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Reference quality assembly of the 3.5-Gb genome of Capsicum annuum from a single linked-read library

Horticulture Research 2018年第1期5卷 890-902页

作者： Amanda M.Hulse-Kemp Shamoni Maheshwari Kevin Stoffel Theresa A.Hill David Jaffe Stephen R.Williams Neil Weisenfeld Srividya Ramakrishnan Vijay Kumar Preyas Shah Michael C.Schatz Deanna M.Church Allen Van Deynze department of Plant Sciences University of CaliforniaDavisCAUSA USDA-ARS genomics and bioinformatics Research Unit RaleighNCUSA department of crop and Soil Sciences North Carolina State UniversityRaleighNCUSA 10x genomics Inc7068 Koll Center ParkwaySuite 401PleasantonCAUSA department of Computer Science Johns Hopkins UniversityBaltimoreMDUSA

Linked-Read sequencing technology has recently been employed successfully for de novo assembly of human genomes,however,the utility of this technology for complex plant genomes is *** evaluated the technology for this purpose by sequencing the 3.5-gigabase(Gb)diploid pepper(Capsicum annuum)genome with a single Linked-Read *** genomes,including pepper,are characterized by long,highly similar repetitive ***,significant effort is used to ensure that the sequenced plant is highly homozygous and the resulting assembly is a haploid *** a phased assembly approach,we targeted a heterozygous F1 derived from a wide cross to assess the ability to derive both haplotypes and characterize a pungency gene with a large insertion/*** Supernova software generated a highly ordered,more contiguous sequence assembly than all currently available *** reference *** 83%of the final assembly was anchored and oriented using four publicly available de novo linkage maps.A comparison of the annotation of conserved eukaryotic genes indicated the completeness of *** validity of the phased assembly is further demonstrated with the complete recovery of both 2.5-Kb insertion/deletion haplotypes of the PUN1 locus in the F1 sample that represents pungent and nonpungent peppers,as well as nearly full recovery of the BUSCO2 gene set within each of the two *** most contiguous pepper genome assembly to date has been generated which demonstrates that Linked-Read library technology provides a tool to de novo assemble complex highly repetitive heterozygous plant *** technology can provide an opportunity to cost-effectively develop high-quality genome assemblies for other complex plants and compare structural and gene differences through accurate haplotype reconstruction.

关键词： Capsicum pepper insertion

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Epigenetics in the modern era of crop improvements

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Science China Life Sciences 2025年

作者： Yan Xue Xiaofeng Cao Xiangsong Chen Xian Deng Xingwang Deng Yong Ding Aiwu Dong Chengguo Duan Xiaofeng Fang Lei Gong Zhizhong Gong Xiaofeng Gu Chongsheng He Hang He Shengbo He Xinjian He Yan He Yuehui He Guifang Jia Danhua Jiang Jianjun Jiang Jinsheng Lai Zhaobo Lang Chenlong Li Qing Li Xingwang Li Bao Liu Bing Liu Xiao Luo Yijun Qi Weiqiang Qian Guodong Ren Qingxin Song Xianwei Song Zhixi Tian Jiawei Wang Yuan Wang Liang Wu Zhe Wu Rui Xia Jun Xiao Lin Xu Zhengyi Xu Wenhao Yan Hongchun Yang Jixian Zhai Yijing Zhang Yusheng Zhao Xuehua Zhong Daoxiu Zhou Ming Zhou Yue Zhou Bo Zhu Jiankang Zhu Qikun Liu College of Life Sciences Institute of Life Science and Green Development Hebei University Biotechnology Research Institute Chinese Academy of Agricultural Sciences College of Biology Hunan Key Laboratory of Plant Functional Genomics and Developmental Regulation Hunan Engineering and Technology Research Center of Hybrid Rapeseed Hunan University Institute of Advanced Agricultural Sciences School of Advanced Agricultural Sciences Peking University State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources Guangdong Laboratory for Lingnan Modern Agriculture South China Agricultural University National Institute of Biological Sciences Key Laboratory of Seed Innovation Institute of Genetics and Developmental Biology Chinese Academy of Sciences School of Advanced Agricultural Sciences Peking-Tsinghua Center for Life Sciences Peking University Synthetic and Functional Biomolecules Center Beijing National Laboratory for Molecular Sciences Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education College of Chemistry and Molecular Engineering Peking University Key Laboratory of Seed Innovation State Key Laboratory of Plant Genomics and National Center for Plant Gene Research Institute of Genetics and Developmental Biology Chinese Academy of Sciences State Key Laboratory of Wheat Improvement Peking University Institute of Advanced Agricultural Sciences Shandong Laboratory of Advanced Agricultural Sciences in Weifang State Key Laboratory of crop Stress Adaptation and Improvement School of Life Sciences Henan University State Key Laboratory of Maize Bio-breeding National Maize Improvement Center Department of Plant Genetics and Breeding China Agricultural University Frontiers Science Center for Molecular Design Breeding China Agricultural University Center for crop Functional genomics and Molecular Breeding China Agricultural University Sanya Institute of China Agricultural University Hainan Yazhou Bay Seed Laboratory Institute of Advan

