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The transcriptional landscape of the developmental switch from regular pollen maturation towards microspore-derived plant regeneration in barley
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作者 Anna Nowicka Martin Kovacik +10 位作者 Anna Maksylewicz Przemysław Kopec Ewa Dubas Monika Krzewska Agnieszka Springer Robert E.Hoffie Diaaeldin S.Daghma Zbynek Milec Ales Pecinka Jochen Kumlehn Iwona Zur 《The Crop Journal》 SCIE CSCD 2024年第4期1064-1080,共17页
Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors.Haploids/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant b... Plant formation from in vitro-cultivated microspores involves a complex network of internal and environmental factors.Haploids/doubled haploids(DHs)derived from in vitro-cultured microspores are widely used in plant breeding and genetic engineering.However,the mechanism underlying the developmental switch from regular pollen maturation towards microspore-derived plant regeneration remains poorly defined.Here,RNA-sequencing was employed to elucidate the transcriptional landscapes of four early stages of microspore embryogenesis(ME)in barley cultivars Golden Promise and Igri,which exhibit contrasting responsiveness to microspore-derived plant formation.Our experiments revealed fundamental regulatory networks,specific groups of genes,and transcription factor(TF)families potentially regulating the developmental switch.We identified a set of candidate genes crucial for genotype-dependent responsiveness/recalcitrance to ME.Our high-resolution temporal transcriptome atlas provides an important resource for future functional studies on the genetic control of microspore developmental transition. 展开更多
关键词 Hordeum vulgare marker gene Microspore embryogenesis Stress response Transcriptome analysis
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Fine-mapping of a candidate gene for web blotch resistance in Arachis hypogaea L.
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作者 Xiaohui Wu Mengyuan Zhang +11 位作者 Zheng Zheng Ziqi Sun Feiyan Qi Hua Liu Juan Wang Mengmeng Wang Ruifang Zhao Yue Wu Xiao Wang Hongfei Liu Wenzhao Dong Xinyou Zhang 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2024年第5期1494-1506,共13页
Peanut(Arachis hypogaea L.)is a globally important oil crop.Web blotch is one of the most important foliar diseases affecting peanut,which results in serious yield losses worldwide.Breeding web blotch-resistant peanut... Peanut(Arachis hypogaea L.)is a globally important oil crop.Web blotch is one of the most important foliar diseases affecting peanut,which results in serious yield losses worldwide.Breeding web blotch-resistant peanut varieties is the most effective and economically viable method for minimizing yield losses due to web blotch.In the current study,a bulked segregant analysis with next-generation sequencing was used to analyze an F2:3 segregating population and identify candidate loci related to web blotch resistance.Based on the fine-mapping of the candidate genomic interval using kompetitive allele-specific PCR(KASP)markers,we identified a novel web blotch resistance-related locus spanning approximately 169 kb on chromosome 16.This region included four annotated genes,of which only Arahy.35VVQ3 had a non-synonymous single nucleotide polymorphism in the coding region between the two parents.Two markers(Chr.16.12872635 and Chr.16.12966357)linked to this gene were shown to be co-segregated with the resistance of peanut web blotch by 72 randomly selected recombinant inbred lines(RIL),which could be used in marker-assisted breeding of resistant peanut varieties. 展开更多
关键词 peanut web blotch bulked segregant analysis KAsP markers resistant gene
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Fast tracking alien gene discovery by molecular markers in a late flowering Chinese cabbage-cabbage translocation line‘AT7–4' 被引量:1
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作者 Hui Li Aixia Gu +12 位作者 Daling Feng Na Li Rui Yang Xinpei Zhang Shuangxia Luo Umer Karamat Qianyun Wang Shuxin Xuan Xueping Chen Yin Lu Yanhua Wang Shuxing Shen Jianjun Zhao 《Horticultural Plant Journal》 SCIE CAS CSCD 2023年第1期89-97,共9页
