11 results on '"Yin, Tongming"'
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2. Additional file 5 of Repeated turnovers keep sex chromosomes young in willows
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Wang, Deyan, Li, Yiling, Li, Mengmeng, Yang, Wenlu, Ma, Xinzhi, Zhang, Lei, Wang, Yubo, Feng, Yanlin, Zhang, Yuanyuan, Zhou, Ran, Sanderson, Brian J., Keefover-Ring, Ken, Yin, Tongming, Smart, Lawrence B., DiFazio, Stephen P., Liu, Jianquan, Olson, Matthew, and Ma, Tao
- Abstract
Additional file 5. Peer review history.
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- 2022
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- View/download PDF
3. Additional file 1 of Repeated turnovers keep sex chromosomes young in willows
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Wang, Deyan, Li, Yiling, Li, Mengmeng, Yang, Wenlu, Ma, Xinzhi, Zhang, Lei, Wang, Yubo, Feng, Yanlin, Zhang, Yuanyuan, Zhou, Ran, Sanderson, Brian J., Keefover-Ring, Ken, Yin, Tongming, Smart, Lawrence B., DiFazio, Stephen P., Liu, Jianquan, Olson, Matthew, and Ma, Tao
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Additional file 1: Fig. S1-S11. Supplementary figure legends and supplementary figures.
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- 2022
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4. Physical interaction between SnRK2 and PP2C is conserved in Populus trichocarpa
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Song, Xueqing, Ohtani, Misato, Hori, Chiaki, Takebayasi, Arika, Hiroyama, Ryoko, Rejab, Nur Ardiyana, Suzuki, Takaomi, Demura, Taku, Yin, Tongming, Yu, Xiang, and Zhuge, Qiang
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physical interaction ,Populus trichocarpa ,yeast two-hybrid ,SnRK2 ,ABA signaling ,PP2C - Abstract
Type 2C protein phosphatase (PP2C) is a central player in abscisic acid (ABA) signaling transduction, which is required for plant growth, development and stress responses. In Arabidopsis, group A PP2Cs inhibit activity of the SNF1-related protein kinases 2 (SnRK2) family via physical interaction. To clarify whether this scheme is conserved in woody plants, we experimentally isolated the genes homologous to three members of group A PP2Cs (PtABI1, PtAHG1 and PtAHG3) and 12 SnRK2s (PtSnRK2.1–2.12) from a model tree Populus trichocarpa, and examined their interaction using a yeast two-hybrid assay. Our results showed that only three PtSnRK2 proteins had a positive interaction with PtPP2Cs: PtSnRK2.10 possessed strong interaction activity with all three PtPP2Cs, while significant, but relatively weak, interactions were observed with PtSnRK2.6 and PtSnRK2.9. These three PtSnRK proteins are grouped into subclass 2 or 3, which are considered to be ABA-dependent kinases in Arabidopsis. These findings suggest that physical interaction between SnRK2 and PP2C is also conserved in poplars and may be involved in the ABA signaling pathway in tree plants.
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- 2015
5. Corrigendum to 'VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity'
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Xu, Yiqing, Bi, Changwei, Wu, Guoxin, Wei, Suyun, Dai, Xiaogang, Yin, Tongming, and Ye, Ning
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General Immunology and Microbiology ,lcsh:R ,lcsh:Medicine ,General Medicine ,Corrigendum ,General Biochemistry, Genetics and Molecular Biology - Published
- 2016
6. The F-Box Gene Family Is Expanded in Herbaceous Annual Plants Relative to Woody Perennial Plants1[W][OA]
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Yang, Xiaohan, Kalluri, Udaya C., Jawdy, Sara, Gunter, Lee E., Yin, Tongming, Tschaplinski, Timothy J., Weston, David J., Ranjan, Priya, and Tuskan, Gerald A.
