Yue‐Ie Hsing

Institute of Plant and Microbial Biology, Academia Sinica

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Blanca San Segundo

Consejo Superior de Investigaciones Científicas

Fu‐Jin Wei

Institute of Plant and Microbial Biology, Academia Sinica

Sonia Campo

Universitat Politècnica de Catalunya

Su‐May Yu

Institute of Molecular Biology, Academia Sinica

Kazunori Okada

The University of Tokyo

Yuan‐Ching Tsai

National Chiayi University

Shiho Tomiyama

The University of Tokyo

Cheng‐Chieh Wu

Institute of Plant and Microbial Biology, Academia Sinica

Cristina Peris-Peris

Center for Research in Agricultural Genomics

Ming‐Tsung Wu

Institute of Plant and Microbial Biology, Academia Sinica

Cooperative Institutions

Academia Sinica

National Taiwan University

Institute of Plant and Microbial Biology, Academia Sinica

International Rice Research Institute

The University of Tokyo

Institute of Agrobiological Sciences

National Chung Hsing University

National Institute of Genetics

Institute of Molecular Biology, Academia Sinica

King Abdullah University of Science and Technology

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Rice Mutant Resources for Gene Discovery

Plant Molecular Biology (2004)

Hirohiko Hirochika Emmanuel Guiderdoni Gynheung An Yue‐Ie Hsing Moo Young Eun

Model Organism

10.1023/b:plan.0000036368.74758.66

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Citations (250)

TEOS1, a Novel Transposable Element Family from Oryza Sativa

Zhōngyāng yánjiūyuàn zhíwùxué huikān/Zhōngyāng yánjiūyuàn zhíwùxué huikān (2003)

Ya‐Ting Chao Chun-Lin Su Teh‐Yuan Chow Pei-Fang Lee Chun-I Chung

We have uncovered a novel group of transposable elements TEOS1. (Transposable Element of Oryza 5ativa) by repeat mining of rice genome sequence data We first identified a TEOS1 element. 6,896 bp in length. from a PAC clone of rice chromosome 5 The presence of long terminal repeats (LTRs) and other diagnostic features such as a primer-binding site (PBS) and a polypurine tract (PPT), indicated that TEOS1 is a group of LTR retrotransposon The internal domain of TEOS1 containing two arrays of tandem repeats and a predicated Tf1gene was characteristically distinct from those of other LTR retrotransposons previously described TEOS1 elements identified were flanked by 5-bp direct repeats. some identified as solo LTRs were flanked by 5-7bp direct repeats The PBS sequence vvas homologous to the 3' end region of tRNA (superscript Arg) The deduced amino acid sequence of Tf1 is dissimilar to that of any known mobility related proteins TEOS1 is probable to be trans-activated by other retrotransposons in the rice genome We have estimated that there are about 300 TEOS1 elements per haploid rice genome The presence of repeats in TEOS1 offers the potential to form secondary structure during replication and transcription, and to serve as a hot spot for transposon insertion, augmenting the dynamics of molecular interactions of the genomic sequences.

Retrotransposon

Direct repeat

Inverted repeat

10.7016/bbas.200301.0001

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Citations (1)

Large-scale phenomics analysis of a T-DNA tagged mutant population

GigaScience (2017)

Hshin‐Ping Wu Fu‐Jin Wei Cheng‐Chieh Wu Shuen‐Fang Lo Liang‐Jwu Chen

Rice, Oryza sativa L., is one of the most important crops in the world. With the rising world population, feeding people in a more sustainable and environmentally friendly way becomes increasingly important. Therefore, the rice research community needs to share resources to better understand the functions of rice genes that are the foundation for future agricultural biotechnology development, and one way to achieve this goal is via the extensive study of insertional mutants. We have constructed a large rice insertional mutant population in a japonica rice variety, Tainung 67. The collection contains about 93 000 mutant lines, among them 85% with phenomics data and 65% with flanking sequence data. We screened the phenotypes of 12 individual plants for each line grown under field conditions according to 68 subcategories and 3 quantitative traits. Both phenotypes and integration sites are searchable in the Taiwan Rice Insertional Mutants Database. Detailed analyses of phenomics data, T-DNA flanking sequences, and whole-genome sequencing data for rice insertional mutants can lead to the discovery of novel genes. In addition, studies of mutant phenotypes can reveal relationships among varieties, cultivation locations, and cropping seasons.

