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Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding 被引量:1
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作者 Haozhe Tan Binghui Tang +10 位作者 Mengling Sun Qiulu Yin Yizan Ma Jianying Li Pengcheng wang Zhonghua Li Guannan Zhao maojun wang Xianlong Zhang Chunyuan You Lili Tu 《The Crop Journal》 SCIE CSCD 2024年第3期866-879,共14页
Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(... Cotton fiber is one of the main raw materials for the textile industry.In recent years,many cotton fiber quality QTL have been identified,but few were applied in breeding.In this study,a genome wide association study(GWAS)of fiber-quality traits in 265 upland cotton breeding intermediate lines(GhBreeding),combined with genome-wide selective sweep analysis(GSSA)and genomic selection(GS),revealed 25 QTL.Most of these QTL were ignored by only using GWAS.The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber,which indicates the credibility of QTL to a certain extent.Then these QTL were verified in other cotton natural populations,5 stable QTL were found having broad potential for application in breeding.Additionally,among these 5 stable QTL,superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently.These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding. 展开更多
关键词 Cotton fiber quality breeding GWAS Genome-wide selective sweep analysis Genomic selection InDel markers
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Genetic interrogation of phenotypic plasticity informs genome-enabled breeding in cotton
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作者 Yuefan Huang Zhengyang Qi +3 位作者 Jianying Li Jiaqi You Xianlong Zhang maojun wang 《Journal of Genetics and Genomics》 SCIE CSCD 2023年第12期971-982,共12页
Phenotypic plasticity, or the ability to adapt to and thrive in changing climates and variable environments, is essential for developmental programs in plants. Despite its importance, the genetic underpinnings of phen... Phenotypic plasticity, or the ability to adapt to and thrive in changing climates and variable environments, is essential for developmental programs in plants. Despite its importance, the genetic underpinnings of phenotypic plasticity for key agronomic traits remain poorly understood in many crops. In this study, we aim to fill this gap by using genome-wide association studies to identify genetic variations associated with phenotypic plasticity in upland cotton (Gossypium hirsutum L.). We identified 73 additive quantitative trait loci (QTLs), 32 dominant QTLs, and 6799 epistatic QTLs associated with 20 traits. We also identified 117 additive QTLs, 28 dominant QTLs, and 4691 epistatic QTLs associated with phenotypic plasticity in 19 traits. Our findings reveal new genetic factors, including additive, dominant, and epistatic QTLs, that are linked to phenotypic plasticity and agronomic traits. Meanwhile, we find that the genetic factors controlling the mean phenotype and phenotypic plasticity are largely independent in upland cotton, indicating the potential for simultaneous improvement. Additionally, we envision a genomic design strategy by utilizing the identified QTLs to facilitate cotton breeding. Taken together, our study provides new insights into the genetic basis of phenotypic plasticity in cotton, which should be valuable for future breeding. 展开更多
关键词 COTTON Phenotype plasticity Genotype-environment interaction Genomic selection Genome-wide association studies
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Comparative genomic analyses reveal cis-regulatory divergence after polyploidization in cotton
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作者 Jiaqi You Min Lin +5 位作者 Zhenping Liu Liuling Pei Yuexuan Long Lili Tu Xianlong Zhang maojun wang 《The Crop Journal》 SCIE CSCD 2022年第6期1545-1556,共12页
Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression ... Polyploidization has long been recognized as a driver for the evolutionary formation of superior plant traits coupled with gene expression novelty.However,knowledge of the effect of regulatory variation on expression changes following polyploidization remains limited.In this study,we characterized transcriptional regulatory divergence by comparing tetraploid cotton with its putative diploid ancestors.We identified 144,827,99,609,and 219,379 Tn5 transposase-hypersensitive sites(THSs)in Gossypium arboreum,G.raimondii,and G.hirsutum,respectively,and found that the conservation of promoter THSs was associated with coordination of orthologous genes expression.This observation was consistent with analysis of transcription-factor binding sites(TFBS)for 262 known motifs:genes with higher TFBS conservation scores(CS)showed less change than those genes with lower TFBS CS in expression levels.TFBS influenced by genomic variation were involved in the novel regulation networks between transcriptional factors and target genes in tetraploid cotton.We describe an example showing that the turnover of TFBS was linked to expression pattern divergence of genes involved in fiber development(fiber-related genes).Our findings reveal the regulatory divergence of the transcriptional network in cotton after polyploidization and characterizes the regulatory relationships of genes contributing to desirable traits. 展开更多
