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78 results on '"Tung, Chih-Wei"'

54. Sexual Recombination and Selection During Domestication of Clonally Propagated Pineapple

Author

VanBuren, Robert, primary, Paris, Margot, additional, Wai, Jennifer, additional, Zhang, Jisen, additional, Huang, Lixian, additional, Zhou, Hongye, additional, Wang, Hao, additional, Hwa, Teh-Yang, additional, Kao, Shu-Min, additional, Choi, Jae Young, additional, Liao, Zhenyang, additional, Lin, Zhicong, additional, Wang, Lulu, additional, Zhang, Xingtan, additional, Yue, Jingjing, additional, Sharma, Anupma, additional, Singh, Ratnesh, additional, Song, Jian, additional, Yim, Won C., additional, Cushman, John C., additional, Paull, Robert, additional, Matsumoto, Tracie, additional, Qin, Yuan, additional, Wu, Qingsong, additional, Wang, Jianping, additional, Yu, Qingyi, additional, Wu, Jun, additional, Zhang, Shaoling, additional, Boches, Peter, additional, Tung, Chih-Wei, additional, ddEeckenbrugge, Geo Coppens, additional, Sanewski, Garth M., additional, Purugganan, Michael D., additional, Bennetzen, Jeffrey L., additional, Lexer, Christian, additional, and Ming, Ray, additional

Published
2018
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55. Corrigendum: Open access resources for genome-wide association mapping in rice

Author

McCouch, Susan R., Wright, Mark H., Tung, Chih-Wei, Maron, Lyza G., McNally, Kenneth L., Fitzgerald, Melissa, Singh, Namrata, DeClerck, Genevieve, Perez, Francisco Agosto, Korniliev, Pavel, Greenberg, Anthony J., Naredo, Ma. Elizabeth B., Mercado, Sheila Mae Q., Harrington, Sandra E., Shi, Yuxin, Branchini, Darcy A., Kuser-Falcão, Paula R., Leung, Hei, Ebana, Kowaru, Yano, Masahiro, Eizenga, Georgia, McClung, Anna, and Mezey, Jason

Subjects
Principal Component Analysis, Genotype, Quantitative Trait Loci, Chromosome Mapping, Computational Biology, Genetic Variation, Agriculture, Epistasis, Genetic, Oryza, Corrigenda, Polymorphism, Single Nucleotide, Access to Information, Plant Breeding, Phenotype, Databases, Genetic, Edible Grain, Alleles, Genome, Plant, Genome-Wide Association Study
Abstract

Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

Published
2016

56. Additional file 2: Table S2. of Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

Author

Schafleitner, Roland, Huang, Shu-Mei, Shui-Hui Chu, Jo-Yi Yen, Lin, Chen-Yu, Miao-Rong Yan, Bharath Krishnan, Liu, Mao-Sen, Hsiao-Feng Lo, Chien-Yu Chen, Chen, Long-Fang, Dung-Chi Wu, Thu-Giang Bui, Srinivasan Ramasamy, Tung, Chih-Wei, and Ramakrishnan Nair

Abstract

Interval mapping of bruchid resistance on physical maps of populations TC1966 x NM94 and V2802. (DOCX 14Â kb)

Published
2016
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57. Additional file 4: Table S4. of Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

Author

Schafleitner, Roland, Huang, Shu-Mei, Shui-Hui Chu, Jo-Yi Yen, Lin, Chen-Yu, Miao-Rong Yan, Bharath Krishnan, Liu, Mao-Sen, Hsiao-Feng Lo, Chien-Yu Chen, Chen, Long-Fang, Dung-Chi Wu, Thu-Giang Bui, Srinivasan Ramasamy, Tung, Chih-Wei, and Ramakrishnan Nair

Subjects
food and beverages
Abstract

Gene content of the reference genome VC1973 in the chromosome 5 QTL interval. (DOCX 18Â kb)

Published
2016
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58. Additional file 5: Figure S1. of Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

Author

Schafleitner, Roland, Huang, Shu-Mei, Shui-Hui Chu, Jo-Yi Yen, Lin, Chen-Yu, Miao-Rong Yan, Bharath Krishnan, Liu, Mao-Sen, Hsiao-Feng Lo, Chien-Yu Chen, Chen, Long-Fang, Dung-Chi Wu, Thu-Giang Bui, Srinivasan Ramasamy, Tung, Chih-Wei, and Ramakrishnan Nair