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fungi ,food and beverages ,Exons ,Plants ,Genome Analysis ,Genes, Plant ,Wood ,Introns ,Phylogeny - Abstract
F-box proteins are generally responsible for substrate recognition in the Skp1-Cullin-F-box complexes that are involved in protein degradation via the ubiquitin-26S proteasome pathway. In plants, F-box genes influence a variety of biological processes, such as leaf senescence, branching, self-incompatibility, and responses to biotic and abiotic stresses. The number of F-box genes in Populus (Populus trichocarpa; approximately 320) is less than half that found in Arabidopsis (Arabidopsis thaliana; approximately 660) or Oryza (Oryza sativa; approximately 680), even though the total number of genes in Populus is equivalent to that in Oryza and 1.5 times that in Arabidopsis. We performed comparative genomics analysis between the woody perennial plant Populus and the herbaceous annual plants Arabidopsis and Oryza in order to explicate the functional implications of this large gene family. Our analyses reveal interspecific differences in genomic distribution, orthologous relationship, intron evolution, protein domain structure, and gene expression. The set of F-box genes shared by these species appear to be involved in core biological processes essential for plant growth and development; lineage-specific differences primarily occurred because of an expansion of the F-box genes via tandem duplications in Arabidopsis and Oryza. The number of F-box genes in the newly sequenced woody species Vitis (Vitis vinifera; 156) and Carica (Carica papaya; 139) is similar to that in Populus, supporting the hypothesis that the F-box gene family is expanded in herbaceous annual plants relative to woody perennial plants. This study provides insights into the relationship between the structure and composition of the F-box gene family in herbaceous and woody species and their associated developmental and physiological features.
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- 2008
7. The Bioenergy Science Center (BESC) and Overcoming Recalcitrance of Populus to Biofuel Production
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Mohnen, Debra, Biswal, Ajaya, Hao Zhangying, Sholes, Tipton, Gelineo-Albersheim, Ivana, Hunt, Kimberly, Darvill, Alan, Hahn, Michael, Kong Yingzhen, Zhou Gongke, Avci, Utku, Adams, Michael, Kataeva, Irina, Yang Sung-Jae, Xu Ying, Yin Yanbin, Chen Huiling, Difazio, Stephen, Slavov, Gancho, Davis, Mark, Sykes, Robert, Decker, Steve, Selig, Mike, Tucker, Melvin, Himmel, Mike, Studer, Michael, Demartini, Jaclyn, Wyman, Charles, Rokhsar, Dan, Goodstein, David, Schwartz, Wendy, Shu Sheng-quiang, Schmutz, Jeremy, Lynd, Lee, Nelson, Rick, Dixon, Richard, Hinchee, Maud, Rottmann, William, Winkeler, Kim, Chang Shujun, Gilna, Paul, Davison, Brian, Yin Tongming, Ranjan, Priya, Abraham, Paul, Robert Hettich, and Tuskan, Gerald
8. Genome-Wide Association Mapping and Genomic Selection for Alfalfa (Medicago sativa) Forage Quality Traits
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Alberto Palmonari, E. Charles Brummer, Paolo Annicchiarico, Elisa Biazzi, Luciano Pecetti, Aldo Tava, Nelson Nazzicari, and Yin, Tongming
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0106 biological sciences ,0301 basic medicine ,Germplasm ,Leaves ,Surfactants ,lcsh:Medicine ,Plant Science ,Lignin ,Biochemistry ,01 natural sciences ,Medicago ,lcsh:Science ,Flowering Plants ,Genome ,Multidisciplinary ,Plant Biochemistry ,Plant Anatomy ,Chromosome Mapping ,food and beverages ,Fabaceae ,Agriculture ,Genomics ,Single Nucleotide ,Plants ,Legumes ,Chemistry ,Neutral Detergent Fiber ,Phenotype ,Physical Sciences ,Genome, Plant ,Research Article ,Medicago sativa ,Biotechnology ,Genetic Markers ,General Science & Technology ,Materials Science ,Detergents ,Quantitative Trait Loci ,Forage ,Quantitative trait locus ,Biology ,Polymorphism, Single Nucleotide ,Quantitative Trait ,03 medical and health sciences ,Quantitative Trait, Heritable ,Genomic Medicine ,Genetic ,Genome-Wide Association Studies ,Genetics ,Plant breeding ,Selection, Genetic ,Polymorphism ,Heritable ,Selection ,Materials by Attribute ,Selection (genetic algorithm) ,Alfalfa ,Human Genome ,fungi ,lcsh:R ,Organisms ,Chemical Compounds ,Biology and Life Sciences ,Computational Biology ,Human Genetics ,Molecular Sequence Annotation ,Plant ,Genome Analysis ,Agronomy ,Plant Breeding ,030104 developmental biology ,Genetic marker ,lcsh:Q ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
