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| 1 | Cloning and expression profiles of 15 genes encoding WRKY transcription factor in wheat (Triticum aestivem L.)显示文摘WRKY proteins are involved in various physiological processes,including biotic and abiotic stress responses,hormone responses and development.However,no systematic identification,expression and function analysis of WRKY genes in wheat were reported.In this study,we isolated 15 wheat cDNAs with complete open reading frame(ORF)encoding putative WRKY proteins using in silico cloning.Phylogenetic analysis indicated that the 15 wheat WRKY genes belonged to three major WRKY groups.Expression analysis revealed that most genes expressed drastically in leaf,except TaWRKY10 which expressed in crown intensively.Four genes were strongly up-reg-ulated with the senescence of leaves.Eight genes were responsive to low temperature,high temperature,NaCl or PEG treatment.More-over,dierential expression patterns were also observed between wheat hybrid and its parents,and some genes were more responsive to PEG treatment in the hybrid.These results demonstrated that wheat WRKY genes are involved in leaf senescing and abiotic stresses.And the changed expression of these WRKY genes in hybrid might contribute to the heterosis by improving the stress tolerance in hybrids. | Hualing Wu Zhongfu Ni Yingyin Yao Ganggang Guo Qixin Sun | 2008 | Progress in Natural Science:Materials International2008，18，6： | 34 |
| 2 | Analysis of genome-wide gene expression in root of wheat hybrid and its parents using Barleyl GeneChip显示文摘以前的研究显示在混血儿和他们的父母之间的那微分基因表情为杂种优势负责。在这篇论文,我们在根报导染色体宽的基因表示分析一高度 heter 用大麦 GeneChip 的耳的种间的混合 3338/2463 和它的父母 inbreds。1187 基因的一个总数在在混合 3338/2463 和它的父母之间的基因表情显示了差别,并且他们能被聚类进八个微分表示模式。进一步的分析表明在这 1187 基因之中, 975 基因显示出高顺序类似到 GenBank 条目,并且代表了多样的功能的范畴,例如新陈代谢,细胞生长和维护,信号 transduction,强调的反应,抄写规定和其它。十四基因为 RT-PCR 分析和 9 的表示模式(64.29%) 被选择基因被证实。显著地, 380 差别表示了基因能在中国春天删除箱上被印射,并且分别地与在七个 homoeologous 组的基因的数字是 158, 148, 121, 140, 132, 94 和 127。有比较印射的表示基因将提供的差别的系统的鉴定的联合推进卓见进杂种优势的分子的基础的理解,这被结束。 | ZHANG Yinhong NI Zhongfu YAO Yingyin ZHAO Jun SUN Oixin | 2006 | Progress in Natural Science:Materials International2006，16，7： | 11 |
| 3 | Wheat genomic study for genetic improvement of traits in China显示文摘Bread wheat(Triticum aestivum L.)is a major crop that feeds 40%of the world’s population.Over the past several decades,advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat,and the genetic basis of agronomically important traits,which promote the breeding of elite varieties.In this review,we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield,end-use traits,flowering regulation,nutrient use efficiency,and biotic and abiotic stress responses,and various breeding strategies that contributed mainly by Chinese scientists.Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools,highthroughput phenotyping platforms,sequencing-based cloning strategies,high-efficiency genetic transformation systems,and speed-breeding facilities.These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture in China and throughout the world. | Jun Xiao Bao Liu Yingyin Yao Zifeng Guo Haiyan Jia Lingrang Kong Aimin Zhang Wujun Ma Zhongfu Ni Shengbao Xu Fei Lu Yuannian Jiao Wuyun Yang Xuelei Lin Silong Sun Zefu Lu Lifeng Gao Guangyao Zhao Shuanghe Cao Qian Chen Kunpu Zhang Mengcheng Wang Meng Wang Zhaorong Hu Weilong Guo Guoqiang Li Xin Ma Junming Li Fangpu Han Xiangdong Fu Zhengqiang Ma Daowen Wang Xueyong Zhang Hong-Qing Ling Guangmin Xia Yiping Tong Zhiyong Liu Zhonghu He Jizeng Jia Kang Chong | 2022 | Science China(Life Sciences)2022，65，9： | 9 |
| 4 | A natural variation in Ribonuclease H-like gene underlies Rht8 to confer“Green Revolution”trait in wheat显示文摘Dear Editor,Introduction of gibberellin(GA)-insensitive Reduced height(Rht)genes,Rht-B1b and Rht-D1b,has resulted in the“Green Revolution”in modern wheat cultivars(Triticum aestivum)that has skyrocketed wheat grain yields worldwide since the 1960s(Peng et al.,1999;Velde et al.,2021).However,Rht-B1b/D1b also reduce coleoptiles,which is undesired in dryland regions where deep planting is essential for seedling establishment(Rebetzke et al.,1999,Rebetzke et al.,2001;Ellis et al.,2004). | Lingling Chai Mingming Xin Chaoqun Dong Zhaoyan Chen Huijie Zhai Junhong Zhuang Xuejiao Cheng Naijiao Wang Jia Geng Xiaobo Wang Ruolin Bian Yingyin Yao Weilong Guo Zhaorong Hu Huiru Peng Guihua Bai Qixin Sun Zhenqi Su Jie Liu Zhongfu Ni | 2022 | Molecular Plant2022，15，3： | 8 |