Abstract

Genotypes of markers for QTLs detected by interval mapping on chromosomes 1, 2, 7 and 10 of TC1966 Ă NM92 or V2802 Ă NM94. (DOCX 1189Â kb)

Published
2016
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65. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform

Author

Thomson, Michael (IRRI-PBGB), Zhao, Keyan (Cornell University, Stanford University), Wright, Mark (Cornell University), McNally, Kenneth (IRRI-PBGB), Rey, Jessica (IRRI-PBGB), Tung, Chih-Wei (Cornell University), Reynolds, Andy (Cornell University), Scheffler, Brian (USDA-ARS Genomics And Bioinformatics Research Unit), Eizenga, Georgia (USDA-ARS Dale Bumpers National Rice Research Center), McClung, Anna (USDA-ARS Dale Bumpers National Rice Research Center), Kim, Hyunjung (Cornell University), Ismail, Abdelbagi (IRRI-PBGB), De Ocampo, Marjorie (IRRI-PBGB), Mojica, Chromewell (IRRI-PBGB), Reveche, Ma. Ymber (IRRI-PBGB), Dilla-Ermita, Christine (IRRI-PBGB), Mauleon, Ramil (IRRI-PBGB), Leung, Hei (IRRI-PBGB), Bustamante, Carlos (Cornell University, and McCouch, Susan (Cornell University)

Published
2014
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66. Identification of single nucleotide polymorphism markers associated with resistance to bruchids (Callosobruchus spp.) in wild mungbean (Vigna radiata var. sublobata) and cultivated V. radiata through genotyping by sequencing and quantitative trait locus analysis

Author

Schafleitner, Roland, primary, Huang, Shu-mei, additional, Chu, Shui-hui, additional, Yen, Jo-yi, additional, Lin, Chen-yu, additional, Yan, Miao-rong, additional, Krishnan, Bharath, additional, Liu, Mao-sen, additional, Lo, Hsiao-feng, additional, Chen, Chien-yu, additional, Chen, Long-fang O., additional, Wu, Dung-chi, additional, Bui, Thu-Giang Thi, additional, Ramasamy, Srinivasan, additional, Tung, Chih-wei, additional, and Nair, Ramakrishnan, additional

Published
2016
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67. Open access resources for genome-wide association mapping in rice

Author

McCouch, Susan R., primary, Wright, Mark H., additional, Tung, Chih-Wei, additional, Maron, Lyza G., additional, McNally, Kenneth L., additional, Fitzgerald, Melissa, additional, Singh, Namrata, additional, DeClerck, Genevieve, additional, Agosto-Perez, Francisco, additional, Korniliev, Pavel, additional, Greenberg, Anthony J., additional, Naredo, Ma. Elizabeth B., additional, Mercado, Sheila Mae Q., additional, Harrington, Sandra E., additional, Shi, Yuxin, additional, Branchini, Darcy A., additional, Kuser-Falcão, Paula R., additional, Leung, Hei, additional, Ebana, Kowaru, additional, Yano, Masahiro, additional, Eizenga, Georgia, additional, McClung, Anna, additional, and Mezey, Jason, additional

Published
2016
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68. An Exhaustive Scan Method for SNP Main Effects and SNP × SNP Interactions Over Highly Homozygous Genomes.

Author

Tsai, Shin-Fu, Tung, Chih-Wei, Tsai, Chen-An, and Liao, Chen-Tuo

Subjects
*SINGLE nucleotide polymorphisms, *HOMOZYGOSITY, *SIMULATION methods & models, *EPISTASIS (Genetics), *GENE expression
Abstract

Genome-wide association studies (GWAS) have been a powerful tool for exploring potential relationships between single-nucleotide polymorphisms (SNPs) and biological traits. For screening out important genetic variants, it is desired to perform an exhaustive scan over a whole genome. However, this is usually a challenging and daunting task in computation, due mainly to the large number of SNPs in GWAS. In this article, we propose a computationally effective algorithm for highly homozygous genomes. Pseudo standard error (PSE) is known to be a highly efficient and robust estimator for the standard deviation of a quantitative trait. We thus develop a statistical testing procedure for determining significant SNP main effects and SNP × SNP interactions associated with a quantitative trait based on PSE. A simulation study is first conducted to evaluate its empirical size and power. It is shown that the proposed PSE-based method can generally maintain the empirical size sufficiently close to the nominal significance level. However, the power investigation indicates that the PSE-based method might lack power in identifying significant effects for low-frequency variants if their true effect sizes are not large enough. A software is provided for implementing the proposed algorithm and its computational efficiency is evaluated through another simulation study. An exhaustive scan is usually done within a very reasonable runtime and a rice genome data set is analyzed by the software. [ABSTRACT FROM AUTHOR]