关键词 COTTON POLYPLOIDIZATION Transcriptional regulation Fiber development
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棉花纤维品质亚基因组遗传解析与模块化设计育种构想 被引量:1
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作者 尤佳琦 王茂军 张献龙 《科学通报》 北大核心 2025年第19期3168-3178,共11页
棉花是我国重要的经济作物,其纤维品质对纺织工业和下游产业的发展至关重要.尽管我国在棉花育种方面取得了显著进展,但优质棉品种的选育仍面临诸多挑战.近年来,华中农业大学棉花遗传改良团队深入研究了主栽棉种异源四倍体陆地棉的“亚... 棉花是我国重要的经济作物,其纤维品质对纺织工业和下游产业的发展至关重要.尽管我国在棉花育种方面取得了显著进展,但优质棉品种的选育仍面临诸多挑战.近年来,华中农业大学棉花遗传改良团队深入研究了主栽棉种异源四倍体陆地棉的“亚基因组不对称性”,揭示了多倍化、驯化和纤维发育过程中亚基因组间的差异;发现亚基因组间的结构变异和同源基因表达偏倚在纤维品质形成中起着关键作用,并提出了“亚基因组模块化设计育种”的新策略,即通过调节亚基因组同源基因的表达差异充分发挥异源多倍体的“加性效应”,从而提升纤维品质.初步探索表明,该策略具有较大的应用潜力,有望突破传统育种的局限,实现棉花纤维品质的进一步提升.未来,结合表观遗传改良以及“基因组+基因编辑”工具组合,有望进一步突破遗传改良的上限,满足市场对高品质棉花的综合需求. 展开更多
关键词 棉花 亚基因组不对称性 驯化 多倍化 纤维品质改良
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RAPID LEAF FALLING 1 facilitates chemical defoliation and mechanical harvesting in cotton
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作者 Bing Zhang Dandan Yue +13 位作者 Bei Han Danfan Bao Xiao Zhang Xuyang Hao Xin Lin Keith Lindsey Longfu Zhu Shuangxia Jin maojun wang Haijiang Xu Mingwei Du Yu Yu Xianlong Zhang Xiyan Yang 《Molecular Plant》 2025年第5期765-782,共18页
Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission ... Chemical defoliation stands as the ultimate tool in enabling the mechanical harvest of cotton, offering economic and environmental advantages. However, the underlying molecular mechanism that triggers leaf abscission through defoliant remains unsolved. In this study, we meticulously constructed a transcriptomic atlas through single-nucleus mRNA sequencing (snRNA-seq) of the abscission zone (AZ) from cotton petiole. We identified two newly-formed cell types, abscission cells and protection layer cells in cotton petiole AZ after defoliant treatment. GhRLF1 (RAPID LEAF FALLING 1), as one of the members of the cytokinin oxidase/dehydrogenase (CKX) gene family, was further characterized as a key marker gene unique to the abscission cells following defoliant treatment. Overexpression of GhRLF1 resulted in reduced cytokinin accumulation and accelerated leaf abscission. Conversely, CRISPR/Cas9-mediated loss of GhRLF1 function appeared to delay this process. Its interacting regulators, GhWRKY70, acting as “Pioneer” activator, and GhMYB108, acting as “Successor” activator, orchestrate a sequential modulation of GhWRKY70/GhMYB108–GhRLF1–CTK (cytokinin) within the AZ to regulate cotton leaf abscission. GhRLF1 not only regulates leaf abscission but also reduces cotton yield. Consequently, transgenic lines that exhibit rapid leaf falling and require less defoliant but show unaffected cotton yield were developed for mechanical harvesting. This was achieved using a defoliant-induced petiole-specific promoter, proPER21, to drive GhRLF1 (proPER21::RLF1). This pioneering biotechnology offers a new strategy for the chemical defoliation of machine-harvested cotton, ensuring stable production and reducing leaf debris in harvested cotton, thereby enhancing environmental sustainability. 展开更多
关键词 abscission cells chemical defoliation snRNA-seq machine-harvested cotton RAPID LEAF FALLING 1
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A comprehensive overview of cotton genomics,biotechnology and molecular biological studies 被引量:18
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作者 Xingpeng Wen Zhiwen Chen +15 位作者 Zuoren Yang maojun wang Shuangxia Jin Guangda wang Li Zhang Lingjian wang Jianying Li Sumbul Saeed Shoupu He Zhi wang Kun wang Zhaosheng Kong Fuguang Li Xianlong Zhang Xiaoya Chen Yuxian Zhu 《Science China(Life Sciences)》 SCIE CAS CSCD 2023年第10期2214-2256,共43页
Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis,which makes it of high research and application value.To date,nu... Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis,which makes it of high research and application value.To date,numerous research on cotton has navigated various aspects,from multi-genome assembly,genome editing,mechanism of fiber development,metabolite biosynthesis,and analysis to genetic breeding.Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers.Mature multiple genome editing systems,such as CRISPR/Cas9,Cas12(Cpf1)and cytidine base editing(CBE),have been widely used in the study of candidate genes affecting fiber development.Based on this,the cotton fiber cell development network has been preliminarily drawn.Among them,the MYB-b HLH-WDR(MBW)transcription factor complex and IAA and BR signaling pathway regulate the initiation;various plant hormones,including ethylene,mediated regulatory network and membrane protein overlap fine-regulate elongation.Multistage transcription factors targeting Ces A 4,7,and 8 specifically dominate the whole process of secondary cell wall thickening.And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development.Furthermore,research on the synthesis of cotton secondary metabolite gossypol,resistance to diseases and insect pests,plant architecture regulation,and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties.This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects,thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction. 展开更多
关键词 COTTON genome assembly genome editing fiber development GOSSYPOL plant architecture oil utilization genetic breeding
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Histone H3 lysine 27 trimethylation suppresses jasmonate biosynthesis and signaling to affect male fertility under high temperature in cotton 被引量:5
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作者 Yanlong Li Miao Chen +12 位作者 Aamir Hamid Khan Yizan Ma Xin He Jing Yang Rui Zhang Huanhuan Ma Chunyang Zuo Yawei Li Jie Kong maojun wang Longfu Zhu Xianlong Zhang Ling Min 《Plant Communications》 SCIE CSCD 2023年第6期96-112,共17页
High-temperature(HT)stress causes male sterility in crops,thus decreasing yields.To explore the possible contribution of histone modifications to male fertility under HT conditions,we defined the histone methylation l... High-temperature(HT)stress causes male sterility in crops,thus decreasing yields.To explore the possible contribution of histone modifications to male fertility under HT conditions,we defined the histone methylation landscape for the marks histone H3 lysine 27 trimethylation(H3K27me3)and histone H3 lysine 4 trimethylation(H3K4me3)by chromatin immunoprecipitation sequencing(ChIP-seq)in two differing upland cotton(Gossypium hirsutum)varieties.We observed a global disruption in H3K4me3 and H3K27me3 modifications,especially H3K27me3,in cotton anthers subjected to HT.HT affected the bivalent H3K4me3–H3K27me3 modification more than either monovalent modification.We determined that removal of H3K27me3 at the promoters of jasmonate-related genes increased their expression,maintaining male fertility under HT in the HT-tolerant variety at the anther dehiscence stage.Modulating jasmonate homeostasis or signaling resulted in an anther indehiscence phenotype under HT.Chemical suppression of H3K27me3 deposition increased jasmonic acid contents and maintained male fertility under HT.In summary,our study provides new insights into the regulation of male fertility by histone modifications under HT and suggests a potential strategy for improving cotton HT tolerance. 展开更多
关键词 high temperature H3K27me3 H3K4me3 cotton anther JASMONATE
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High-quality Gossypium hirsutum and Gossypium barbadense genome assemblies reveal the landscape and evolution of centromeres 被引量:5
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作者 Xing Chang Xin He +8 位作者 Jianying Li Zhenping Liu Ruizhen Pi Xuanxuan Luo Ruipeng wang Xiubao Hu Sifan Lu Xianlong Zhang maojun wang 《Plant Communications》 SCIE CSCD 2024年第2期135-150,共16页
Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and... Centromere positioning and organization are crucial for genome evolution;however,research on centro-mere biology is largely influenced by the quality of available genome assemblies.Here,we combined Oxford Nanopore and Pacific Biosciences technologies to de novo assemble two high-quality reference genomes for Gossypium hirsutum(TM-1)and Gossypium barbadense(3-79).Compared with previously published reference genomes,our assemblies show substantial improvements,with the contig N50 improved by 4.6-fold and 5.6-fold,respectively,and thus represent the most complete cotton genomes to date.These high-quality reference genomes enable us to characterize 14 and 5 complete centromeric regions for G.hirsutum and G.barbadense,respectively.Our data revealed that the centromeres of allotetraploid cotton are occupied by members of the centromeric repeat for maize(CRM)and Tekay long terminal repeat families,and the CRM family reshapes the centromere structure of the At subgenome after polyploidization.These two intertwined families have driven the convergent evolution of centromeres between the two subgenomes,ensuring centromere function and genome stability.In addition,the reposi-tioning and high sequence divergence of centromeres between G.hirsutum and G.barbadense have contributed to speciation and centromere diversity.This study sheds light on centromere evolution in a sig-nificant crop and provides an alternative approach for exploring the evolution of polyploid plants. 展开更多