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades,our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

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Development of Chlorella pyrenoidosa EMS mutants with enhanced biomass and lipid content for biofuel production

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Systems Microbiology and Biomanufacturing 2023年第4期3卷 693-701页

作者： M.Vidya Vani P.Osman Basha N.Rajesh K.Riazunnisa department Biotechnology and bioinformatics Yogi Vemana UniversityKadapaAndhra Pradesh 516005India department Genetics and genomics Yogi Vemana UniversityKadapaAndhra Pradesh 516005India

Biodiesel production from microalgae depends on algal biomass production through autotrophic cultivation,and it has a lot of potential as a feasible alternative source of *** lethal and mutagenic effects of ethyl methanesulphonate(EMS)are investigated in the present study on the organism Chlorella pyrenoidosa for the generation of paler *** *** wild-type strain was treated with 0.1,0.2,and 0.5 M EMS doses and the colonies that appeared after 20 days of growth on a solid TAP medium were analyzed,and a total of two mutant colonies with less pigmentation were *** CPM1(10.02±0.03 and 3.12±0.04µg/ml)and CPM2(9.55±0.0 and 32.84±0.03µg/ml)mutants had lower chloro-phyll a and b and carotenoids content than wild *** produced significant biomass(1.34-and 1.31-fold enhanced biomass in CPM1 and CPM2)and lipid content than the wild *** findings suggest that genetic modification of *** has the potential to produce strains with increased biomass productivity and lipid content for biofuel production.

关键词： Chlorella pyrenoidosa Random mutagenesis Ethyl methanesulphonate(EMS) Chlorophyll mutants

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Ectopic Overexpression of Wheat Adenosine Diphosphate-ribosylation Factor,TaARF,Increases Growth Rate in Arabidopsis

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Journal of Integrative Plant Biology 2009年第1期51卷 35-44页

作者： Yingyin Yao Zhongfu Ni Jinkun Du Zongfu Han Yan Chen Qingbo Zhang Qixin Sun department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and UtilizationMinistry of Education Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agdculture Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

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 this study, real-time quantitative reverse transcription-polymerase chain reaction analysis indicated that the TaARF transcript was preferentially expressed in root, node and crown, and the accumulation of TaARF mRNA in hybrid was more than 1.5-fold higher than that in two parents. In order to understand possible roles of the putative wheat ARF gene, TaARF was overexpressed in Arabidopsis, and the transgenic plants were characterized. We show that ectopic overexpression of TaARF in Arabidopsis leads to increased leaf area, increased growth rate and earlier transition to flowering, suggesting that TaARF plays significant roles in growth and development. This study provides evidence demonstrating that TaARF plays important roles in growth and development and we speculate that the upregulated expression of this gene might contribute to the heterosis observed in wheat root and leaf growth.

关键词： adenosine diphosphate-ribosylation factor Arabidopsis ectopic heterosis overexpression wheat.

