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| 1 | A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era显示文摘Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference versions.Demands for clade-specific homology inference and analysis have increased in the pangenomic era.Here we present a novel method,GeneTribe(http://gffzz6c7fcf032cb94ff5s66k0bvvfbwn56vbf.ffgz.tsg.suse.edu.cn/genetribe/),for homology inference among genetically similar genomes that incorporates gene collinearity and shows bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and scalability.The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and rye.We built Triticeae-GeneTribe(http://gffzzaeec8df70e7c4b21h66k0bvvfbwn56vbf.ffgz.tsg.suse.edu.cn/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions.With macrocollinearity analysis,we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events.With collinearity analysis at both the macro-and microscale,we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vm2,which evolved as a combined result of genome translocation,duplication,and polyploidization and gene loss events.Our work provides a useful practice for connecting emerging genome assemblies,with awareness of the extensive polyploidy in plants,and will help researchers efficiently exploit genome sequence re-sources. | Yongming Chen Wanjun Song Xiaoming Xie Zihao Wang Panfeng Guan Huiru Peng Yuannian Jiao Zhongfu Ni Qixin Sun Weilong Guo | 2020 | Molecular Plant2020，13，12： | 14 |
| 2 | Molecular mapping of QTLs for root response to phosphorus deficiency at seedling stage in wheat (Triticum aestivum L.)显示文摘Phosphorus (P) deficiency in the soil is one of the major abiotic stresses that limit plant growth and crop productivity throughout the world. Development of cultivars with improved P-deficiency tolerance is an efficient strategy for sustainable agriculture. Plant roots play an important role in crop growth and development, especially in nutrient uptake and improvement of P-efficiency. Mapping quantitative trait loci (QTLs) for root traits and their response to low P stress at seedling stage will facilitate the development of P-efficient wheat cultivars. In this study, 30 QTLs (LOD>2.0) were mapped for the three root traits, such as root length, root number and root dry matter under different P supply conditions and their response to P-stress. These QTLs were distributed on 14 chromosomes, with each of the 5 QTLs explaining more than 10% phenotype variance. Analyses showed that root traits and their response to P-deficiency were controlled by different QTLs. In addition, alleles with positive effects were separated on both parents, and wheat cultivars with improved P-efficiency could be developed by accumulating these positive effect alleles together. | Li Zhenxing Ni Zhongfu Peng Huiru Liu Zhiyong Nie Xiuling Xu Shengbao Liu Gang Sun Qixin | 2007 | Progress in Natural Science:Materials International2007，17，10： | 8 |
| 3 | 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 |
| 4 | Molecular dissection of plant height QTLs using recombinant inbred lines from hybrids between common wheat (Triticum aestivum L.) and spelt wheat (Triticum spelta L.)显示文摘In wheat, plant height is an important agronomic trait, and a number of quantitative trait loci (QTLs) controlling plant height have been located. In this study, using the conditional and unconditional QTL mapping methods, combined with data from five different growth stages over two years of field trials, the developmental behavior for plant height in wheat was dissected. Nine unconditional QTLs and 8 conditional QTLs were identified, of which 6 were detected by both methods. None of the 11 QTLs was detected at all of the 5 investigated developmental stages, but 7 QTLs were detected at certain stages in both years. Further analysis identified 9 unconditional QTLs at different stages, which could explain the phenotypic variation from 4.81% to 17.35%. It was noteworthy that one major QTL designated QHt-4B-2, which was located on chromosome 4B, was detected on May 18 and 25 in both years, and its genetic contributions to plant height ranged from 13.42% to 16.13%. Moreover, of the 8 conditional QTLs identified, six were detected in both years, in the order of QHt-3B→QHt-4B-1→QHt-4B-2→QHt-4D→QHt-5A and QHt-2B expressed at the same developmental stage. The results indicate that QTL expression during plant height development is selective and in a temporal order. | LIU Gang XU ShengBao NI ZhongFu XIE ChaoJie QIN DanDan LI Jing LU LaHu ZHANG JinPing PENG HuiRu SUN QiXin | 2011 | Chinese Science Bulletin2011，56，18： | 6 |
