DNA methylation polymorphism and stability in Chinese indica hybrid rice

Peng, Hai; Jiang, Guicheng; Zhang, Jing; Zhang, Weixiong; Zhai, Wenxue

doi:10.1007/s11427-013-4576-z

Cited by 8 publications

(3 citation statements)

References 36 publications

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“…Identification of epialleles underlying natural variation will be an important issue in future rice breeding [24,36]. Epigenetic alleles may be involved in diverse phenomenaranging from development to genome evolution and defense against transposons [37].…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

Wang

Huang

Qiao

et al. 2015

Biochemical and Biophysical Research Communications

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DNA methylation, which is one of the best understood epigenetic phenomena, plays an important role in plant responses to environmental stimuli. The rice introgression line IL177-103 and its recurrent parent IR64, which show contrasting salt stress tolerance, were used to characterize DNA methylation changes under salt stress and subsequent recovery using methylation-sensitive amplified polymorphism (MSAP) analysis. The introgression line IL177-103 showed significantly improved tolerance to salinity, as represented by higher relative water content, endogenous abscisic acid content, activity of reactive oxygen species scavenging enzymes, and lower Na(+) concentration in shoots, compared with IR64. The MSAP results showed that less than 10.5% of detected DNA methylation sites were genotype specific, in line with their similar genetic background. Salt-induced DNA methylation changes in both genotypes were mostly detected in roots, and the major portion of the salt-induced DNA demethylation/methylation alterations remained even after recovery, implying their inheritance in the present generation. Furthermore, a few sites with stable DNA methylation differences were identified between salt-tolerant IL177-103 and salt-sensitive IR64, thus providing genotype-specific epigenetic markers. Collectively, these results provide valuable data for further dissection of the molecular mechanisms of salt-stress response and tolerance in rice.

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Section: Discussionmentioning

confidence: 99%

Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

Wang

Huang

Qiao

et al. 2015

Biochemical and Biophysical Research Communications

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“…Second, it is important to articulate that the true essence of functional genomics in the context of rice breeding must be deeply rooted to the ability to identify meaningful sequence variation across an allelic series, understanding how such sequence variation contributes to differences in gene function, and whether differences in gene function are due simply to sequence variation (alleles) or differential DNA methylation in the absence of drastic sequence variation (epialleles). More and more examples of homologous genes that vary in expression in the absence of meaningful sequence variation are being reported in the literature (Peng and Zhang, 2009 ; Hai et al, 2013 ; Zheng et al, 2013 ). Understanding the organization and distribution of critical regulatory element modules within the upstream sequences of intraspecific or interspecific homologs has the potential to provide another layer of information for understanding the contribution of ‘ epiallelic variation ’ to phenotypic variation.…”

Section: Discussionmentioning

confidence: 99%

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Reyes

Mohanty

Yun

et al. 2015

Rice

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Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.

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“…For instance, generally stable inheritance with rare examples of unexpected patterns has been shown in recombinant inbred populations of maize (Eichten et al 2013 ; Li et al 2014 ). Still, non-Mendelian epi-inheritance was reported in maize (Zhao et al 2008 ), rice (Peng et al 2013 ) and soybean (Schmitz et al 2013 ). It could be that some DMRs are associated with proximal structural variation and are in general reasonably faithfully inherited in conjunction with the genetic polymorphism.…”

Section: Prospects and Limits Of Using Cwr Epigenetic Variation In Cr...mentioning

confidence: 99%

Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

et al. 2022

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Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.

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DNA methylation polymorphism and stability in Chinese indica hybrid rice

Cited by 8 publications

References 36 publications

Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

Comparative analysis of DNA methylation changes in two rice genotypes under salt stress and subsequent recovery

Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining

Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation

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