Genetic progress for forage quality has been poor in alfalfa (Medicago sativa L.), the most-grown forage legume worldwide. This study aimed at exploring opportunities for marker-assisted selection (MAS) and genomic selection of forage quality traits based on breeding values of parent plants. Some 154 genotypes from a broadly-based reference population were genotyped by genotyping-by-sequencing (GBS), and phenotyped for leaf-to-stem ratio, leaf and stem contents of protein, neutral detergent fiber (NDF) and acid detergent lignin (ADL), and leaf and stem NDF digestibility after 24 hours (NDFD), of their dense-planted half-sib progenies in three growing conditions (summer harvest, full irrigation; summer harvest, suspended irrigation; autumn harvest). Trait-marker analyses were performed on progeny values averaged over conditions, owing to modest germplasm × condition interaction. Genomic selection exploited 11,450 polymorphic SNP markers, whereas a subset of 8,494 M. truncatula-aligned markers were used for a genome-wide association study (GWAS). GWAS confirmed the polygenic control of quality traits and, in agreement with phenotypic correlations, indicated substantially different genetic control of a given trait in stems and leaves. It detected several SNPs in different annotated genes that were highly linked to stem protein content. Also, it identified a small genomic region on chromosome 8 with high concentration of annotated genes associated with leaf ADL, including one gene probably involved in the lignin pathway. Three genomic selection models, i.e., Ridge-regression BLUP, Bayes B and Bayesian Lasso, displayed similar prediction accuracy, whereas SVR-lin was less accurate. Accuracy values were moderate (0.3-0.4) for stem NDFD and leaf protein content, modest for leaf ADL and NDFD, and low to very low for the other traits. Along with previous results for the same germplasm set, this study indicates that GBS data can be exploited to improve both quality traits (by genomic selection or MAS) and forage yield.
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- 2017
9. High-density genetic linkage map construction and QTL mapping of grain shape and size in the wheat population Yanda1817 × Beinong6
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Hao Wang, Shenghui Zhou, Ling Wang, Meihua Yu, Lin Fu, Shuhong Ouyang, Huiru Peng, Chengguo Yuan, Jingzhong Xie, Xiaojie Zhao, Jun Han, Yong Liang, Yan Zhang, Yongxing Chen, Zhenzhong Wang, Jie Li, Qixin Sun, Deyun Zhang, Lixin Wang, Jiao-Jiao Chen, Jirui Wang, Guoxin Wang, Ping Lu, Delin Li, Yu Cui, Chen Dang, Yao Xiao, Zhiyong Liu, Ming-Cheng Luo, Jinxia Qin, Li-li Wang, Mingshan You, Qiuhong Wu, Dong Zhang, Yin-Lian Huang, and Yin, Tongming
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Genetic Linkage ,General Science & Technology ,Population ,Quantitative Trait Loci ,lcsh:Medicine ,Biology ,Quantitative trait locus ,Environment ,Polymorphism, Single Nucleotide ,Quantitative Trait ,Quantitative Trait, Heritable ,Gene mapping ,Inclusive composite interval mapping ,Humans ,Inbreeding ,Gene–environment interaction ,Polymorphism ,education ,lcsh:Science ,Heritable ,Triticum ,Genetic Association Studies ,Genetics ,education.field_of_study ,Multidisciplinary ,Genome ,lcsh:R ,Chromosome Mapping ,Genomics ,Single Nucleotide ,Plant ,Marker-assisted selection ,Phenotype ,Genetic marker ,Microsatellite ,lcsh:Q ,Gene-Environment Interaction ,Genome, Plant ,Biotechnology ,Research Article ,Microsatellite Repeats - Abstract