Flowering time is an important agronomic trait of Chinese cabbage with late flowering being a primary breeding objective.In our previous work,we obtained Chinese cabbage-cabbage translocation lines that contained seve... Flowering time is an important agronomic trait of Chinese cabbage with late flowering being a primary breeding objective.In our previous work,we obtained Chinese cabbage-cabbage translocation lines that contained several beneficial cabbage genes.Cabbage-specific molecular markers show that these genes were coming from chromosome C01 of cabbage.In this study,we investigated the inheritance of flowering time in a couple of translocation lines and analyzed the transmission rate of molecular markers in the offspring.Consequently,we obtained the late flowering Chinese cabbage-cabbage translocation line‘AT7–4’in which the flowering time was later than that of‘85–1’by about 7 days under 4-week vernalization.Based on previous studies of the genomes of Chinese cabbage and cabbage,we located the cabbage-specific molecular markers that were closely linked at the top of the chromosome A01 in the F2mapping population generated by self-crossing F1s derived from a cross between the translocation line‘AT7–4’and Chinese cabbage‘14–36’.Five flowering-related genes in the alien fragment were found by functional annotation and their molecular markers were developed.This study lays the foundation for the future improvement of Chinese cabbage varieties using A-C translocation lines. 展开更多
关键词 Chinese cabbage Translocation line Alien gene Molecular marker Late flowering
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Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean
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作者 Yanzhu Su Xiaoshuai Hao +11 位作者 Weiying Zeng Zhenguang Lai Yongpeng Pan Can Wang Pengfei Guo Zhipeng Zhang Jianbo He Guangnan Xing Wubin Wang Jiaoping Zhang Zudong Sun Junyi Gai 《The Crop Journal》 SCIE CSCD 2024年第1期232-243,共12页
Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network g... Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade tolerance.An improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with both.Annotation of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth stages.From the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the network.Altogether,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network. 展开更多
关键词 Soybean(Glycine max(L.)Merr.) SHADE-TOLERANCE Restricted two-stage multi-locus genomewide association study based on gene/allele sequence markers(GASM-RTM-GWAS) Shade-tolerance index(STI) Relative cell length(RCL) Transcriptome
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Identification of KASP markers and putative genes for pre-harvest sprouting resistance in common wheat(Triticum aestivum L.) 被引量:1
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作者 Guannan Liu Daniel Mullan +3 位作者 Aimin Zhang Hui Liu Dongcheng Liu Guijun Yan 《The Crop Journal》 SCIE CSCD 2023年第2期549-557,共9页
Common wheat(Triticum aestivum L.)is the most important crop in the world and a typical allopolyploid with a large and complex genome.Pre-harvest sprouting(PHS)leads to a significant reduction in grain quality worldwi... Common wheat(Triticum aestivum L.)is the most important crop in the world and a typical allopolyploid with a large and complex genome.Pre-harvest sprouting(PHS)leads to a significant reduction in grain quality worldwide.PHS is a complex trait with related QTL located on different chromosomes.However,the study of markers and genes related to PHS resistance is limited especially for whitegrained wheat.Four pairs of near isogenic lines(NILs)from a white-grained wheat cross of CharaDM5637B*8 targeting a major QTL for PHS resistance(Qphs.ccsu-3A.1)on wheat chromosme 3AL were genotyped using the 90K SNP Illumina iSelect array.Ten SNPs were identified,with a 75%-100%consistency between genotype and phenotype in the resistant or susceptible isolines.The 10 SNPs were converted to cost-effective kompetitive allele-specific PCR(KASP)markers.Screening of 48 wheat cultivars with different phenotypes of PHS identified four KASP markers with 81.3%-85.4%conformity between genotype and phenotype.Further investigation revealed that the four SNPs(BS00022245_51,Kukri_c49927_151,BS00022884_51 and BS00110550_51)corresponding to the four validated KASP markers are residing in three independent genes(TraesCS3A03G1072800,TraesCS3A03G1072400,TraesCS3A03G1071800)close to each other with a distance of 4.28-4.48 Mb to the targeted QTL.These three annotated genes have potential functions related to PHS resistance.Our study revealed that combined use of NILs and the 90K SNP chip is a powerful approach for developing KASP markers and mining functional genes in wheat.The KASP markers for PHS resistance on chromosome 3AL are useful for high-throughput evaluation and marker-assisted selection,and the three identified genes could lead to a better understanding of the genetic pathways controlling PHS. 展开更多
关键词 Pre-harvest sprouting(PHS) KASP marker Functional genes Chromosome 3AL 90K SNP assay Near-isogenic lines