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Cloning and expression profiles of 15 genes encoding WRKY transcription factor in wheat (Triticum aestivem L.)

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Progress in Natural Science:Materials International 2008年第6期18卷 697-705页

作者： Hualing Wu,Zhongfu Ni,Yingyin Yao,Ganggang Guo,Qixin Sun* department of Plant Genetics&Breeding and State Key Laboratory for Agrobiotechnology,Key Laboratory of crop Heterosis and Utilization,Ministry of Education,Key Laboratory of crop genomics and Genetic Improvement,Ministry of Agriculture/Beijing Key Laboratory of crop Genetic Improvement,China Agricultural University,Beijing 100094,China department of Plant Genetics & Breeding and State Key Laboratory for Agrobiotechnology Key Laboratory of Crop Heterosis and Utilization Ministry of Education Key Laboratory of Crop Genomics and Genetic Improvement Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement China Agricultural University Beijing 100094 China

WRKY proteins are involved in various physiological processes,including biotic and abiotic stress responses,hormone responses and ***,no systematic identification,expression and function analysis of WRKY genes in wheat were *** this study,we isolated 15 wheat cDNAs with complete open reading frame(ORF)encoding putative WRKY proteins using in silico *** analysis indicated that the 15 wheat WRKY genes belonged to three major WRKY *** analysis revealed that most genes expressed drastically in leaf,except TaWRKY10 which expressed in crown *** genes were strongly up-reg-ulated with the senescence of *** genes were responsive to low temperature,high temperature,NaCl or PEG ***-over,dierential expression patterns were also observed between wheat hybrid and its parents,and some genes were more responsive to PEG treatment in the *** results demonstrated that wheat WRKY genes are involved in leaf senescing and abiotic *** the changed expression of these WRKY genes in hybrid might contribute to the heterosis by improving the stress tolerance in hybrids.

关键词： Wheat WRKY transcription factor Gene cloning Gene expression Heterosis

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Development of near-isogenic lines for a major QTL controlling grain number per spike in bread wheat

Development of near-isogenic lines for a major QTL controlli...

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第十四届全国植物基因组学大会

作者： Ruiru Cheng Xinyi Wu Yulong Huang Dong Yu Hongshen Wan Zhengqiang Ma The Applied Plant genomics Laboratory Crop Genomics and Bioinformatics CentreNanjing Agricultural University

Near-isogenic lines(NILs) are ideal materials for investigating functions of genes of *** we report the development of NILs for a major QTL,***-4B affecting grain number per spike(GN),which was originally detected in ... 详细信息

关键词： near-isogenic lines grain number per spike

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Development and evaluation of near-isogenic lines for grain weight QTLs in wheat

Development and evaluation of near-isogenic lines for grain ...

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第十四届全国植物基因组学大会

作者： Yulong Huang Xinyi Wu Ruiru Cheng Dong Yu Hongshen Wan Zhengqiang Ma The Applied Plant genomics Laboratory Crop Genomics and Bioinformatics CentreNanjing Agricultural University

Grain weight,as one of three major components of yield,has a great influence on yield ***,it is important to identify grain weight-determining genes and understand the mechanisms underlying grain weight ***-2D, ***-4B... 详细信息

关键词： near-isogenic lines grain weight

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Identification of a novel class of seed development-related proline-rich protein genes in Wheat

Identification of a novel class of seed development-related ...

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第六届全国小麦基因组学及分子育种大会

作者： Haiyan Jia Shirong Liu Shengwei Ma Li Ma Zhengqiang Ma The Applied Plant genomics Lab Crop Genomics and Bioinformatics CenterNanjing Agricultural University

Yield formation of plants are governed by a large network of genes under complicated regulation,for which our understanding is still at the infant *** this study,a novel class of seed development-related proline-rich protein(PRP)genes,consisting of at least four homologs,was identified in ***,they are distinct from the previously described five classes of plant ***-quantitative RT-PCR showed that these wheat PRPs were mainly expressed in reproductive organs,and their expression levels were reduced gradually as the seeds *** of these genes,TaPRP.1,were fused to a Actin1 promoter and transformed into a wheat cultivar through particle *** transgenic lines had significantly higher unit grain weight than the non-transgenic control in three different trials and showed a higher level of TaPRP.1expression.