High-density genetic linkage maps are necessary for precisely mapping quantitative trait loci (QTLs) controlling grain shape and size in wheat. By applying the Infinium iSelect 9K SNP assay, we have constructed a high-density genetic linkage map with 269 F 8 recombinant inbred lines (RILs) developed between a Chinese cornerstone wheat breeding parental line Yanda1817 and a high-yielding line Beinong6. The map contains 2431 SNPs and 128 SSR & EST-SSR markers in a total coverage of 3213.2 cM with an average interval of 1.26 cM per marker. Eighty-eight QTLs for thousand-grain weight (TGW), grain length (GL), grain width (GW) and grain thickness (GT) were detected in nine ecological environments (Beijing, Shijiazhuang and Kaifeng) during five years between 2010-2014 by inclusive composite interval mapping (ICIM) (LOD ≥ 2.5). Among which, 17 QTLs for TGW were mapped on chromosomes 1A, 1B, 2A, 2B, 3A, 3B, 3D, 4A, 4D, 5A, 5B and 6B with phenotypic variations ranging from 2.62% to 12.08%. Four stable QTLs for TGW could be detected in five and seven environments, respectively. Thirty-two QTLs for GL were mapped on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 4D, 5A, 5B, 6B, 7A and 7B, with phenotypic variations ranging from 2.62% to 44.39%. QGl.cau-2A.2 can be detected in all the environments with the largest phenotypic variations, indicating that it is a major and stable QTL. For GW, 12 QTLs were identified with phenotypic variations range from 3.69% to 12.30%. We found 27 QTLs for GT with phenotypic variations ranged from 2.55% to 36.42%. In particular, QTL QGt.cau-5A.1 with phenotypic variations of 6.82-23.59% was detected in all the nine environments. Moreover, pleiotropic effects were detected for several QTL loci responsible for grain shape and size that could serve as target regions for fine mapping and marker assisted selection in wheat breeding programs.
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- 2015
10. Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium
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Andrew Farmer, E. Charles Brummer, Yuanhong Han, Ho Julie, Yanling Wei, Ananta Acharya, Xuehui Li, Maria J. Monteros, and Yin, Tongming
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Linkage disequilibrium ,Heredity ,Population genetics ,lcsh:Medicine ,Genome-wide association study ,Plant Science ,Breeding ,Plant Genetics ,Linkage Disequilibrium ,Plant Genomics ,Cluster Analysis ,lcsh:Science ,Phylogeny ,Oligonucleotide Array Sequence Analysis ,Genetics ,Principal Component Analysis ,Multidisciplinary ,Medicago ,biology ,Linkage (Genetics) ,food and beverages ,Agriculture ,Genomics ,Single Nucleotide ,Plant Dormancy ,Seasons ,Research Article ,SNP array ,Medicago sativa ,Genetic Markers ,General Science & Technology ,Genotypes ,Population ,Crops ,Single-nucleotide polymorphism ,Polymorphism, Single Nucleotide ,Genome Analysis Tools ,Genetic variation ,Genome-Wide Association Studies ,Polymorphism ,Biology ,Genetic association ,Crop Genetics ,Quantitative Traits ,Complex Traits ,fungi ,lcsh:R ,Human Genome ,Computational Biology ,Reproducibility of Results ,Genetic Variation ,biology.organism_classification ,Genetics, Population ,Genetic Polymorphism ,lcsh:Q ,Population Genetics - Abstract
A large set of genome-wide markers and a high-throughput genotyping platform can facilitate the genetic dissection of complex traits and accelerate molecular breeding applications. Previously, we identified about 0.9 million SNP markers by sequencing transcriptomes of 27 diverse alfalfa genotypes. From this SNP set, we developed an Illumina Infinium array containing 9,277 SNPs. Using this array, we genotyped 280 diverse alfalfa genotypes and several genotypes from related species. About 81% (7,476) of the SNPs met the criteria for quality control and showed polymorphisms. The alfalfa SNP array also showed a high level of transferability for several closely related Medicago species. Principal component analysis and model-based clustering showed clear population structure corresponding to subspecies and ploidy levels. Within cultivated tetraploid alfalfa, genotypes from dormant and nondormant cultivars were largely assigned to different clusters; genotypes from semidormant cultivars were split between the groups. The extent of linkage disequilibrium (LD) across all genotypes rapidly decayed to 26 Kbp at r(2) = 0.2, but the rate varied across ploidy levels and subspecies. A high level of consistency in LD was found between and within the two subpopulations of cultivated dormant and nondormant alfalfa suggesting that genome-wide association studies (GWAS) and genomic selection (GS) could be conducted using alfalfa genotypes from throughout the fall dormancy spectrum. However, the relatively low LD levels would require a large number of markers to fully saturate the genome.