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Population Genetic Structure in Apricot (Prunus armeniaca L.) Cultivars Revealed by Fluorescent-AFLP Markers in Southern Xinjiang,China 被引量:13
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作者 苑兆和 陈学森 +3 位作者 何天明 冯建荣 冯涛 张春雨 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第11期1037-1047,共11页
Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot (Prunus armeniaca L.) cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous R... Population-wide genetic structure was studied using fluorescent-AFLP markers on 85 apricot (Prunus armeniaca L.) cultivars collected from Kuche, Kashi, Hetian in the Tarim Basin, southern Xinjiang Uygur Autonomous Region of China. The purpose of this study was to determine the genetic structure and genotypic diversity among the different eco-geographical populations. Based on the results from this study, 8 pairs of fluorescent-AFLP primers showed clear electrophoregram and high polymorphism amongst the 64 pairs of EcoR Ⅰ/Mse Ⅰ (Mse Ⅰ - a FAM fluorescent marked primer) primers screened. There was a significant polymorphic difference for the same primer pair in different populations and for the same population with different primer pairs. The percentage of polymorphic loci (P) at species level was higher than Kuche, Hetian, Kashi population levels, respectively. The Nei's gene diversity index (H) and Shannon's information index (I) at species level were higher than those of Kuche, Hetian, and Kashi at population level, respectively. H and I of Kuche population were the highest amongst the three populations. Apricot population genetic diversity was found mainly within the population, Genetic differentiation coefficient between populations (GST) was 0.0882. Gene flow Nm between the populations was 5.1689. Population genetic identity was between 0.9772-0.9811 and genetic distance was between 0.0191-0.0232. These results further indicated that the similarity between populations was higher and the genetic distance between populations was smaller. The UPGMA cluster analysis indicates that the geographical populations at Kuche, Kashi, Hetian were relatively independent Mendelian populations. Concurrently, there was also partial gene exchange between the populations. All the evidences indicated that the genetic diversity in Kuche population was the highest, suggesting that it could be a transition population from wild apricot to cultivated apricot. There were abundant genetic diversities in apricot cultivar populations in southern Xinjiang, China, which provide promising germplasm for further breeding and theoretical basis for biodiversity conservation and utilization for apricot population in this area. 展开更多
关键词 Prunus armeniaca POPULATION AFLP marker genetic structure' gene flow
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ACC Synthase Gene (ACSG) as a Possible Molecular Marker for Female Lines in Cucumber 被引量:11
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作者 叶波平 白书农 曹宗巽 《Acta Botanica Sinica》 CSCD 2000年第7期765-766,共2页
利用本实验室根据已知序列分离得到的ACC合酶基因 (ACSG)为探针对不同黄瓜 (CucumissativusL .)品种(系 )的基因组DNA进行Southern杂交 ,初步分析了该基因与黄瓜性别表型之间的相关性。发现在所检测的 10个不同品系中 ,ACSG与雌性系表... 利用本实验室根据已知序列分离得到的ACC合酶基因 (ACSG)为探针对不同黄瓜 (CucumissativusL .)品种(系 )的基因组DNA进行Southern杂交 ,初步分析了该基因与黄瓜性别表型之间的相关性。发现在所检测的 10个不同品系中 ,ACSG与雌性系表型之间存在明显的相关关系 ,而且这种相关关系在不同的实验中具有良好的重复性。ACSG基因可能是鉴定黄瓜雌性系的一个分子标记。 展开更多
关键词 CUCUMBER ACC synthase gene female lines molecular marker
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Development of RAPD Markers and SCAR Markers Linked to Bentazon Susceptible Lethality Gene in Rice 被引量:2
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作者 向太和 杨剑波 +6 位作者 李莉 倪大虎 杨前进 朱启升 汪秀峰 张毅 黄大年 《Acta Botanica Sinica》 CSCD 2003年第2期223-228,共6页
Rice cultivar Norin 8 and its mutant Norin 8m harbour bentazon resistance trait and bentazon susceptibility trait respectively. A total of 360 arbitrary 10-mer oligonucleotide primers were screened on the genomic DNA ... Rice cultivar Norin 8 and its mutant Norin 8m harbour bentazon resistance trait and bentazon susceptibility trait respectively. A total of 360 arbitrary 10-mer oligonucleotide primers were screened on the genomic DNA of Norin 8 and Norin 8m with RAPD technique. Among which, five primers produced seven polymorphic RAPD bands between Norin 8 and Norin 8m. Amplified RAPD polymorphic products were cloned and sequenced. The sequences were used to design primers for PCR. Five SCAR markers, SCAR/G18/883, SCAR/G18/890, SCAR/G18/919/948, SCAR/D10/1237 and SCAR/F03/1186, were developed from OPG18/943, OPG18/972, OPD10/1248 and OPF03/1198. F-2 progeny of 320 individuals was analyzed to map SCAR markers in relationship to ben