Genetic variation through Dissociation (Ds) insertional mutagenesis system for rice in Korea: progress and current status

Park, Dong-Soo; Park, Soo-Kwon; Han, Sang‐Ik; Wang, Hoe-Jeong; Jun, Nam-Soo; Manigbas, Norvie L.; Woo, Young‐Min; Ahn, Byoung-Ohg; Yun, Doh-Won; Yoon, Ung-Han; Kim, Yonghwan; Lee, Myung Chul; Kim, Doh-Hoon; Nam, Min‐Hee; Han, Chang‐deok; Kang, Hang-Won; Yi, Gihwan

doi:10.1007/s11032-009-9300-0

Cited by 18 publications

(14 citation statements)

References 33 publications

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“…The Dongjin cultivar synthesizes relatively low levels of flavonoids. We used the Ac/Ds gene-trap system to generate Dongjin mutants that express high levels of flavonoids (20,21). We analyzed flanking sequence tags (FSTs) in order to verify the transgenic cultivars.…”

Section: Mutant Ricementioning

confidence: 99%

Multi-Layered Screening Method Identification of Flavonoid-Specific Genes, using Transgenic Rice

Kim

Lim

Park

et al. 2013

Biotechnology & Biotechnological Equipment

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Section: Mutant Ricementioning

confidence: 99%

Multi-Layered Screening Method Identification of Flavonoid-Specific Genes, using Transgenic Rice

Kim

Lim

Park

et al. 2013

Biotechnology & Biotechnological Equipment

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“…A twoelement Ac/Ds gene trap system was successfully established in rice to generate a collection of stable, unlinked and single-copy Ds transposants 25 . In Korea, 115,000 Ds insertion lines have been generated through the Ac/Ds gene trap system using Dongjin japonica rice 26 .…”

Section: Original Researchmentioning

confidence: 99%

“…White rice seeds were used to Dongjin cultivar because Ds lines of black rice were generated with the Ac/Ds gene trap system using Dongjin cultivar 26 . Black rice seeds were screened over 2 years.…”

Section: Ricementioning

confidence: 99%

Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

et al. 2010

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To better understand the functional characterization of anthocyanin gene expression in black rice, we performed a detailed computational examination. The experiment was performed using the newly designed 135K Oryza sativa microarray to assess gene expression at three time points after the heading stage in Ds insertion lines. Transcription factors related to anthocyanin pigmentation biosynthesis were clustered. A total of 8,517 genes exhibited greater than 2.5-fold up-or downregulation in each comparison between three rice groups and three seed developmental stages. The resultant 82 transcription factor genes found to be associated with anthocyanin were classified into 12 groups. In addition, 12 unknown and hypothetical genes were identified from comparisons between the white cultivar and two black Ds insertion mutants tested. We identified 12 unknown and hypothetical genes involved in anthocyanin biosynthesis. These genes likely play either a regulatory role in the anthocyanin production process or are related to anthocyanin metabolism during flavonoid biosynthesis. While these genes require further characterization and validation, the results here underline the potential use of the newly designed microarray.

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“…Various DNA transposons such as Ac, Ds, En and Spm have been used to construct insertional rice lines (Chin et al 1999;Upadhyaya et al 2002;Greco et al 2003;Kolesnik et al 2004;Kumar et al 2005;van Enckevort et al 2005;Jung et al 2008;Park et al 2007;Park et al 2009). Similarly, knockout genes can also be isolated by FSTs.…”

Section: Strategies For Rice Functional Genomicsmentioning

confidence: 99%

“…Miyao et al (2007) have investigated around 50,000 Tos17 insertion lines and found that nearly half of the lines showed mutant phenotype. Park et al (2009) have analyzed 115,000 Ds insertion lines in their phenotype variation and various physiological and agronomical variations were observed with the rate at around 3.6%. In addition, for better utilization of these lines, several rice mutant phenotype databases are also established Miyao et al 2007;Larmande et al 2008).…”

Section: Rice Mutant Resources and Databases For Rice Functional Genomentioning

confidence: 99%

Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis

Jiang

Ramachandran

2010

Biotechnol Lett

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Rice is the first cereal genome to be completely sequenced. Since the completion of its genome sequencing, considerable progress has been made in multiple areas including the whole genome annotation, gene expression profiling, mutant collection, etc. Here, we summarize the current status of rice genome annotation and review the methodology of assigning biological functions to hundreds of thousands of rice genes as well as discuss the major limitations and the future perspective in rice functional genomics. Available data analysis shows that the rice genome encodes around 32,000 protein-coding genes. Expression analysis revealed at least 31,000 genes with expression evidence from full-length cDNA/EST collection or other transcript profiling. In addition, we have summarized various strategies to generate mutant population including natural, physical, chemical, T-DNA, transposon/retrotransposon or gene silencing based mutagenesis. Currently, more than 1 million of mutants have been generated and 27,551 of them have their flanking sequence tags. To assign biological functions to hundreds of thousands of rice genes, global co-operations are required, various genetic resources should be more easily accessible and diverse data from transcriptomics, proteomics, epigenetics, comparative genomics and bioinformatics should be integrated to better understand the functions of these genes and their regulatory mechanisms.

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Genetic variation through Dissociation (Ds) insertional mutagenesis system for rice in Korea: progress and current status

Cited by 18 publications

References 33 publications

Multi-Layered Screening Method Identification of Flavonoid-Specific Genes, using Transgenic Rice

Multi-Layered Screening Method Identification of Flavonoid-Specific Genes, using Transgenic Rice

Computational identification of seed-specific transcription factors involved in anthocyanin production in black rice

Assigning biological functions to rice genes by genome annotation, expression analysis and mutagenesis

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