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- 2014
11. A genetic linkage map of Sole (Solea solea): A tool for evolutionary and comparative analyses of exploited (flat)fishes
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Hans Komen, Eveline Diopere, Filip Volckaert, Gregory E. Maes, Martien A. M. Groenen, and Yin, Tongming
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Evolutionary Genetics ,0106 biological sciences ,Genetic Linkage ,lcsh:Medicine ,comparative genomics ,01 natural sciences ,Genome ,Flatfish ,Natural Selection ,senegalensis ,Genome Sequencing ,lcsh:Science ,Genome Evolution ,Gasterosteus aculeatus ,Phylogeny ,time ,Genetics ,0303 health sciences ,Multidisciplinary ,Oryzias latipes ,pleuronectiformes ,biology ,turbot scophthalmus-maximus ,Genomics ,Tetraodon nigroviridis ,Flatfishes ,Microsatellite ,Oreochromis niloticus [Nile tilapia] ,Research Article ,Common sole ,Genome evolution ,Evolutionary Processes ,common sole ,Marine Biology ,Animal Breeding and Genomics ,Polymorphism, Single Nucleotide ,Synteny ,010603 evolutionary biology ,Molecular Genetics ,Evolution, Molecular ,03 medical and health sciences ,Scophthalmus maximus ,Solea solea [Sole] ,Phylogenetics ,Evolutionary Adaptation ,Animals ,Fokkerij en Genomica ,14. Life underwater ,marine fishes ,Molecular Biology Techniques ,Sequencing Techniques ,Molecular Biology ,030304 developmental biology ,Comparative genomics ,Evolutionary Biology ,Population Biology ,lcsh:R ,Biology and Life Sciences ,Computational Biology ,Fisheries Science ,microsatellite markers ,biology.organism_classification ,populations ,WIAS ,lcsh:Q ,divergence ,Population Genetics - Abstract
Linkage maps based on markers derived from genes are essential evolutionary tools for commercial marine fish to help identify genomic regions associated with complex traits and subject to selective forces at play during exploitation or selective breeding. Additionally, they allow the use of genomic information from other related species for which more detailed information is available. Sole (solea solea L.) is a commercially important flatfish species in the North Sea, subject to overexploitation and showing evidence of fisheries-induced evolutionary changes in growth- and maturation-related traits. Sole would definitely benefit from a linkage map to better understand how evolution has shaped its genome structure. This study presents a linkage map of sole based on 423 single nucleotide polymorphisms derived from expressed sequence tags and 8 neutral microsatellite markers. The total map length is 1233.8 cM and consists of 38 linkage groups with a size varying between 0 to 92.1 cM. Being derived from expressed sequence tags allowed us to align the map with the genome of four model fish species, namely medaka (Oryzias latipes), Nile tilapia (Oreochromis niloticus), three-spined stickleback (Gasterosteus aculeatus) and green spotted pufferfish (Tetraodon nigroviridis). This comparison revealed multiple conserved syntenic regions with all four species, and suggested that the linkage groups represent 21 putative sole chromosomes. The map was also compared to the linkage map of turbot (Scophthalmus maximus), another commercially important flatfish species and closely related to sole. For all putative sole chromosomes (except one) a turbot homolog was detected, confirming the even higher degree of synteny between these two flatfish species. ispartof: PLoS One vol:9 issue:12 ispartof: location:United States status: published
- Published
- 2014
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