or Ben genes. SCAR markers of SCAR/G18/883, SCAR/G18/890, SCAR/G18/919/948 were shown to cosegregate with ben or Ben genes, and SCAR/D10/1237 to be linked of Ben gene with a distance of (14.8 +/- 2.1) cM. The genetic linkage to ben gene and SCAR markers was identified by a pair of near isogenic lines H121 and Hben121. Southern blotting analysis and segregation ratio of F-2 progeny revealed that OPG18/943 and OPG18/972 were single-copy in genome, and locus of OPG18/943 and OPG18/972 were allelic and sequence tagged sites. It is the first report on molecular markers linked to ben or Ben genes. The markers are useful to marker-assisted selection for the breeding and tag ben gene with map-based cloning. 展开更多
关键词 rice ( Oryza saliva ) bentazon susceptible lethality gene RAPD marker SCAR marker
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Screening and Application of SSR Markers of Resistant Gene against Rice Stripe Virus 被引量:1
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作者 蔡之军 姚海根 +2 位作者 姚坚 殷跃军 李守俊 《Plant Diseases and Pests》 CAS 2010年第6期7-11,共5页
[Objective] New SSR primers were designed and screened to apply in the backcross breeding for modified resistance against rice stripe virus.[Method] The conventional late japonica rice varieties including 502 with hig... [Objective] New SSR primers were designed and screened to apply in the backcross breeding for modified resistance against rice stripe virus.[Method] The conventional late japonica rice varieties including 502 with high resistance to stripe virus,Xiushui 09 with high susceptibility to stripe virus and their derived strains were adopted as the test materials,SSR and SAPR markers were used to locate RSV1 gene with high resistance against stripe virus,and three pairs of SSR markers (M-11-1,M-11-2,M-11-3) were further designed.Through screening and analysis,M-11-3 was selected as the RSV1 detection marker gene for tracking RSV1 gene,thus RSV1 gene was successfully introduced to the backcross breeding of late japonica rice varieties such as Xiushui 09,and the resistance expression of different strains was identified.[Result]The resistance of improved strains against stripe virus was significantly higher than Xiushui 09,the resistance of most strains was close to the level of donor,and the expression of resistance among years was stable.Therefore,the resistance effect of RSV1 gene used in the test was very obvious,which was accurate with the assisted selection of RSV1 gene linked markers M-11-3.[Conclusion]The study certified the feasibility of molecular markers application in resistance improvement against rice stripe virus,which also showed that optimization and development of new marker genes could effectively improve the efficiency of marker-assisted selection. 展开更多
关键词 RICE Strip virus RSV1 gene Molecule marker assisted selection
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Screening and Application of Molecular Markers for Starch Synthesis-related Genes in Rice
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作者 姚姝 刘燕清 +8 位作者 强新涛 赵春芳 于新 周丽慧 陈涛 赵庆勇 朱镇 张亚东 王才林 《Agricultural Science & Technology》 CAS 2016年第1期29-33,共5页
In this study, the genotypes of starch synthesis-related genes were systematically screened from different rice varieties using molecular markers. The results showed that starch synthesis-related genes were highly pol... In this study, the genotypes of starch synthesis-related genes were systematically screened from different rice varieties using molecular markers. The results showed that starch synthesis-related genes were highly polymorphic between indica and japonica varieties, as they greatly variated among indica varieties, but were conserved among japonica varieties. The genotypes of two indica varieties9311 and Minghui 63 were more similar to that of japonica varieties. Two or three alleles of six starch synthesis-related genes were found in 28 japonica parental varieties. Four genotypes of two soluble starch synthase genes, SSIIa and SSIIIa,were detected in 88 stable lines derived from the cross of Kanto 194/ Wujing 13 using molecular markers. 展开更多
关键词 Rice(Oryza sativa L Starch synthesis-related gene Molecular marker High quality
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Mapping of a Major Stripe Rust Resistance Gene in Chinese Native Wheat Variety Chike Using Microsatellite Markers 被引量:4
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作者 刘方慧 牛永春 +1 位作者 邓晖 檀根甲 《Journal of Genetics and Genomics》 SCIE CAS CSCD 北大核心 2007年第12期1123-1130,共8页