| 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 | A MITE insertion into the 3′-UTR regulates the transcription of TaHSP16.9 in common wheat显示文摘Miniature inverted-repeat transposable elements(MITEs) are a type of DNA transposon frequently inserted into promoters, untranslated regions(UTR), introns, or coding sequences of genes. We found a 276-bp tourist-like MITE insertion in the 3′-UTR of a 16.9 k Da small heat shock protein gene(TaH SP16.9-3A) on chromosome 3A of common wheat. Haplotype analysis revealed two haplotypes, s HSP-W(wild type without MITE insertion) and s HSP-M(mutant with MITE insertion), present in wheat germplasm. Both semiquantitative PCR and quantitative real-time PCR analyses showed increased transcription levels of TaH SP16.9-3A in s HSP-M compared with those of s HSP-W after heat treatment at 42 °C. It appeared that the MITE insertion into the 3′-UTR enhances the transcription of TaH SP16.9-3A. | Jingting Li Zhenzhong Wang Huiru Peng Zhiyong Liu | 2014 | The Crop Journal2014，2，6： | 5 |
| 7 | Genetic improvement of heat tolerance in wheat:Recent progress in understanding the underlying molecular mechanisms显示文摘As a cool season crop, wheat(Triticum aestivum L.) has an optimal daytime growing temperature of 15 ℃ during the reproductive stage. With global climate change, heat stress is becoming an increasingly severe constraint on wheat production. In this review, we summarize recent progress in understanding the molecular mechanisms of heat tolerance in wheat. We firstly describe the impact of heat tolerance on morphology and physiology and its potential effect on agronomic traits. We then review recent discoveries in determining the genetic and molecular factors affecting heat tolerance, including the effects of phytohormone signaling and epigenetic regulation. Finally, we discuss integrative strategies to improve heat tolerance by utilization of existing germplasm including modern cultivars, landraces and related species. | Zhongfu Ni Hongjian Li Yue Zhao Huiru Peng Zhaorong Hu Mingming Xin Qixin Sun | 2018 | The Crop Journal2018，6，1： | 4 |
| 8 | 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 |
| 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 | Molecular mapping of a dominant non-glaucousness gene from synthetic hexaploid wheat (Triticum aestivum L.)显示文摘 | Qing Liu Zhongfu Ni Huiru Peng Wei Song Zhiyong Liu Qixin Sun | 2007 | Euphytica (-)2007，，1： | 2 |
| 11 | 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 |
| 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://gffzzaeec8df70e7c4b21h66k0bvvfbwn56vbf.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 | The PCDD/F and PBDD/F pollution in the ambient atmosphere of Shanghai, China显示文摘 | Huiru Li Jialiang Feng Guoying Sheng Senlin Lü Jiamo Fu Ping’an Peng Ren Man | 2007 | Chemosphere2007，，4： | 1 |
| 14 | 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 |
| 15 | The PCDD/F and PBDD/F pollution in the ambient atmosphere of Shanghai, China显示文摘 | Huiru Li Jialiang Feng Guoying Sheng Senlin Lü Jiamo Fu Ping’an Peng Ren Man | 2007 | Chemosphere2007，，4： | 1 |
| 16 | Metabolomic analysis of the response of growing pigs to dietary l-arginine supplementation显示文摘 | Qinghua He Xiangfeng Kong Guoyao Wu Pingping Ren Huiru Tang Fuhua Hao Ruilin Huang Tiejun Li Bie Tan Peng Li Zhiru Tang Yulong Yin Yongning Wu | 2009 | Amino Acids2009，，1： | 1 |
| 17 | Paleo-position of the North China craton within the supercontinent Columbia: Constraints from new paleomagnetic results显示文摘 | Huiru Xu Zhenyu Yang Peng Peng Joseph G. Meert Rixiang Zhu | 2014 | Precambrian Research2014，，： | 1 |
| 18 | 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 |
| 19 | Molecular mapping of a dominant non-glaucousness gene from synthetic hexaploid wheat (Triticum aestivum L.)显示文摘 | Qing Liu Zhongfu Ni Huiru Peng Wei Song Zhiyong Liu Qixin Sun | 2007 | Euphytica (-)2007，，1： | 1 |
| 20 | Metabolomic analysis of the response of growing pigs to dietary l-arginine supplementation显示文摘 | Qinghua He Xiangfeng Kong Guoyao Wu Pingping Ren Huiru Tang Fuhua Hao Ruilin Huang Tiejun Li Bie Tan Peng Li Zhiru Tang Yulong Yin Yongning Wu | 2009 | Amino Acids2009，，1： | 1 |
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