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Evolution of plant microRNA gene families

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Cell Research 2007年第3期17卷 212-218页

作者： aili li~1 long mao~(1,2) ~1institute of crop sciences,chinese academy of agricultural sciences and the national key facility for crop gene resources and genetic improvement (NFCRI),beoing 100081,china ~2Department of Biological sciences,Northern Illinois University,DeKalb,IL 60115,USA institute of crop sciences Chinese Academy of Agricultural Sciences and The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) Beijing 100081 China.

MicroRNAs(miRNAs)are important post-transcriptional regulators of their target genes in plants and animals,miR-NAs are usually 20-24 nucleotides *** their unusually small sizes,the evolutionary history of miRNA genefamilies seems to be similar to their protein-coding *** contrast to the small but abundant miRNA familiesin the animal genomes,plants have fewer but larger miRNA gene *** of plant miRNA gene familiesare often highly similar,suggesting recent expansion via tandem gene duplication and segmental duplication *** many miRNA genes are conserved across plant species,the same gene family varies significantly in size andgenomic organization in different species,which may cause dosage effects and spatial and temporal differences in targetgene *** this review,we summarize the current progress in understanding the evolution of plant miRNA genefamilies.

关键词： microRNAs post-transcriptional regulation tandem duplication segmental duplication

Effects of Glyphosate on target-sites and non-target sites of herbicide in soybean apical bud

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Effects of Glyphosate on target-sites and non-target sites o...

SQUAMOSA Promoter-Binding Protein-like Transcription Factors:Star Players for Plant Growth and Development

第十三届全国植物基因组学大会

作者： ling-Xue Jiang~(1,2),long-Guo Jin~1,Yong Guo~1,Bo Tao~2,li-Juan Qiu~(1*) 1 The national key facility for crop gene resources and genetic improvement(NFCRI), institute of crop Science,chinese academy of agricultural sciences,Beijing 100081,china 2 College of Agriculture,Northeast agricultural University,Harbin,Heilongjiang,150030, china

Glyphosate,which is a broad spectrum and non-selective herbicide,has been widely used for weed *** transformed the exogenous 5-enolypyruvylshikimate- 3-phosphate synthase gene(EPSPS) into soybean,soybean had high resistance to *** order to get knowledge of mRNA expression patterns and affect mechanisms of glyphosate in soybean apical bud,Digital gene Expression Profiling (DGE) was used to identify discriminating responses of soybean apical bud to 2.10

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Journal of Integrative Plant Biology 2010年第11期52卷 946-951页

作者： Xiaobo Chen Zenglin Zhang Danmei liu Kai Zhang aili li long mao national key facility for crop gene resources and genetic improvement (NFCRI) MOA Key Laboratory of Crop Germplasm & BiotechnologyInstitute of Crop ScienceChinese Academy of Agricultural Sciences (CAAS)Beijing 100081China

SQUAMOSA Promoter-Binding Protein-like （SPL） genes encode plantspecific transcription factors that play important roles in plant phase transition,flower and fruit development,plant architecture,gibberellins signaling,sporogenesis,and response to copper and fungal *** Arabidopsis,many SPL genes are post-transcriptionally regulated by the microRNA （miRNA） miR156,among which AtSPL9 in turn positively regulates the expression of the second miRNA *** miR156AtSPL9-miR172 regulatory pathway plays critical roles during juvenile to adult leaf development and the miR156-SPLs feedback interaction persists all through the plant development,which may be conserved in other *** the present paper,we provide a concise review on the most recent progress in the regulatory mechanisms associated with plant SPL transcription factors,especially in relation to *** potential application of these discoveries in agriculture is briefly discussed.

关键词： CARRIER proteins geneS GIBBERELliNS PLANT hormones TRANSCRIPTION

The Battle to Sequence the Bread Wheat Genome:A Tale of the Three Kingdoms

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Genomics, Proteomics & Bioinformatics 2020年第3期18卷 221-229页

作者： Jiantao Guan Diego F.Garcia Yun Zhou Rudi Appels aili li long mao national key facility for crop gene resources and genetic improvement Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China Collaborative Innovation Center of crop Stress Biology&institute of Plant Stress Biology School of Life ScienceHenan UniversityKaifeng 475004China AgriBio Centre for AgriBioscienceDepartment of Economic DevelopmentJobsTransportand ResourcesLa Trobe UniversityMelbourneVIC 3083Australia

In the year 2018,the world witnessed the finale of the race to sequence the genome of the world’s most widely grown crop,the common *** has been known to bear a notoriously large and complicated genome of a polyploidy nature.A decade competition to sequence the wheat genome initiated with a single consortium of multiple countries,taking a conventional strategy similar to that for sequencing Arabidopsis and rice,became ferocious over time as both sequencing technologies and genome assembling methodologies *** different stages,multiple versions of genome sequences of the same variety(e.g.,chinese Spring)were produced by several groups with their special ***,16 years after the rice genome was finished and 9 years after that of maize,the wheat research community now possesses its own reference *** with these genomics tools,wheat will reestablish itself as a model for polyploid plants in studying the mechanisms of polyploidy evolution,domestication,genetic and epigenetic regulation of homoeolog expression,as well as defining its genetic diversity and breeding on the genome *** enhanced resolution of the wheat genome should also help accelerate development of wheat cultivars that are more tolerant to biotic and/or abiotic stresses with better quality and higher yield.

