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Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb

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Abstract

We have reported previously that introgression by Zizania latifolia resulted in extensive DNA methylation changes in the recipient rice genome, as detected by a set of pre-selected DNA segments. In this study, using the methylation-sensitive amplified polymorphism (MSAP) method, we globally assessed the extent and pattern of cytosine methylation alterations in three typical introgression lines relative to their rice parent at ∼2,700 unbiased genomic loci each representing a recognition site cleaved by one or both of the isoschizomers, HpaII/MspI. Based on differential digestion by the isoschizomers, it is estimated that 15.9% of CCGG sites are either fully methylated at the internal Cs and/or hemi-methylated at the external Cs in the rice parental cultivar Matsumae. In comparison, a statistically significant increase in the overall level of both methylation types was detected in all three studied introgression lines (19.2, 18.6, 19.6%, respectively). Based on comparisons of MSAP profiles between the isoschizomers within the rice parent and between parent and the introgression lines, four major groups of MSAP banding patterns are recognized, which can be further divided into various subgroups as a result of inheritance of, or variation in, parental methylation patterns. The altered methylation patterns include hyper- and hypomethylation changes, as well as inter-conversion of hemi- to full-methylation, or vice versa, at the relevant CCGG site(s). Most alterations revealed by MSAP in low-copy loci can be validated by DNA gel blot analysis. The changed methylation patterns are uniform among randomly selected individuals for a given introgression line within or among selfed generations. Sequencing on 31 isolated fragments that showed different changing patterns in the introgression line(s) allowed their mapping onto variable regions on one or more of the 12 rice chromosomes. These segments include protein-coding genes, transposon/retrotransposons and sequences with no homology. Possible causes for the introgression-induced methylation changes and their implications for genome evolution and crop breeding are discussed.

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Acknowledgments

This study was supported by the Program for Changjiang Scholars and Innovative Research Team (PCSIRT) in University, the National Natural Science Foundation of China (30430060, 30370768), and the State Key Basic Research and Development Plan of China (2005CB120805). We are indebted to two anonymous reviewers for critical and constructive suggestions to improve this manuscript. We are also grateful to Dr. Jonathan Lamb of the University of Missouri-Columbia, USA, for editing the English. This work has been carried out in compliance with the current laws governing biological experimentation in China.

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Authors and Affiliations

  1. Laboratory of Plant Molecular Epigenetics, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024, China

    Z. Y. Dong, Y. M. Wang, Z. J. Zhang, X. Y. Lin, X. F. Ou & B. Liu

  2. Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun, 130024, China

    Y. Shen

  3. Division of Biological Sciences, University of Missouri, Columbia, MO, 65211, USA

    F. P. Han

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  1. Z. Y. Dong
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Correspondence to B. Liu.

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Communicated by E. Guiderdoni

Z. Y. Dong and Y. M. Wang have equally contributed to the work.

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Dong, Z.Y., Wang, Y.M., Zhang, Z.J. et al. Extent and pattern of DNA methylation alteration in rice lines derived from introgressive hybridization of rice and Zizania latifolia Griseb. Theor Appl Genet 113, 196–205 (2006). https://doi.org/10.1007/s00122-006-0286-2

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