| 5 | Shaping polyploid wheat for success:Origins,domestication,and the genetic improvement of agronomic traits显示文摘Bread wheat(Triticum aestivum L.,AABBDD,2 n=6 x=42),which accounts for most of the cultivated wheat crop worldwide,is a typical allohexaploid with a genome derived from three diploid wild ancestors.Bread wheat arose and evolved via two sequential allopolyploidization events and was further polished through multiple steps of domestication.Today,cultivated allohexaploid bread wheat has numerous advantageous traits,including adaptive plasticity,favorable yield traits,and extended end-use quality,which have enabled its cultivation well beyond the ranges of its tetraploid and diploid progenitors to become a global staple food crop.In the past decade,rapid advances in wheat genomic research have considerably accelerated our understanding of the bases for the shaping of complex agronomic traits in this polyploid crop.Here,we summarize recent advances in characterizing major genetic factors underlying the origin,evolution,and improvement of polyploid wheats.We end with a brief discussion of the future prospects for the design of gene cloning strategies and modern wheat breeding. | Jie Liu Yingyin Yao Mingming Xin Huiru Peng Zhongfu Ni Qixin Sun | 2022 | Journal of Integrative Plant Biology2022，64，2： | 5 |
| 6 | Genomic and genic sequence variation in synthetic hexaploid wheat (AABBDD) as compared to their parental species显示文摘In order to understand the genomic changes during the evolution of hexaploid wheat, two sets of synthetic hexaploid wheat from hybridization between maternal tetraploid wheat (AABB) and paternal diploid goat grass (DD) were used for DNA-AFLP and single strand conformation polymorphism (SSCP) analysis to determine the genomic and genic variation in the synthetic hexaploid wheat. Results indicated that more DNA sequences from paternal diploid species were eliminated in the synthetic hexaploid wheat than from maternal tetraploid wheat, suggesting that genome from parental species of lower ploidity tends to be eliminated preferentially. However, sequence variation detected by SSCP procedure was much lower than those detected by DNA-AFLP, which indicated that much less variation in the genic regions occurred in the synthetic hexaploid wheat, and sequence variations detected by DNA-AFLP could be derived mostly from non-coding regions and repetitive sequences. Our results also indicated that sequence variation in 4 genes can be detected in hybrid F1, which suggested that this type of sequence variation could be resulted from distant hybridization. It was interesting to note that 3 out of the 4 genes were mapped and clustered on the long arm of chromosome 2D, which indicated that variation in genic sequences in synthetic hexaploid wheat might not be a randomized process. | Lihong Nie Zongfu Han Lahu Lu Yingyin Yao Qixin Sun Zhongfu Ni | 2008 | Progress in Natural Science:Materials International2008，18，5： | 4 |
| 7 | Ectopic expression of VRT-A2 underlies the origin of Triticum polonicum and Triticum petropavlovskyi with long outer glumes and grains显示文摘Polish wheat (Triticum polonicum) is a unique tetraploid wheat species characterized by an elongated outer glume. The genetic control of the long-glume trait by a single semi-dominant locus, P1 (from Polish wheat), was established more than 100 years ago, but the underlying causal gene and molecular nature remain elusive. Here, we report the isolation of VRT-A2, encoding an SVP-clade MADS-box transcription factor, as the P1 candidate gene. Genetic evidence suggests that in T. polonicum, a naturally occurring sequence rearrangement in the intron-1 region of VRT-A2 leads to ectopic expression of VRT-A2 in floral organs where the long-glume phenotype appears. Interestingly, we found that the intron-1 region is a key ON/OFF molecular switch for VRT-A2 expression, not only because