Chike (accession number Su1900), a Chinese native wheat (Triticum aestivum L.) variety, is resistant to the currently prevailing physiological races of Puccinia striiformis Westend. f. sp. tritici in China. Geneti... Chike (accession number Su1900), a Chinese native wheat (Triticum aestivum L.) variety, is resistant to the currently prevailing physiological races of Puccinia striiformis Westend. f. sp. tritici in China. Genetic analysis indicated that resistance to the physiological race CY32 of the pathogen in the variety was controlled by one dominant gene. In this study, BSA (bulked segregant analysis) methods and SSRs (simple sequence repeats) marker polymorphic analysis are used to map the gene. The resistant and susceptible DNA bulks were prepared from the segregating F2 population of the cross between Taichung 29, a susceptible variety as maternal parent, and Chike as paternal parent. Over 400 SSR primers were screened, and five SSR markers Xwmc44, Xgwm259, Xwmc367, Xcfa2292, and Xbarc80 on the chromosome arm 1BL were found to be polymorphic between the resistant and the susceptible DNA bulks as well as their parents. Genetic linkage was tested on segregating F2 population with 200 plants, including 140 resistant and 60 susceptible plants. All the five SSR markers were linked to the stripe rust resistance gene in Chike. The genetic distances for the markers Xwmc44, Xgwm259, Xwmc367, Xcfa2292, and Xbarc80 to the target gene were 8.3 cM, 9.1 cM, 17.2 cM, 20.6 cM, and 31.6 cM, respectively. Analysis using 21 nulli-tetrasomic Chinese Spring lines further confirmed that all the five markers were located on chromosome lB. On the basis of the above results, it is reasonable to assume that the major stripe rust resistance gene YrChk in Chike was located on the chromosome arm 1BL, and its comparison with the other stripe rust resistance genes located on 1B suggested that YrChk may be a novel gene that provides the resistance against stripe rust in Chike. Exploration and utilization of resources of disease resistance genes in native wheat varieties will be helpful both to diversify the resistance genes and to amend the situation of resistance gene simplification in the commercial wheat cultivars in China. 展开更多
关键词 WHEAT native variety Puccinia striiformis resistance gene microsatellite marker gene mapping
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Single-cell and spatial heterogeneity landscapes of mature epicardial cells 被引量:1
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作者 Jianlin Du Xin Yuan +7 位作者 Haijun Deng Rongzhong Huang Bin Liu Tianhua Xiong Xianglin Long Ling Zhang Yingrui Li Qiang She 《Journal of Pharmaceutical Analysis》 SCIE CAS CSCD 2023年第8期894-907,共14页
Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with... Tbx18,Wt1,and Tcf21 have been identified as epicardial markers during the early embryonic stage.However,the gene markers of mature epicardial cells remain unclear.Single-cell transcriptomic analysis was performed with the Seurat,Monocle,and CellphoneDB packages in R software with standard procedures.Spatial transcriptomics was performed on chilled Visium Tissue Optimization Slides(10x Genomics)and Visium Spatial Gene Expression Slides(10x Genomics).Spatial transcriptomics analysis was performed with Space Ranger software and R software.Immunofluorescence,whole-mount RNA in situ hybridization and X-gal staining were performed to validate the analysis results.Spatial transcriptomics analysis revealed distinct transcriptional profiles and functions between epicardial tissue and non-epicardial tissue.Several gene markers specific to postnatal epicardial tissue were identified,including Msln,C3,Efemp1,and Upk3b.Single-cell transcriptomic analysis revealed that cardiac cells from wildtype mouse hearts(from embryonic day 9.5 to postnatal day 9)could be categorized into six major cell types,which included epicardial cells.Throughout epicardial development,Wt1,Tbx18,and Upk3b were consistently expressed,whereas genes including Msln,C3,and Efemp1 exhibited increased expression during the mature stages of development.Pseudotime analysis further revealed two epicardial cell fates during maturation.Moreover,Upk3b,Msln,Efemp1,and C3 positive epicardial cells were enriched in extracellular matrix signaling.Our results suggested Upk3b,Efemp1,Msln,C3,and other genes were mature epicardium markers.Extracellular matrix signaling was found to play a critical role in the mature epicardium,thus suggesting potential therapeutic targets for heart regeneration in future clinical practice. 展开更多
关键词 Epicardial cells gene markers Single-cell sequencing Spatial transcriptomics
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Mapping of Fertility Restoring Gene for Aegilops kotschyi Cytoplasmic Male Sterility in Wheat Using SSR Markers 被引量:13