Published
2017
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69. The bracteatuspineapple genome and domestication of clonally propagated crops

Author

Chen, Li-Yu, VanBuren, Robert, Paris, Margot, Zhou, Hongye, Zhang, Xingtan, Wai, Ching Man, Yan, Hansong, Chen, Shuai, Alonge, Michael, Ramakrishnan, Srividya, Liao, Zhenyang, Liu, Juan, Lin, Jishan, Yue, Jingjing, Fatima, Mahpara, Lin, Zhicong, Zhang, Jisen, Huang, Lixian, Wang, Hao, Hwa, Teh-Yang, Kao, Shu-Min, Choi, Jae Young, Sharma, Anupma, Song, Jian, Wang, Lulu, Yim, Won C., Cushman, John C., Paull, Robert E., Matsumoto, Tracie, Qin, Yuan, Wu, Qingsong, Wang, Jianping, Yu, Qingyi, Wu, Jun, Zhang, Shaoling, Boches, Peter, Tung, Chih-Wei, Wang, Ming-Li, Coppens d’Eeckenbrugge, Geo, Sanewski, Garth M., Purugganan, Michael D., Schatz, Michael C., Bennetzen, Jeffrey L., Lexer, Christian, and Ming, Ray

Abstract

Domestication of clonally propagated crops such as pineapple from South America was hypothesized to be a ‘one-step operation’. We sequenced the genome of Ananas comosusvar. bracteatusCB5 and assembled 513 Mb into 25 chromosomes with 29,412 genes. Comparison of the genomes of CB5, F153 and MD2 elucidated the genomic basis of fiber production, color formation, sugar accumulation and fruit maturation. We also resequenced 89 Ananasgenomes. Cultivars ‘Smooth Cayenne’ and ‘Queen’ exhibited ancient and recent admixture, while ‘Singapore Spanish’ supported a one-step operation of domestication. We identified 25 selective sweeps, including a strong sweep containing a pair of tandemly duplicated bromelain inhibitors. Four candidate genes for self-incompatibility were linked in F153, but were not functional in self-compatible CB5. Our findings support the coexistence of sexual recombination and a one-step operation in the domestication of clonally propagated crops. This work guides the exploration of sexual and asexual domestication trajectories in other clonally propagated crops.

Published
2019
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70. High-throughput single nucleotide polymorphism genotyping for breeding applications in rice using the BeadXpress platform

Author

Thomson, Michael J., primary, Zhao, Keyan, additional, Wright, Mark, additional, McNally, Kenneth L., additional, Rey, Jessica, additional, Tung, Chih-Wei, additional, Reynolds, Andy, additional, Scheffler, Brian, additional, Eizenga, Georgia, additional, McClung, Anna, additional, Kim, Hyunjung, additional, Ismail, Abdelbagi M., additional, de Ocampo, Marjorie, additional, Mojica, Chromewell, additional, Reveche, Ma. Ymber, additional, Dilla-Ermita, Christine J., additional, Mauleon, Ramil, additional, Leung, Hei, additional, Bustamante, Carlos, additional, and McCouch, Susan R., additional

Published
2011
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71. Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

Author

Zhao, Keyan, primary, Tung, Chih-Wei, additional, Eizenga, Georgia C., additional, Wright, Mark H., additional, Ali, M. Liakat, additional, Price, Adam H., additional, Norton, Gareth J., additional, Islam, M. Rafiqul, additional, Reynolds, Andy, additional, Mezey, Jason, additional, McClung, Anna M., additional, Bustamante, Carlos D., additional, and McCouch, Susan R., additional

Published
2011
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73. Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

Author

Zhao, Keyan, primary, Wright, Mark, additional, Kimball, Jennifer, additional, Eizenga, Georgia, additional, McClung, Anna, additional, Kovach, Michael, additional, Tyagi, Wricha, additional, Ali, Md. Liakat, additional, Tung, Chih-Wei, additional, Reynolds, Andy, additional, Bustamante, Carlos D., additional, and McCouch, Susan R., additional

Published
2010
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74. Development of genome-wide SNP assays for rice