it recruits transcriptional repressors, but also because it confers intron-mediated transcriptional enhancement. Genotypic analyses using wheat accessions indicated that the P1 locus is likely derived from a single natural mutation in tetraploid wheat, which was subsequently inherited by hexaploid T. petropavlovskyi. Taken together, our findings highlight the promoter-proximal intron variation as a molecular basis for phenotypic differentiation, and thus species formation in Triticum plants. | Jing Liu Zhaoyan Chen Zhihui Wang Zhaoheng Zhang Xiaoming Xie Zihao Wang Lingling Chai Long Song Xuejiao Cheng Man Feng Xiaobo Wang Yanhong Liu Zhaorong Hu Jiewen Xing Zhenqi Su Huiru Peng Mingming Xin Yingyin Yao Weilong Guo Qixin Sun Jie Liu Zhongfu Ni | 2021 | Molecular Plant2021，14，9： | 4 |
| 8 | Cloning and characterization of an up-regulated GA 20-oxidase gene in hybrid maize显示文摘Previous studies revealed that GA content and metabolism are positively correlated with a faster shoot growth rate of hybrid,and recently,genes participating in both GA biosynthesis and GA response pathways were also found to be differentially expressed between wheat hybrid and its parental inbreds. In this study,an up-regulated GA 20-oxidase gene in a maize hybrid,designated ZmGA20,was cloned. ZmGA20 contains an open reading frame (ORF) encoding 391 amino acid residues. BLASTX searches in GenBank revealed that the ZmGA20 is homologous to the sequences of GA20ox proteins from different species,and analysis also indicated that ZmGA20 had typical features of GA 20-oxidase proteins,including a 'LPWKET' sequence. Semi-quantitative RT-PCR analysis showed that ZmGA20 was expressed in different tissues and/or organs. The expression level of ZmGA20 in the hybrid was higher than that in two parents (in roots,leaves,stems and embryo,and ears). The abundance of ZmGA20 transcript was equal to that of the highly expressed parents,which provided molecular evidence for the observed GA content heterosis in maize hybrids. | Jinkun Du Yingyin Yao Zhongfu Ni Qixin Sun | 2009 | Progress in Natural Science:Materials International2009，19，2： | 4 |
| 9 | Transcriptome Comparison of Susceptible and Resistant Wheat in Response to Powdery Mildew Infection显示文摘Powdery mildew(Pm) caused by the infection of Blumeria graminis f.sp.tritici(Bgt) is a worldwide crop disease resulting in significant loss of wheat yield.To profile the genes and pathways responding to the Bgt infection,here,using Affymetrix wheat microarrays,we compared the leaf transcriptomes before and after Bgt inoculation in two wheat genotypes,a Pm-susceptible cultivar Jingdong 8(S) and its near-isogenic line(R) carrying a single Pm resistant gene Pm30.Our analysis showed that the original gene expression status in the S and R genotypes of wheat was almost identical before Bgt inoculation,since only 60 genes exhibited differential expression by P = 0.01 cutoff.However,12 h after Bgt inoculation,3014 and 2800 genes in the S and R genotype,respectively,responded to infection.A wide range of pathways were involved,including cell wall fortification,flavonoid biosynthesis and metabolic processes.Furthermore,for the first time,we show that sense-antisense pair genes might be participants in wheat-powdery mildew interaction.In addition,the results of qRT-PCR analysis on several candidate genes were consistent with the microarray data in their expression patterns.In summary,this study reveals leaf transcriptome changes before and after powdery mildew infection in wheat near-isogenic lines,suggesting that powdery mildew resistance is a highly complex systematic response involving a large amount of gene regulation. | Mingming Xin Xiangfeng Wang Huiru Peng Yingyin Yao Chaojie Xie Yao Han ZhongfuNi Qixin Sun | 2012 | Genomics, Proteomics & Bioinformatics2012，10，2： | 3 |
| 10 | Epigenetic modification contributes to the expression divergence of three T a EXPA 1 homoeologs in hexaploid wheat ( T riticum aestivum )显示文摘 | Zhaorong Hu Zongfu Han Na Song Lingling Chai Yingyin Yao Huiru Peng Zhongfu Ni Qixin Sun | 2013 | New Phytol2013，，4： | 2 |