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作者 LIU Bao-shen, SUN Qi-xin, GAO Qing-rong, SUN Lan-zhen, XIE Chao-jie, LI Chuan-you, NI Zhong-fu and DOU Bing-de( Agronomy Department, Shandong Agricultural University, Taian 271018, P.R.China Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100094 , P. R . China ) 《Agricultural Sciences in China》 CAS CSCD 2002年第8期845-849,共5页
LK783 was found to be a good fertility restorer for K-type male sterility of wheat. Microsatel-lite markers were employed to map the major restoring gene in LK783. Maintainer and restorer DNA pools were established us... LK783 was found to be a good fertility restorer for K-type male sterility of wheat. Microsatel-lite markers were employed to map the major restoring gene in LK783. Maintainer and restorer DNA pools were established using the extreme sterile and fertile plants among (KJ5418A//911289/LK783)F1 population, respectively. Seventy-nine sets of SSR primers were screened for polymorphism between the two pools, 6 of which were found polymorphic. Linkage analysis showed that Xgwm11, Xgwm18, Xgwm264a and Xgwm273 were linked to the restoring gene in LK783, while Xgwm11, Xgwm18 and Xgwm273 were co-segregated. The distance between the Rf gene in LK783 and the three co-segregated markers was 6.54 ± 4.37 cM, the distance between Rf gene and Xgwm264a was 5. 71 ± 4.10 cM. The four SSR markers were located on chromosome IBS by amplifying the DNA of nulli-tetrasomics and ditelosomics of CS with the 4 sets of primers, indicating that the major restoring gene in LK783 was located on IBS, but the relative location of the gene was different from Rfv1, allelism of the two genes should be further investigated. The breeding for new fertility restorer lines of K-type cytoplasmic male sterility in wheat would be facilitated by using the four polymorphic markers. 展开更多
关键词 Wheat ( Triticum aestivum) Cytoplasmic male sterility Restoring gene Molecular marker MICROSATELLITE
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InDel and SNP Markers and Their Applications in Map-based Cloning of Rice Genes 被引量:8
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作者 Cun-hong PAN Ai-hong LI +9 位作者 Zheng-yuan DAI Hong-xi ZHANG Guang-qing LIU Zi-bin WANG Yu-yin MA Yue-jun YIN Ya-fang ZHANG Shi-min ZUO Zong-xiang CHEN Xue-biao PAN 《Rice science》 SCIE 2008年第4期251-258,共8页
High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymo... High-density markers are necessary for map-based cloning of rice genes, but the currently available markers are not satisfactory enough. InDel (insertion-deletion length polymorphism) and SNP (single nucleotide polymorphism) are the new generation of molecular markers and can basically meet the need of fine mapping. InDel and SNP markers can be developed through bioinformatics. These markers are valuable markers with the characters of low cost, high specificity and stability. This article introduced the methods for designing InDel and SNP markers, taking the mapping of a rice rolled leaf gene as an example. In addition, some key factors in improving the design efficiency were also discussed. 展开更多
关键词 RICE molecular marker insertion-deletion length polymorphism single nucleotide polymorphism BIOINFORMATICS gene mapping rolled leaf gene
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Genetic Analysis and Preliminary Mapping of a Highly Male-Sterile Gene in Foxtail Millet(Setaria italica L.Beauv.) Using SSR Markers 被引量:7
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作者 WANG Jun WANG Zhi-lan +8 位作者 YANG Hui-qing YUAN Feng GUO Er-hu TIAN Gang AN Yuan-huai LI Hui-xia WANG Yu-wen DIAO Xian-min GUO Ping-yi 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2013年第12期2143-2148,共6页
Breeding of male-sterile lines has become the mainstream for the heterosis utilization in foxtail millet,but the genetic basis of most male-sterile lines used for the hybrid is still an area to be elucidated.In this s... Breeding of male-sterile lines has become the mainstream for the heterosis utilization in foxtail millet,but the genetic basis of most male-sterile lines used for the hybrid is still an area to be elucidated.In this study,a highly male-sterile line Gao146A was investigated.Genetic analysis indicated that the highly male-sterile phenotype was controlled by a single recessive gene a single recessive gene.Using F 2 population derived from cross Gao146A/K103,one gene controlling the highly male- sterility,tentatively named as ms1,which linked to SSR marker b234 with genetic distance of 16.7 cM,was mapped on the chromosome VI.These results not only laid the foundation for fine mapping of this highly male-sterile gene,but also helped to accelerate the improvement of highly male-sterile lines by using molecular marker assisted breeding method. 展开更多