Author

McCouch, Susan R., primary, Zhao, Keyan, additional, Wright, Mark, additional, Tung, Chih-Wei, additional, Ebana, Kaworu, additional, Thomson, Michael, additional, Reynolds, Andy, additional, Wang, Diane, additional, DeClerck, Genevieve, additional, Ali, Md. Liakat, additional, McClung, Anna, additional, Eizenga, Georgia, additional, and Bustamante, Carlos, additional

Published
2010
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75. Gramene QTL database: development, content and applications

Author

Ni, Junjian, primary, Pujar, Anuradha, additional, Youens-Clark, Ken, additional, Yap, Immanuel, additional, Jaiswal, Pankaj, additional, Tecle, Isaak, additional, Tung, Chih-Wei, additional, Ren, Liya, additional, Spooner, William, additional, Wei, Xuehong, additional, Avraham, Shuly, additional, Ware, Doreen, additional, Stein, Lincoln, additional, and McCouch, Susan, additional

Published
2009
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76. Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice.

Author

Yan, Jian, Aboshi, Takako, Teraishi, Masayoshi, Strickler, Susan R., Spindel, Jennifer E., Tung, Chih-Wei, Takata, Ryo, Matsumoto, Fuka, Maesaka, Yoshihiro, McCouch, Susan R., Okumoto, Yutaka, Mori, Naoki, and Jander, Georg

Subjects
NICOTIANA benthamiana, TYROSINE, PLANT exudates, GENE expression, BIOSYNTHESIS, RICE, AMINO acids, JASMONIC acid
Abstract

Non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. A targeted search for jasmonate-induced metabolites in cultivated rice (Oryza sativa) identified (R)-β-tyrosine, an isomer of the common amino acid (S)-α-tyrosine in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temperate japonica cultivars. Genetic mapping identified a candidate gene on chromosome 12, which was confirmed to encode a tyrosine aminomutase (TAM1) by transient expression in Nicotiana benthamiana and in vitro enzyme assays. A point mutation in TAM1 eliminated β-tyrosine production in Nipponbare. Rice cultivars that do not produce β-tyrosine have a chromosome 12 deletion that encompasses TAM1. Although β-tyrosine accumulation was induced by the plant defense signaling molecule jasmonic acid, bioassays with hemipteran and lepidopteran herbivores showed no negative effects at physiologically relevant β-tyrosine concentrations. In contrast, root growth of Arabidopsis thaliana and other tested dicot plants was inhibited by concentrations as low as 1 μM. As β-tyrosine is exuded into hydroponic medium at higher concentrations, it may contribute to the allelopathic potential of rice. [ABSTRACT FROM AUTHOR]

Published
2015
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78. miR-196a enhances polymerization of neuronal microfilaments through suppressing IMP3 and upregulating IGF2 in Huntington's disease.

Author

Yang HI, Huang PY, Chan SC, Tung CW, Cheng PH, Chen CM, and Yang SH

Abstract

Huntington's disease (HD) is one of the inheritable neurodegenerative diseases, and these diseases share several similar pathological characteristics, such as abnormal neuronal morphology. miR-196a is a potential target to provide neuroprotective functions, and has been reported to enhance polymerization of neuronal microtubules in HD. While microtubules and microfilaments are two important components of the neuronal cytoskeleton, whether miR-196a improves neuronal microfilaments is still unknown. Here, we identify insulin-like growth factor 2 mRNA binding protein 3 (IMP3), and show that miR-196a directly suppresses IMP3 to increase neurite outgrowth in neurons. In addition, IMP3 disturbs neurite outgrowth in vitro and in vivo , and worsens the microfilament polymerization. Moreover, insulin-like growth factor-II (IGF2) is identified as the downstream target of IMP3, and miR-196a downregulates IMP3 to upregulate IGF2, which increases microfilamental filopodia numbers and activates Cdc42 to increase neurite outgrowth. Besides, miR-196a increases neurite outgrowth through IGF2 in different HD models. Finally, higher expression of IMP3 and lower expression IGF2 are observed in HD transgenic mice and patients, and increase the formation of aggregates in the HD cell model. Taken together, miR-196a enhances polymerization of neuronal microfilaments through suppressing IMP3 and upregulating IGF2 in HD, supporting the neuroprotective functions of miR-196a through neuronal cytoskeleton in HD., Competing Interests: The authors declare no competing interests., (© 2022 The Author(s).)

Published
2022
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