| 11 | Ectopic Overexpression of Wheat Adenosine Diphosphate-ribosylation Factor,TaARF,Increases Growth Rate in Arabidopsis显示文摘Differential gene expression between hybrids and their parents is considered to be associated with heterosis. However,the physiological functions and possible contribution to heterosis of these differentially expressed genes are unknown.We have isolated one hybrid upregulated gene encoding putative wheat ADP-ribosylation factor, designated TaARF. In thisstudy, real-time quantitative reverse transcription-polymerase chain reaction analysis indicated that the TaARF transcriptwas preferentially expressed in root, node and crown, and the accumulation of TaARF mRNA in hybrid was more than1.5-fold higher than that in two parents. In order to understand possible roles of the putative wheat ARF gene, TaARFwas overexpressed in Arabidopsis, and the transgenic plants were characterized. We show that ectopic overexpression ofTaARF in Arabidopsis leads to increased leaf area, increased growth rate and earlier transition to flowering, suggestingthat TaARF plays significant roles in growth and development. This study provides evidence demonstrating that TaARFplays important roles in gr owth and development and we speculate that the upregulated expression of this gene mightcontribute to the heterosis observed in wheat root and leaf growth. | Yingyin Yao Zhongfu Ni Jinkun Du Zongfu Han Yan Chen Qingbo Zhang Qixin Sun | 2009 | Journal of Integrative Plant Biology2009，51，1： | 2 |
| 12 | A wheat integrative regulatory network from large-scale complementary functional datasets enables trait-associated gene discovery for crop improvement显示文摘Gene regulation is central to all aspects of organism growth,and understanding it using large-scale functional datasets can provide a whole view of biological processes controlling complex phenotypic traits in crops.However,the connection between massive functional datasets and trait-associated gene discovery for crop improvement is still lacking.In this study,we constructed a wheat integrative gene regulatory network(wGRN)by combining an updated genome annotation and diverse complementary functional datasets,including gene expression,sequence motif,transcription factor(TF)binding,chromatin accessibility,and evolutionarily conserved regulation.wGRN contains 7.2 million genome-wide interactions covering 5947 TFs and 127439 target genes,which were further verified using known regulatory relationships,condition-specific expression,gene functional information,and experiments.We used wGRN to assign genome-wide genes to 3891 specific biological pathways and accurately prioritize candidate genes associated with complex phenotypic traits in genome-wide association studies.In addition,wGRN was used to enhance the interpretation of a spike temporal transcriptome dataset to construct high-resolution networks.We further unveiled novel regulators that enhance the power of spike phenotypic trait prediction using machine learning and contribute to the spike phenotypic differences among modern wheat accessions.Finally,we developed an interactive webserver,wGRN(http://gffzzaeec8df70e7c4b21hxvcwcu9bvfp96cuu.ffgz.tsg.suse.edu.cn/wGRN),for the community to explore gene regulation and discover trait-associated genes.Collectively,this community resource establishes the foundation for using large-scale functional datasets to guide trait-associated gene discovery for crop improvement. | Yongming Chen Yiwen Guo Panfeng Guan Yongfa Wang Xiaobo Wang Zihao Wang Zhen Qin Shengwei Ma Mingming Xin Zhaorong Hu Yingyin Yao Zhongfu Ni Qixin Sun Weilong Guo Huiru Peng | 2023 | Molecular Plant2023，16，2： | 1 |