关键词： Common wheat Homoeologous genomes Polyploid Sequencing Triticum aestivum

Wheat functional genomics in the era of next generation sequencing: An update

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The crop Journal 2018年第1期6卷 7-14页

作者： Meiling Jia Jiantao Guan Zhiwen Zhai Shuaifeng Geng Xueyong Zhang long mao aili li national key facility for crop gene resources and genetic improvement Institute of Crop ScienceChinese Academy of Agricultural Sciences

Bread wheat is not only an important cereal crop but also a model for study of an allopolyploid plant with a large, highly repetitive genome. Advances in next-generation sequencing(NGS) technology provide needed throughput to conquer the enormous size of the wheat genome. Multiple high quality reference genome sequences will soon be available. Full-scale wheat functional genomics studies are dawning. In this review we highlight the available tools and methodologies for wheat functional genomics research developed with the assistance of NGS technology and recent progress, particularly the concerted effort in generating multiple reference genomes, strategies to attain genome-wide genetic variation, genome-wide association studies, mutant population generation, and NGS-supported gene cloning and functional characterization. These resources and platforms lay a solid foundation for wheat research, leading to a new era of wheat functional genomics that will bridge the gap between genotype and *** of wheat genomes and gene functions should assist in genomics-assisted selection and facilitate breeding of elite varieties for sustainable agriculture in china and the world.

关键词： GWAS NGS TILliNG Triticum aestivum

Natural variation of GmFNSII-2 contributes to drought resistance by modulating enzyme activity in soybean

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The crop Journal 2024年第2期12卷 529-539页

作者： Huihui Gao Pengcheng Wei Yongzhe Gu Pengbin Tang Yifan Shen Lei Yang linxin Dong Haowei Zheng Kuo Shu Mayamiko Masangano Bin Dong long Miao Jiajia li lijuan Qiu Xiaobo Wang School of Agronomy Anhui Agricultural UniversityHefei 230036AnhuiChina State key Laboratory of crop gene resources and Breeding The National Key Facility for Crop Gene Resources and Genetic Improvement(NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement(MOA)Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

As an essential crop that provides vegetable oil and protein,soybean(Glycine max(L.)Merr.)is widely planted all over the ***,the scarcity of water resources worldwide has seriously impacted on the quality and yield of *** address this,exploring excellent genes for improving drought resistance in soybean is *** this study,we identified natural variations of GmFNSII-2(flavone synthase II)significantly affect the drought resistance of *** sequence analysis of GmFNSII-2 in 632 cultivated and 44 wild soybeans nine haplotypes were *** full-length allele GmFNSII-2^(C),but not the truncated allele GmFNSII-2^(A) possessing a nonsense nucleotide variation,increased enzyme *** research found that GmDREB3,known to increase soybean drought resistance,bound to the promoter region of GmFNSII-2^(C).GmDREB3 positively regulated the expression of GmFNSII-2^(C),increased flavone synthase abundance and improved the drought ***,a singlebase mutation in the GmFNSII-2^(C) promoter generated an additional drought response element(CCCCT),which had stronger interaction strength with GmDREB3 and increased its transcriptional activity under drought *** frequency of drought-resistant soybean varieties with Hap 1(Pro:GmFNSII-2^(C))has increased,suggesting that this haplotype may be selected during soybean *** summary,GmFNSII-2^(C) could be used for molecular breeding of drought-tolerant soybean.