关键词 genome assembly centromere architecture convergent evolution POLYPLOIDIZATION
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Identification of rural courtyards’utilization status using deep learning and machine learning methods on unmanned aerial vehicle images in north China 被引量:2
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作者 maojun wang Wenyu Xu +1 位作者 Guangzhong Cao Tao Liu 《Building Simulation》 SCIE EI CSCD 2024年第5期799-818,共20页
The issue of unoccupied or abandoned homesteads(courtyards)in China emerges given the increasing aging population,rapid urbanization and massive rural-urban migration.From the aspect of rural vitalization,land-use pla... The issue of unoccupied or abandoned homesteads(courtyards)in China emerges given the increasing aging population,rapid urbanization and massive rural-urban migration.From the aspect of rural vitalization,land-use planning,and policy making,determining the number of unoccupied courtyards is important.Field and questionnaire-based surveys were currently the main approaches,but these traditional methods were often expensive and laborious.A new workflow is explored using deep learning and machine learning algorithms on unmanned aerial vehicle(UAV)images.Initially,features of the built environment were extracted using deep learning to evaluate the courtyard management,including extracting complete or collapsed farmhouses by Alexnet,detecting solar water heaters by YOLOv5s,calculating green looking ratio(GLR)by FCN.Their precisions exceeded 98%.Then,seven machine learning algorithms(Adaboost,binomial logistic regression,neural network,random forest,support vector machine,decision trees,and XGBoost algorithms)were applied to identify the rural courtyards’utilization status.The Adaboost algorithm showed the best performance with the comprehensive consideration of most metrics(Accuracy:0.933,Precision:0.932,Recall:0.984,F1-score:0.957).Results showed that identifying the courtyards’utilization statuses based on the courtyard built environment is feasible.It is transferable and cost-effective for large-scale village surveys,and may contribute to the intensive and sustainable approach to rural land use. 展开更多
关键词 unoccupied homesteads courtyard built environment inner courtyard management GLR solar water heaters machine learning algorithms
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Physical mechanism of field modulation effects in ion implanted edge termination of vertical GaN Schottky barrier diodes 被引量:1
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作者 Ruiyuan Yin Chiachia Li +6 位作者 Bin Zhang Jinyan wang Yunyi Fu Cheng P.Wen Yilong Hao Bo Shen maojun wang 《Fundamental Research》 CAS 2022年第4期629-634,共6页
In this study,the physical properties of F ion-implanted GaN were thoroughly studied,and the related electric-field modulation mechanisms in ion-implanted edge termination were revealed.Transmission electron microscop... In this study,the physical properties of F ion-implanted GaN were thoroughly studied,and the related electric-field modulation mechanisms in ion-implanted edge termination were revealed.Transmission electron microscopy re.sults indicate that the ion-implanted region maintains a single-crystal structure even with the implantation of high-energy F ions,indicating that the high resistivity of the edge termination region is not induced by amorphization.Alternately,ion implantation-induced deep levels could compensate the electrons and lead to a highly resistive layer In addition to the bulk ffect,the direct bombardment of high-energy F ions resulted in a rough and nitrogen-deficient surface,which was confirmed via atomic force microscopy(AFM)and X-ray photoelectron spectroscopy,The implanted surface with a large density of nitrogen vacancies can accommodate electrons,and it is more conductive than the bulk in the implanted region,which is validated via spreading resistance profiling and conductive AFM measurements.Under reverse bias,the implanted surface can spread the potential in the lateral direction,whereas the acceptor traps capture electrons acting as space charges,shifting the peak electric field into the bulk region in the vertical direction.As a result,the Schottky barrier diode terminated with high-energy F ion-implanted regions exhibits a breakdown voltage of over 1.2 kv. 展开更多
关键词 lon implantation Edge termination Electri field modulationeffect GAN Schottky barrier diodes
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