Inheritance and alteration of genome methylation in F1 hybrid rice

Takamiya, Tomoko; Hosobuchi, Saeko; Noguchi, T.; Asai, Kenji; Nakamura, Eiji; Habu, Yoshiki; Paterson, Andrew H.; Iijima, Hiroshi; Murakami, Yasufumi; Okuizumi, Hisato

doi:10.1002/elps.200700784

Cited by 15 publications

(9 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The methylation pattern of reciprocal cross F1 generation have four types, namely monomorphism, demethylation, hypermethylation and hypomethylation, but they are mainly composed of type hypermethylation. This conclusion is basically identical to the research conclusion of Wang [33], but is not the same finding in corn, Arabidopsis thaliana [12,39], larch [34] and rice [40]. Related studies [34] have shown that methylation means that genes translate from activation to suppression; however, demethylation means that genes translate from suppression to activation.…”

Section: Discussionsupporting

confidence: 80%

Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

Zhang

et al. 2016

IJMS

View full text Add to dashboard Cite

In this study, we selected natural polyploidy loach (diploid, triploid and tetraploid) and hybrid F1 generation obverse cross (4 × 2) and inverse cross (2 × 4) by diploids and tetraploids as the research model. The MSAP (methylation-sensitive amplified polymorphism) reaction system was established by our laboratory to explore methylation levels and pattern diversification features at the whole genome level of the polyploidy loach. The results showed that the total methylation and full methylation rates decreased on increased ploidy individuals; moreover, the hemimethylation rate showed no consistent pattern. Compared with diploid loach, the methylation patterns of tetraploid sites changed 68.17%, and the methylation patterns of triploid sites changed 73.05%. The proportion of hypermethylation genes is significantly higher than the proportion of demethylation genes. The methylation level of reciprocal cross F1 generation is lower than the male diploid and higher than the female tetraploid. The hemimethylation and total methylation rate of the cross hybrid F1 generation is significantly higher than the orthogonal F1 generation (p < 0.01). After readjusting, the methylation pattern of genome DNA of reciprocal hybrids changed 69.59% and 72.83%, respectively.

show abstract

Section: Discussionsupporting

confidence: 80%

Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

Zhang

et al. 2016

IJMS

View full text Add to dashboard Cite

show abstract

“…The methylation status of the parental Nipponbare and Kasalath, 9 NKF 1 plants (NK1 to NK9), and 9 KNF 1 plants (KN1 to KN9) was analyzed by an RLGS method with combinations of Not I– Msp I– Bam HI (hereafter [ Msp I] pattern) or Not I- Hpa II- Bam HI ([ Hpa II] pattern) restriction enzymes [22, 25]. Briefly, 0.4 μ g of genomic DNA was treated with 2 U DNA polymerase I (Nippon Gene, Tokyo, Japan) in 10 μ L of blocking buffer (10 mM Tris-HCl, pH 7.4, 10 mM MgCl 2 , 1 mM dithiothreitol (DTT), 0.4 μ M dGTP, 0.2 μ M dCTP, 0.4 μ M ddATP, and 0.4 μ M ddTTP) at 37°C for 20 minutes.…”

Section: Methodsmentioning

confidence: 99%

“…indica cv. Kasalath by RLGS, and detected altered inheritance and demethylation of specific RLGS spots in F1 plants [25]. In this study, we analyzed the appearance or disappearance of two altered spots in reciprocal F1 hybrids and selfed progeny, and detected an unexpected allelic expression bias.…”

Section: Introductionmentioning

confidence: 96%

The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance inF1Hybrids

Takamiya

Hosobuchi

Noguchi

et al. 2009

Comparative and Functional Genomics

Self Cite

View full text Add to dashboard Cite

We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath) of rice (Oryza sativa L.) using restriction landmark genome scanning (RLGS), and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the applicability of RLGS for scanning of non-Mendelian inheritance of DNA methylation and biased allelic expression.

show abstract

“…If so, all isolated Hpa II fragments of the (-, +) MH type should contain at least one additional internal CCGG site; indeed, this was reported for all such sequenced fragments [41]. Internal CCGG sequences were also identified in Hpa II-specific fragments obtained from restriction landmark genome scanning of A. thaliana and rice, and their CmCGG methylation status was confirmed by Southern blot hybridization and/or by polymerase chain reaction (PCR) [42,43]. More evidence for the presence of internal CmCGG site(s) in the fragments of the (-, +) MH type comes from MSAP analysis of seven swine tissues where approximately 26.2% and 25.7% of MH patterns were of the (+, -) and (-, +) type, respectively [21].…”

Section: Resultsmentioning

confidence: 89%

How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles?

2014

View full text Add to dashboard Cite

BackgroundDNA methylation plays a key role in development, contributes to genome stability, and may also respond to external factors supporting adaptation and evolution. To connect different types of stimuli with particular biological processes, identifying genome regions with altered 5-methylcytosine distribution at a genome-wide scale is important. Many researchers are using the simple, reliable, and relatively inexpensive Methylation Sensitive Amplified Polymorphism (MSAP) method that is particularly useful in studies of epigenetic variation. However, electrophoretic patterns produced by the method are rather difficult to interpret, particularly when MspI and HpaII isoschizomers are used because these enzymes are methylation-sensitive, and any C within the CCGG recognition motif can be methylated in plant DNA.ResultsHere, we evaluate MSAP patterns with respect to current knowledge of the enzyme activities and the level and distribution of 5-methylcytosine in plant and vertebrate genomes. We discuss potential caveats related to complex MSAP patterns and provide clues regarding how to interpret them. We further show that addition of combined HpaII + MspI digestion would assist in the interpretation of the most controversial MSAP pattern represented by the signal in the HpaII but not in the MspI profile.ConclusionsWe recommend modification of the MSAP protocol that definitely discerns between putative hemimethylated mCCGG and internal CmCGG sites. We believe that our view and the simple improvement will assist in correct MSAP data interpretation.

show abstract

Inheritance and alteration of genome methylation in F1 hybrid rice

Cited by 15 publications

References 48 publications

Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

Analysis of Different Ploidy and Parent–Offspring Genomic DNA Methylation in the Loach Misgurnus anguillicaudatus

The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance inF1Hybrids

How to interpret Methylation Sensitive Amplified Polymorphism (MSAP) profiles?

Contact Info

Product

Resources

About