关键词 foxtail millet(Setaria italic L.Beauv.) highly male-sterility gene mapping SSR marker
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Development of Simple Functional Markers for Low Glutelin Content Gene 1 (Lgc1) in Rice (Oryza sativa) 被引量:7
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作者 CHEN Tao TIAN Meng-xiang ZHANG Ya-dong ZHU Zhen ZHAO Ling ZHAO Qing-yong LIN Jing ZHOU Li-hui WANG Cai-lin 《Rice science》 SCIE 2010年第3期173-178,共6页
Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelincontent gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and Gl... Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelincontent gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice. 展开更多
关键词 Oryza sativa low glutelin-content gene functional marker double polymerase chain reaction
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Transcriptome analysis of salt-responsive genes and SSR marker exploration in Carex rigescens using RNA-seq 被引量:4
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作者 LI Ming-na LONG Rui-cai +6 位作者 FENG Zi-rong LIU Feng-qi SUN Yan ZHANG Kun KANG Jun-mei WANG Zhen CAO Shi-hao 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2018年第1期184-196,共13页
Carex rigescens (Franch.) V. Krecz is a wild turfgrass perennial species in the Carex genus that is widely distributed in salinised areas of northern China. To investigate genome-wide salt-response gene networks in ... Carex rigescens (Franch.) V. Krecz is a wild turfgrass perennial species in the Carex genus that is widely distributed in salinised areas of northern China. To investigate genome-wide salt-response gene networks in C. rigescens, transcriptome analysis using high-throughput RNA sequencing on C. rigescens exposed to a 0.4% salt treatment (Cr_Salt) was compared to a non-salt control (Cr_Ctrl). In total, 57 742 546 and 47 063 488 clean reads were obtained from the Cr Ctrl and Cr Salt treatments, respectively. Additionally, 21 954 unigenes were found and annotated using multiple databases. Among these unigenes, 34 were found to respond to salt stress at a statistically significant level with 6 genes up-regulated and 28 downregulated. Specifically, genes encoding an EF-hand domain, ZFP and AP2 were responsive to salt stress, highlighting their roles in future research regarding salt tolerance in C. rigescens and other plants. According to our quantitative RT-PCR results, the expression pattern of all detected differentially expressed genes were consistent with the RNA-seq results. Furthermore, we identified 11 643 simple sequence repeats (SSRs) from the unigenes. A total of 144 amplified successfully in the C. rigescens cultivar LOping 1, and 69 of them reflected polymorphisms between the two genotypes tested. This is the first genome-wide transcriptome study of C. rigescens in both salt-responsive gene investigation and SSR marker exploration. Our results provide further insights into genome annotation, novel gene discovery, molecular breeding and comparative genomics in C. rigescens and related grass species. 展开更多
关键词 salt stress Carex rigescens TRANSCRIPTOME differentially expressed genes SSR markers
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Molecular Marker Assisted Selection for Yield-Enhancing Genes in the Progeny of Minghui63 x O. rufipogon 被引量:7
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作者 WANGYue-guang DENGQi-yun +7 位作者 LIANGFeng-shan XlNGQuan-hua LIJi-ming XONGYue-dong SUNShi-mong GUOBao-tai YUANLong-ping WANGBin 《Agricultural Sciences in China》 CAS CSCD 2004年第2期89-93,共5页
Two yield-enhancing genes (yld1.1 and yld2.1) are located on chromosomes 1 and 2 respectivelyin a weedy relative of cultivated rice, Oryza rufipogon. SSR markers RM9 and RM166 are closelylinked with the two loci respe... Two yield-enhancing genes (yld1.1 and yld2.1) are located on chromosomes 1 and 2 respectivelyin a weedy relative of cultivated rice, Oryza rufipogon. SSR markers RM9 and RM166 are closelylinked with the two loci respectively. Minghui63 (MH63) has been a widely used restorationline in hybrid rice production in China during the past two decades. The F1 of cross 'MH63O.rufipogon' was backcrossed with MH63 generation by generation. RM9 and RM166 were used toselect the plants from the progeny of the backcross populations. The results were as follows:(1) In BC2F1 population, the percentage of the individuals which have RM9 and RM166 amplifiedbands simultaneously was 12.2%, while in the BC3F1 population, that was 16.3%. (2) Among 400individuals of BC3F1, four yield-promising plants were obtained, with yield being 30% more thanthat of MH63. (3) The products amplified by primer RM166 in O. rufipogon and MH63 weresequenced. It was found that the DNA fragment sequence amplified by RM166 from MH63 was 101 bpshorter than that from O. rufipogon. The 101bp sequence is a part of an intron of the PCNA(proliferating cell nuclear antigen) gene. 展开更多