关键词： wheat proline-rich protein grain weight

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Characterization of two wheat(Triticum aestivum L.) lesion mimic mutants resulted from mutation of a pair of orthologs

Characterization of two wheat(Triticum aestivum L.) lesion m...

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第六届全国小麦基因组学及分子育种大会

作者： Haiyan Jia Wen Wen Shirong Liu Zhongxin Kong Min Fan Zhengqiang Ma The Applied Plant genomics Lab Crop Genomics and Bioinformatics CenterNanjing Agricultural University

Physiological disorder caused by gene mutations in plants could result in lesion mimics(LMs).Plants with LMs have a phenotype similar to those with programmed cell death(PCD)invoked by pathogens and are thus used in the investigation of mechanisms underlying *** identify new genes involved in PCD,two wheat LM mutants,Met0187 and Mfh0014,were *** two mutants were obtained from a tetraploid wheat treated with ethylmethyl sulfide(EMS) and from a hexaploid wheat with dry seeds irradiated with fast neutrons,*** exhibited spontaneous lesions,around which HO accumulation and autofluorescence were detected or *** necrotic phenotype was temperature-sensitive and appeared only when the plants were grown under 16℃ condition and not when grown under conditions above 20℃.Three examined PCD marker genes showed differential expression patterns between the wild and mutant genotypes,indicating that Met0187 and Mfh0014 were PCD-related *** than the necrotic phenotype,dwarfing was also observed for the *** GA application restored the mutants’ *** involved in the GA biosynthesis pathway displayed lower expression level,suggesting that GA biosynthesis was compromised in Met0187 and *** analysis indicated that a single recessive gene mutation caused the mutant phenotype in both Met0187 and *** mutated genes were mapped to homologous intervals of chromosomes 6A and 6B,respectively,implying they are orthologs.

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Map-based cloning of Fhb1 revealed unique mutation of a well-conserved gene resulting in resistance to wheat Fusarium head blight

Map-based cloning of Fhb1 revealed unique mutation of a well...

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第八届全国小麦基因组学及分子育种大会

作者： Zhengqiang Ma Guoqiang Li Jiyang Zhou Haiyan Jia Shulin Xue Na Li Min Fan Zhongxin Kong Zhongxia Gao Yanjun Luo Li Jia Yunxiao Ding Xia An Yang Yuan Shengwei Ma Ge Jiang Yao Wang Wenxing Liu Bin Qin Jicai Fan Rongrong Zhang Qianqian Kong Congfu Ran Applied Plant genomics Laboratory Crop Genomics and Bioinformatics CentreNanjing Agricultural University

Head or ear blight caused by Fusarium *** can devastate staple cereal crops,particularly *** of resistant cultivars is currently the best control measure,but lack of understanding of resistance mechanisms has greatly hindered the breeding *** the FHB-resistant germplasm Wangshuibai,we previously identified a major QTL on chromosome 3 BS conferring resistance to spread within spike,the type II *** clone this gene,NIL isogenic lines of this QTL and the Sumai 3 FHBI QTL,developed using FHB-susceptible lines Mianyang 99-323 and PH691,were used in secondary segregation population *** recombinants identified in these populations,both QTL were fine *** the constructed BAC physical map,they were confined to a common 26.8 kb interval containing only three ***-based analysis demonstrated that Wangshuibai and Sumai3 contain an identical FHB resistance gene in the target *** FHB1 candidate was determined based on sequence comparison and transcriptional profiling analysis,and was confirmed through haplotyping and transgenic *** gene is conserved among plants,but a unique mutation of the 3 BS homolog causes shift of its start codon,consequently,results in the function in FHB resistance.

关键词： Fhb1 Map-based cloning Fusarium head blight

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