Phenomics

Insertional mutagenesis

10.1093/gigascience/gix055

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Citations (11)

MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

Figshare (2015)

Patricia Baldrich Sonia Campo Ming‐Tsung Wu Tze-Tze Liu Yue‐Ie Hsing

MicroRNAs (miRNAs) are small non-coding RNAs that have important regulatory functions in plant growth, development, and response to abiotic stress. Increasing evidence also supports that plant miRNAs contribute to immune responses to pathogens. Here, we used deep sequencing of small RNA libraries for global identification of rice miRNAs that are regulated by fungal elicitors. We also describe 9 previously uncharacterized miRNAs in rice. Combined small RNA and degradome analyses revealed regulatory networks enriched in elicitor-regulated miRNAs supported by the identification of their corresponding target genes. Specifically, we identified an important number of miRNA/target gene pairs involved in small RNA pathways, including miRNA, heterochromatic and trans-acting siRNA pathways. We present evidence for miRNA/target gene pairs implicated in hormone signaling and cross-talk among hormone pathways having great potential in regulating rice immunity. Furthermore, we describe miRNA-mediated regulation of Conserved-Peptide upstream Open Reading Frame (CPuORF)-containing genes in rice, which suggests the existence of a novel regulatory network that integrates miRNA and CPuORF functions in plants. The knowledge gained in this study will help in understanding the underlying regulatory mechanisms of miRNAs in rice immunity and develop appropriate strategies for rice protection.

Rice plant

10.6084/m9.figshare.1451383.v3

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Characterization of a 10 cM region of rice chromosome 5

Zhōngyāng yánjiūyuàn zhíwùxué huikān/Zhōngyāng yánjiūyuàn zhíwùxué huikān (2001)

Teh‐Yuan Chow Ya‐Ting Chao Sumei Liu Hong-Pang Wu Mu-Kuei Chu

Rice is a model species for the cereals and a good candidate for genome sequencing due to its relatively small genome (430 Mb), dense physical and genetic maps, and good transgenic systems. As part of an international effort to decode the rice genome, a PAC clone localized at 10 cM of chromosome 5 is completely determined for its sequence using shotgun libraries of its two inserts, 2-kb and 5-kb in length. In total 2,998 sequencing reads were used for the assembly of the final sequence, covering 175,439 bp. This sequence may code for at least 28 putative proteins, as deduced from computational search for homology with other known coding sequences and EST, or predicted using GenScan package. Also present in this sequence are simple repeats, palindrome and retrotransposons. On the basis of these findings, the gene density in the gene-rich region of rice genome is about 6 kb/gene.

Retrotransposon

Homology

Sequence (biology)

Source

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Retrotranspositional landscape of Asian rice revealed by 3000 genomes

Nature Communications (2018)

Marie‐Christine Carpentier Ernandes Manfroi Fu‐Jin Wei Hshin‐Ping Wu Éric Lasserre

The recent release of genomic sequences for 3000 rice varieties provides access to the genetic diversity at species level for this crop. We take advantage of this resource to unravel some features of the retrotranspositional landscape of rice. We develop software TRACKPOSON specifically for the detection of transposable elements insertion polymorphisms (TIPs) from large datasets. We apply this tool to 32 families of retrotransposons and identify more than 50,000 TIPs in the 3000 rice genomes. Most polymorphisms are found at very low frequency, suggesting that they may have occurred recently in agro. A genome-wide association study shows that these activations in rice may be triggered by external stimuli, rather than by the alteration of genetic factors involved in transposable element silencing pathways. Finally, the TIPs dataset is used to trace the origin of rice domestication. Our results suggest that rice originated from three distinct domestication events.