关键词 Oryza rufipogon Yield-enhancing gene Molecular marker assisted selection (MAS)
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Gene expression profiles of hepatic cell-type specific marker genes in progression of liver fibrosis 被引量:5
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作者 Yoshiyuki Takahara Mitsuo Takahashi +5 位作者 Hiroki Wagatsuma Fumihiko Yokoya Qing-Wei Zhang Mutsuyo Yamaguchi Hiroyuki Aburatani Norifumi Kawada 《World Journal of Gastroenterology》 SCIE CAS CSCD 2006年第40期6473-6499,共27页
AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis.METHODS: Marker genes were identified for different types of hepatic cel... AIM: To determine the gene expression profile data for the whole liver during development of dimethylni-trosamine (DMN)-induced hepatic fibrosis.METHODS: Marker genes were identified for different types of hepatic cells, including hepatic stellate cells (HSCs), Kupffer cells (including other inflammatory cells), and hepatocytes, using independent temporal DNA microarray data obtained from isolated hepatic cells. RESULTS: The cell-type analysis of gene expression gave several key results and led to formation of three hypotheses: (1) changes in the expression of HSC-specific marker genes during fibrosis were similar to gene expression data in in vitro cultured HSCs, suggesting a major role of the self-activating characteristics of HSCs in formation of fibrosis; (2) expression of mast cell-specific marker genes reached a peak during liver fibrosis, suggesting a possible role of mast cells in formation of fibrosis; and (3) abnormal expression of hepatocyte-specific marker genes was found across several metabolic pathways during fibrosis, including sulfur-containing amino acid metabolism, fatty acid metabolism, and drug metabolism, suggesting a mechanistic relationship between these abnormalities and symptoms of liver fibrosis. CONCLUSION: Analysis of marker genes for specific hepatic cell types can identify the key aspects of fibro-genesis. Sequential activation of inflammatory cells and the self-supporting properties of HSCs play an important role in development of fibrosis. 展开更多
关键词 Liver fibrosis gene expression Microarray DIMETHYLNITROSAMINE marker genes Hepatic stellate cell Kupffer cell HEPATOCYTES Metabolic pathway
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Identification of Molecular Markers for a Aphid Resistance Gene in Sorghum and Selective Efficiency Using These Markers 被引量:3
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作者 CHANG Jin-hua CUI Jiang-hui +1 位作者 XUE Wei ZHANG Qing-wen 《Journal of Integrative Agriculture》 SCIE CAS CSCD 2012年第7期1086-1092,共7页
In this study, an F2 segregated population obtained by hybridization between the aphid-sensitive sorghum strain Qiansan and aphid-resistant cultivar Henong 16 was used to establish an aphid-resistant pool and an aphid... In this study, an F2 segregated population obtained by hybridization between the aphid-sensitive sorghum strain Qiansan and aphid-resistant cultivar Henong 16 was used to establish an aphid-resistant pool and an aphid-sensitive pool. 192 pairs of AFLP (amplified fragment length polymorphism) marker primers were screened in these pools using BSA (bulked segregant analysis). Three pairs of EcoR I-CTG/Mse I-CCT, EcoR I-CTG/Mse I-CAT, and EcoR I-AGT/Mse I-CCC showed linkage with aphis resistance. EcoR I-CTG/Mse I-CCT-475, EcoR I-CTG/Mse I-CAT-390, and EcoR I-AGT/Mse I-CCC- 350 (E42/M52-350) were mapped within 6, 10, and 13 cM distances with the aphid-resistant gene by using Mapmaker 3.0 software. The bands amplified by EcoR I-CTG/Mse I-CCT-475 and EcoR I-CTG/Mse I-CAT-390 were extracted, cloned, and sequenced. Specific primers of SCAR (sequence characterized amplified regions) were then designed from these bands. A specific band of 300 bp was amplified by a pair of SCAR primers designed based on the sequence obtained from the EcoR I-CTG/Mse I-CAT-390 marker. The SCAR marker was named SCAS0. The marker was used to detect the F2, BC1, and F2:3 populations. The selective efficiency was 86.8, 91.1, and 86.3% in the BC1, F2, and F2:3 populations, respectively. The average selective efficiency was 88.2%. 展开更多
关键词 sorghum bicolor aphid resistance gene molecular marker SCAR molecular assistant selection
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