU QIFA WANG JIHUA | 2004 | International Journal of Remote Sensing2004，25，13： | 1 |
| 9 | Molecular marker heterozygosity and hybrid performance in indica and japonica rice显示文摘 | Qifa Zhang Z. Q. Zhou G. P. Yang C. G. Xu K. D. Liu M. A. Saghai Maroof | 1996 | Theoretical and Applied Genetics1996，，8： | 1 |
| 10 | An in-situ Technique for Producing Low-Cost Agricultural Biochar显示文摘Application of biochar to agricultural soils is effective to sequester atmospheric carbon and improve soil quality, but current pyrolysis and transportation costs are high, making biochar too costly to be used at the field scale. This study developed a new in-situ technique, burning and soil covering(B-SC), which can be used by farmers for production of biochar with crop residue. In this study,the air-dried feedstocks, elephant grass and corn residue, were burnt in situ for biochar production in the field. After approximately 90% of the leaves were combusted, the burning process was dramatically slowed down by covering the feedstock with soil. The biochar yield averaged 18.0 ± 1.3(n = 15) and 13.7 ± 1.3(n = 10) kg per 100 kg air-dried feedstock for the elephant grass and corn residue,respectively. The biochar properties were suitable for soil improvement. The inputs for biochar production of the B-SC process only included low labor force, open field, feedstock(e.g., grass and crop residue), and simple tools. The operation time for processing 10 kg of the corn residue by an individual farmer was 24.4 ± 4.1 min(n = 10). As compared with the conventional field burning process, the B-SC process drastically shortened the time for biomass burning and generated a significantly lower emission of smoke and thermal energy. This simple technique can be particularly practical and effective for farmers to improve the soils of poor quality in China. | ZHOU Qifa Benjamin A.HOUGE Zhaohui TONG Bin GAO Guodong LIU | 2018 | Pedosphere2018，28，4： | 1 |
| 11 | Design and implementation of high frequency ultrasound pulsed-wave Doppler using FPGA显示文摘 | Hu Changhong Zhou Qifa | 2008 | IEEE Transactions on Ultrasonic Ferroelectrics and Frequency Control2008，55，9： | 1 |
| 12 | Overexpressed glutamine synthetase gene modifies nitrogen metabolism and abiotic stress responses in rice显示文摘 | Hongmei Cai Ying Zhou Jinghua Xiao Xianghua Li Qifa Zhang Xingming Lian | 2009 | Plant Cell Reports2009，，3： | 1 |
| 13 | Global genome expression analysis of rice in response to drought and high-salinity stresses in shoot, flag leaf, and panicle显示文摘 | Junli Zhou Xiangfeng Wang Yuling Jiao Yonghua Qin Xigang Liu Kun He Chen Chen Ligeng Ma Jian Wang Lizhong Xiong Qifa Zhang Liumin Fan Xing Wang Deng | 2007 | Plant Molecular Biology2007，，5： | 1 |
| 14 | Molecular monitoring and stepwise preemptive therapy for Epstein–Barr virus viremia after allogeneic stem cell transplantation显示文摘 | Qifa Liu Li Xuan Hui Liu Fen Huang Hongsheng Zhou Zhiping Fan Ke Zhao Meiqing Wu Lanping Xu Xiao Zhai Fuhua Zhang Can Liu Jing Sun Xiaojun Huang | 2013 | Am. J. Hematol2013，，7： | 1 |
| 15 | Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs显示文摘 | Yi Huang Lida Zhang Jianwei Zhang Dejun Yuan Caiguo Xu Xianghua Li Daoxiu Zhou Shiping Wang Qifa Zhang | 2006 | Plant Molecular Biology (-)2006，，4： | 1 |
| 16 | Coded excitation using biphase-coded pulse with mismatched filters for high- frequency ultrasound imaging 显示文摘 | Hu Changhong Liu Ruibin Zhou Qifa | 2006 | Ultrasonics2006，44，： | 1 |
| 17 | Structure and raman spectroscopy of nanocrystalline TiO2 powder derived by sol-gel process显示文摘 | Zhou Qifa Wu Shanghua | 1997 | Chin Plays Lett1997，14，4： | 1 |
| 18 | Comparison of upper leaf and lower leaf of rice plants in response to supplemental nitrogen levels显示文摘 | Zhou Qifa Wang Jihua | 2002 | Journal of Plant Nutrition2002，26，： | 1 |
| 19 | Spectral indices redefined in detecting nitrogen availability for wheat canopy显示文摘 | Zhao Chunjiang Zhou Qifa Wang Jihua | 2004 | Communications in Soil Science and Plant Analysis2004，35，： | 1 |
| 20 | Band selection for analyzing wheat water status under field conditions using relative depth indices (RDI)显示文摘 | Zhao Chunjiang Zhou Qifa Wang Jihua | 2004 | International Journal of Remote Sensing2004，25，： | 1 |
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