Retrotransposon

Japonica rice

10.1038/s41467-018-07974-5

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Citations (128)

DPX-3778 promotes proliferation of tobacco callus in vitro

Planta (1978)

Wei‐Chin Chang Yue‐Ie Hsing

Kinetin

Callus

Triethanolamine

10.1007/bf00390263

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Citations (2)

MicroRNA-mediated regulation of gene expression in the response of rice plants to fungal elicitors

Figshare (2015)

Patricia Baldrich Sonia Campo Ming‐Tsung Wu Tze-Tze Liu Yue‐Ie Hsing

Rice plant

10.6084/m9.figshare.1451383.v1

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Citations (0)

Interaction of small RNA–8105 and the intron of IbMYB1 RNA regulates IbMYB1 family genes through secondary siRNAs and DNA methylation after wounding

The Plant Journal (2013)

Jeng‐Shane Lin Chih‐Ching Lin Yu‐Chi Li Ming‐Tsung Wu Mong‐Hsun Tsai

Small RNAs (sRNAs) play important roles in plants under stress conditions. However, limited research has been performed on the sRNAs involved in plant wound responses. In the present study, a novel wounding-induced sRNA, sRNA8105, was identified in sweet potato (Ipomoea batatas cv. Tainung 57) using microarray analysis. It was found that expression of sRNA8105 increased after mechanical wounding. Furthermore, Dicer-like 1 (DCL1) is required for the sRNA8105 precursor (pre-sRNA8105) to generate 22 and 24 nt mature sRNA8105. sRNA8105 targeted the first intron of IbMYB1 (MYB domain protein 1) before RNA splicing, and mediated RNA cleavage and DNA methylation of IbMYB1. The interaction between sRNA8105 and IbMYB1 was confirmed by cleavage site mapping, agro-infiltration analyses, and use of a transgenic sweet potato over-expressing pre-sRNA8105 gene. Induction of IbMYB1-siRNA was observed in the wild-type upon wounding and in transgenic sweet potato over-expressing pre-sRNA8105 gene without wounding, resulting in decreased expression of the whole IbMYB1 gene family, i.e. IbMYB1 and the IbMYB2 genes, and thus directing metabolic flux toward biosynthesis of lignin in the phenylpropanoid pathway. In conclusion, sRNA8105 induced by wounding binds to the first intron of IbMYB1 RNA to methylate IbMYB1, cleave IbMYB1 RNA, and trigger production of secondary siRNAs, further repressing the expression of the IbMYB1 family genes and regulating the phenylpropanoid pathway.

10.1111/tpj.12238

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Citations (23)

Promoter Activity of a Soybean Gene Encoding a Seed Maturation Protein, GmPM9

Zhōngyāng yánjiūyuàn zhíwùxué huikān/Zhōngyāng yánjiūyuàn zhíwùxué huikān (2000)

Pei-Fang Lee Yue‐Ie Hsing Teh‐Yuan Chow

Late embryogenesis abundant (LEA) proteins are synthesized during the late stages of seed development and have been widely reported in monocot and dicot plants. In order to understand the developmental regulation of the promoter of a soybean gene encoding LEA protein GmPM9, we fused a series of fragments of the promoter region to the β-glucuronidase (GUS) reporter gene (uirA) and transformed the resulting constructs (pZP966, pZP572, pZP51O, pZP294 and pZPll4) into Arabidopsis thaliana. GUS enzyme activities were detected in mature seeds and cotyledons and hypocotyls of seedlings in transgenic plants containing any one of the five constructs; they were not detected in other tissues at different developmental stages. During seed development, GUS began to appear at 10 days after flowering (DAF) and increased rapidly to a maximum in the mature seeds at 14 DAF. The longest promoter construct (pZP966) enabled the transgenic plants to exhibit the highest GUS activity, whereas the shortest construct (pZP1 14) was sufficient to direct the expression of the GUS gene at a detectable level. The above findings indicate that the promoter of gGmPM9 can be used to express desirable genes in seeds during late seed maturation. The expression of the GUS gene could be induced in the leaves of the transgenic plants containing pZP966 by salt and desiccation, but not by ABA treatment.

GUS reporter system

10.7016/bbas.200007.0175

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Citations (11)