| 13 | New lysine-acetylated proteins screened by immunoaffinity and liquid chromatography-mass spectrometry显示文摘The lack of selective extraction specific for lysine-acetylated proteins has been a major problem in the field of acetylation biology,though acetylation plays a key role in many biological processes.In this paper,we report for the first time the proteomic screening of lysine-acetylated proteins from a mouse liver tissue,by a new approach of immunoaffinity purification of lysine-acetylated peptides combined with nano-HPLC/MS/MS analysis.We have found 20 lysine-acetylated proteins with 21 lysine-acetylated sites,among which 12 lysine-acetylated proteins and 16 lysine-acetylated sites have never been reported before.Notably,three acetyltransferases harboring in mitochondrion are newly discovered acetyltransferases responsible for the acetylation of nonhistone proteins.We have explored the significant patterns of residue preference by the hierarchical clustering analysis of amino acid residues surrounding acetylation sites,which could be helpful to the prediction of new sites of lysine acetylation.Our findings provide more candidates for studying the important roles played by acetylation in diverse cellular pathways and related human diseases. | ZHANG Bing ZHAO Chao LUO KaiXuan YAN GuoQuan YAO Jun WANG YingYin LU HaoJie FAN HuiZhi YANG PengYuan | 2010 | Science China Chemistry2010，53，1： | 1 |
| 14 | Identification of differentially expressed proteins between hybrid and parents in wheat (Triticum aestivum L.) seedling leaves显示文摘 | Xiao Song Zhongfu Ni Yingyin Yao Yinhong Zhang Qixin Sun | 2009 | Theoretical and Applied Genetics2009，，2： | 1 |
| 15 | Wheat Dof transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gene during wheat seed development显示文摘 | Guoqing Dong Zhongfu Ni Yingyin Yao Xiuling Nie Qixin Sun | 2007 | Plant Molecular Biology2007，，1： | 1 |
| 16 | Expression divergence of TaMBD2 homoeologous genes encoding methyl CpG-binding domain proteins in wheat ( Triticum aestivum L.)显示文摘 | Zhaorong Hu Ying Yu Rui Wang Yingyin Yao Huiru Peng Zhongfu Ni Qixin Sun | 2010 | Gene2010，，1： | 1 |
| 17 | Identification of differentially expressed genes in leaf and root between wheat hybrid and its parental inbreds using PCR-based cDNA subtraction显示文摘 | Yingyin Yao Zhongfu Ni Yinhong Zhang Yan Chen Yuhua Ding Zongfu Han Zhiyong Liu Qixin Sun | 2005 | Plant Molecular Biology2005，，3： | 1 |
| 18 | Wheat Dot transcription factor WPBF interacts with TaQM and activates transcription of an alpha-gliadin gent during wheat seed development 显示文摘 | Guoqing Dong Zhongfu Ni Yingyin Yao | 2007 | Plant Molecular Biology2007，63，1： | 1 |
| 19 | Isolation and characterization of 18 genes encoding α- and β-expansins in wheat (Triticum aestivum L.)显示文摘 | Zhan Lin Zhongfu Ni Yi Zhang Yingyin Yao Haiyan Wu Qixin Sun | 2005 | Molecular Genetics and Genomics2005，，5： | 1 |
| 20 | Sequencing and comparative analyses of Aegilops tauschii chromosome arm 3DS reveal rapid evolution of Triticeae genomes显示文摘Bread wheat(Triticum aestivum,AABBDD) is an allohexaploid species derived from two rounds of interspecific hybridizations.A high-quality genome sequence assembly of diploid Aegilops tauschii,the donor of the wheat D genome,will provide a useful platform to study polyploid wheat evolution.A combined approach of BAC pooling and next-generation sequencing technology was employed to sequence the minimum tiling path(MTP) of 3176 BAC clones from the short arm of Ae.tauschii chromosome 3(At3DS).The final assembly of 135 super-scaffolds with an N50 of 4.2 Mb was used to build a247-Mb pseudomolecule with a total of 2222 predicted protein-coding genes.Compared with the orthologous regions of rice,Brachypodium,and sorghum,At3 DS contains 38.67%more genes.In comparison to At3 DS,the short arm sequence of wheat chromosome 3B(Ta3BS) is 95-Mb large in size,which is primarily due to the expansion of the non-centromeric region,suggesting that transposable element(TE) bursts in Ta3 B likely occurred there.Also,the size increase is accompanied by a proportional increase in gene number in Ta3 BS.We found that in the sequence of short arm of wheat chromosome 3D(Ta3DS),there was only less than 0.27%gene loss compared to At3 DS.Our study reveals divergent evolution of grass genomes and provides new insights into sequence changes in the polyploid wheat genome. | Jingzhong Xie Naxin Huo Shenghui Zhou Yi Wang Guanghao Guo Karin R.Deal Shuhong Ouyang Yong Liang Zhenzhong Wang Lichan Xiao Tingting Zhu Tiezhu Hu Vijay Tiwari Jianwei Zhang Hongxia Li Zhongfu Ni Yingyin Yao Huiru Peng Shengli Zhang Olin D.Anderson Patrick E.McGuire Jan Dvorak Ming-Cheng Luo Zhiyong Liu Yong Q.Gu Qixin Sun | 2017 | Journal of Genetics and Genomics2017，44，1： | 1 |
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