Application of RLGS Method for Detection of Alteration in Tissue Cultured Plants

Takamiya, Tomoko; Ohtake, Yuhko; Hosobuchi, Saeko; Noguchi, T.; Kawase, Makoto; Murakami, Yasufumi; Okuizumi, Hisato

doi:10.6090/jarq.42.151

Cited by 5 publications

(4 citation statements)

References 11 publications

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“…We collected leaf blades and sheaths of Nipponbare, Kasalath, and F1 plants grown for 8 wk. Total genomic DNA was isolated by the CTAB extraction method, with modifications as described previously 39–41. We used 0.4 μg of genomic DNA and performed RLGS with the restriction enzyme combination Not I– Msp I– Bam HI or Not I– Hpa II– Bam HI (NEB, Beverly, MA, USA), as described previously 38.…”

Section: Methodsmentioning

confidence: 99%

Inheritance and alteration of genome methylation in F1 hybrid rice

Takamiya¹,

Hosobuchi²,

Noguchi³

et al. 2008

Electrophoresis

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We analyzed the inheritance of DNA methylation in the first filial generation(F1) hybrid of Oryza sativa L. ("Nipponbare"x"Kasalath") by restriction landmark genome scanning (RLGS). Most parental RLGS spots were found in the F1, but eight spots (4%) showed abnormal inheritance: seven of the eight spots were missing in the F1, and one was newly detected in the F1. Here we show demethylation at restriction enzyme sites in the F1. We also found a candidate site of stable heterozygous methylation in the genome. These results show the applicability of the RLGS method for analysis of the inheritance and alteration of methylation in F1 hybrid plants.

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Section: Methodsmentioning

confidence: 99%

Inheritance and alteration of genome methylation in F1 hybrid rice

Takamiya¹,

Hosobuchi²,

Noguchi³

et al. 2008

Electrophoresis

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“…We performed RLGS with combinations of the BspEI and EcoRI (BspEI-EcoRI) restriction enzymes as described in Okamoto et al (2006) and Takamiya et al (2008). Briefly, (1) blocking nicks and gaps in mat rush genomic DNA (0.4 µg) were treated with 10 units of DNA polymerase I (Nippon Gene, Tokyo, Japan) in 50 µL of 1 × blocking buffer (50 mM Tris-HCl, pH 7.4, 100 mM NaCl, 10 mM dithiothreitol (DTT) [αS].…”

Section: Restriction Landmark Genome Scanningmentioning

confidence: 99%

“…RLGS spot cloning was conducted according to Takamiya et al (2008) and Watanabe & Hayashizaki (1997). Briefly, a target RLGS spot was punched out of the dried gel of the mat rush cultivar 'Shimomasuda,' which is the mater-nal parent of 'Hinomidori,' and soaked with TE (pH 8.0).…”

Section: Rlgs Spot Cloningmentioning

confidence: 99%

A Sequence-tagged Site Marker for Identifying the Japanese Mat Rush (<i>Juncus effusus</i>) Cultivar ‘Hinomidori’

Noguchi

Hosobuchi

Takamiya

et al. 2017

JARQ

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We have developed a genetic marker that can identify a registered variety of mat rush in Japan. A vegetatively propagated plant, mat rush is cultivated and used as the material for the surface layer of tatami mats in Japan. Because it has been difficult to detect DNA polymorphism among mat rush cultivars, we applied restriction landmark genome scanning (RLGS) to discriminate mat rush cultivars. RLGS is a genome analysis technique that can detect many DNA polymorphisms as spots separated by two-dimensional electrophoresis. By cloning the DNA of spots specific to the superior mat rush cultivar 'Hinomidori' detected by RLGS, we developed a sequence-tagged site (STS) marker for polymerase chain reaction (PCR) analyses. This STS marker makes it possible to distinguish 'Hinomidori' specifically from other mat rush cultivars. The strategy of developing the STS marker in this study is applicable to other vegetatively propagated plants that are characterized by difficult DNA polymorphism detection.

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“…Moreover, the RLGS method can be applied to the detection of genomic variation in plant tissue culture [Takamiya et al 2008B]. The genome DNA of 2 ramets obtained from one seed of rice was extracted and analyzed for RLGS with the combination of NotI-HpaII-BamHI and with NotI-MspI-BamHI to compare their pattern.…”

Section: Various Aspects On Dna Methylation Rolesmentioning

confidence: 99%