关键词： Drought stress Flavone synthase GmFNSII-2 Natural variation Drought response element

CRISPR/Cas9:A powerful tool for crop genome editing

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The crop Journal 2016年第2期4卷 75-82页

作者： Gaoyuan Song Meiling Jia Kai Chen Xingchen Kong Bushra Khattak Chuanxiao Xie aili li long mao national key facility for crop gene resources and genetic improvement Institute of Crop ScienceChinese Academy of Agricultural Sciences

The CRISPR/Cas9 technology is evolved from a type II bacterial immune system and represents a new generation of targeted genome editing technology that can be applied to nearly all organisms. Site-specific modification is achieved by a single guide RNA(usually about 20nucleotides) that is complementary to a target gene or locus and is anchored by a protospaceradjacent motif. Cas9 nuclease then cleaves the targeted DNA to generate double-strand breaks(DSBs), which are subsequently repaired by non-homologous end joining(NHEJ) or homology-directed repair(HDR) mechanisms. NHEJ may introduce indels that cause frame shift mutations and hence the disruption of gene functions. When combined with double or multiplex guide RNA design, NHEJ may also introduce targeted chromosome deletions,whereas HDR can be engineered for target gene correction, gene replacement, and gene knock-in. In this review, we briefly survey the history of the CRISPR/Cas9 system invention and its genome-editing mechanism. We also describe the most recent innovation of the CRISPR/Cas9 technology, particularly the broad applications of modified Cas9 variants, and discuss the potential of this system for targeted genome editing and modification for crop improvement.

关键词： CRISPR/Cas9 Double-strand break Genome editing TALENs ZFNs

Divergence in homoeolog expression of the grain length-associated gene GASR7 during wheat allohexaploidization

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The crop Journal 2015年第1期3卷 1-9页

作者： Dongdong Zhang Bingnan Wang Junmin Zhao Xubo Zhao lianquan Zhang Dengcai liu lingli Dong Daowen Wang long mao aili li national key facility for crop gene resources and genetic improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Triticeae Research institute Sichuan Agricultural University The State key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyChinese Academy of Sciences

Hexaploid wheat has triplicated homoeologs for most of the genes that are located in subgenomes A, B, and D. GASR7, a member of the Snakin/GASA gene family, has been associated with grain length development in wheat. However, little is known about divergence of its homoeolog expression in wheat polyploids. We studied the expression patterns of the GASR7 homoeologs in immature seeds in a synthetic hexaploid wheat line whose kernels are slender like those of its maternal parent(Triticum turgidum, AABB, PI 94655) in contrast to the round seed shape of its paternal progenitor(Aegilops tauschii, DD, AS2404). We found that the B homoeolog of GASR7 was the main contributor to the total expression level of this gene in both the maternal tetraploid progenitor and the hexaploid progeny, whereas the expression levels of the A and D homoeologs were much lower. To understand possible mechanisms regulating different GASR7 homoeologs, we firstly analyzed the promoter sequences of three homoeologous genes and found that all of them contained gibberellic acid(GA) response elements, with the TaG ASR7 B promoter(pT aG ASR7B) uniquely characterized by an additional predicted transcriptional enhancer. This was confirmed by the GA treatment of spikes where all three homoeologs were induced, with a much stronger response for TaG ASR7 B. McrB C enzyme assays showed that the methylation status at pT aG ASR7 D was increased during allohexaploidization, consistent with the repressed expression of TaG ASR7 D. For pT aG ASR7 A, the distribution of repetitive sequence-derived 24-nucleotide(nt) small interfering RNAs(siR NAs) were found which suggests possible epigenetic regulation because 24-nt siR NAs are known to mediate RNA-dependent DNA methylation. Our results thus indicate that both genetic and epigenetic mechanisms may be involved in the divergence of GASR7 homoeolog expression in polyploid wheat.

关键词： TaGASR7 Gibberellic acid Triticum aestivum Polyploidy

The soft glumes of common wheat are sterile-lemmas as determined by the domestication gene Q

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The crop Journal 2019年第1期7卷 113-117页

作者： Gaoyuan Song Guoliang Sun Xingchen Kong Meiling Jia Ke Wang Xingguo Ye Yun Zhou Shuaifeng Geng long mao aili li national key facility for crop gene resources and genetic improvement Institute of Crop Sciences Chinese Academy of Agricultural Sciences Collaborative Innovation Center of crop Stress Biology Institute of Plant Stress Biology School of Life Science Henan University

The Q gene in common wheat encodes an APETALA2(AP2) transcription factor that causes the free threshing attribute. Wheat spikelets bearing several florets are subtended by a pair of soft glumes that allow free liberation of seeds. In wild species, the glumes are tough and rigid,making threshing difficult. However, the nature of these "soft glumes", caused by the domestication allele Q is not clear. Here, we found that over expression of Q in common wheat leads to homeotic florets at glume positions. We provide phenotypic, microscopy, and marker genes evidence to demonstrate that the soft glumes of common wheat are in fact lemma-like organs, or so-called sterile-lemmas. By comparing the structures subtending spikelets in wheat and other crops such as rice and maize, we found that AP2 genes may play conserved functions in grasses by manipulating vestigial structures, such as floret-derived soft glumes in wheat and empty glumes in rice. Conversion of these seemingly vegetative organs to reproductive organs may be useful in yield improvement of crop species.

关键词： Floret development Spike morphology Sterile lemma Wheat