Cytoplasmic effects on DNA methylation between male sterile lines and the maintainer in wheat (Triticum aestivum L.)

Male sterile cytoplasm plays an important role in hybrid wheat, and three-line system including male sterile (A line), its maintainer (B line) and restoring (R line) has played a major role in wheat hybrid production. It is well known that DNA methylation plays an important role in gene expression regulation during biological development in wheat. However, no reports are available on DNA methylation affected by different male sterile cytoplasms in hybrid wheat. We employed a methylation-sensitive amplified polymorphism technique to characterize nuclear DNA methylation in three male sterile cytoplasms. A and B lines share the same nucleus, but have different cytoplasms which is male sterile for the A and fertile for the B. The results revealed a relationship of DNA methylation at these sites specifically with male sterile cytoplasms, as well as male sterility, since the only difference between the A lines and B line was the cytoplasm. The DNA methylation was markedly affected by male sterile cytoplasms. K-type cytoplasm affected the methylation to a much greater degree than T-type and S-type cytoplasms, as indicated by the ratio of methylated sites, ratio of fully methylated sites, and polymorphism between A lines and B line for these cytoplasms. The genetic distance between the cytoplasm and nucleus for the K-type is much greater than for the T- and S-types because the former is between Aegilops genus and Triticum genus and the latter is within Triticum genus between Triticum spelta and Triticum timopheevii species. Thus, this difference in genetic distance may be responsible for the variation in methylation that we observed.     

DNA polymorphism in Allium cepa cytoplasms and its implications concerning the origin of onions

Summary Mitochondrial and chloroplast DNA was isolated from fertile and cytoplasmic male sterile cultivars of cultivated onions. Restriction fragment length polymorphism led to the distinction between cytoplasms S and M. Mitochondrial DNA patterns from S cytoplasms appeared dentical and characterized mostly male sterile lines. An open-pollinated variety was found to bear this cytoplasm and thought to be the origin of S types. Mitochondrial DNA patterns from M cytoplasms were subdivided into four types, M₁ and M₂ corresponding to normal N cytoplasm, M₃ and M₄ probably corresponding to T cytoplasms. S and M cytoplasms were also distinguished by chloroplast DNA restriction patterns. Our results confirm previous genetic distinction between S, N and T cytoplasms.     

Mitochondrial DNA modifications associated with cytoplasmic male sterility in rice

Summary Mitochondrial DNA was isolated from fertile and cytoplasmic male sterile lines of rice. Restriction analysis showed specific modifications in the male sterile cytoplasm. In addition to the major mitochondrial DNA, three small plasmid-like DNA molecules were detected by agarose gel electrophoresis in both cytoplasms. An additional molecule was specifically found in the sterile cytoplasm. These mitochondrial DNA modifications support the hypothesis of the mitochondrial inheritance of the cytoplasmic male sterility in rice.     

Patterns of cytosine methylation in an elite rice hybrid and its parental lines, detected by a methylation-sensitive amplification polymorphism technique

DNA methylation is known to play an important role in the regulation of gene expression in eukaryotes. In this study, we assessed the extent and pattern of cytosine methylation in the rice genome, using the technique of methylation-sensitive amplified polymorphism (MSAP), which is a modification of the amplified fragment length polymorphism (AFLP) method that makes use of the differential sensitivity of a pair of isoschizomers to cytosine methylation. The tissues assayed included seedlings and flag leaves of an elite rice hybrid, Shanyou 63, and the parental lines Zhenshan 97 and Minghui 63. In all, 1076 fragments, each representing a recognition site cleaved by either or both of the isoschizomers, were amplified using 16 pairs of selective primers. A total of 195 sites were found to be methylated at cytosines in one or both parents, and the two parents showed approximately the same overall degree of methylation (16.3%), as revealed by the incidence of differential digestion by the isoschizomers. Four classes of patterns were identified in a comparative assay of cytosine methylation in the parents and hybrid; increased methylation was detected in the hybrid compared to the parents at some of the recognition sites, while decreased methylation in the hybrid was detected at other sites. A small proportion of the sites was found to be differentially methylated in seedlings and flag leaves; DNA from young seedlings was methylated to a greater extent than that from flag leaves. Almost all of the methylation patterns detected by MSAP could be confirmed by Southern analysis using the isolated amplified fragments as probes. The results clearly demonstrate that the MSAP technique is highly efficient for large-scale detection of cytosine methylation in the rice genome. We believe that the technique can be adapted for use in other plant species. Received: 23 October 1998 / Accepted: 11 January 1999     

Variation and Patterns of DNA Methylation in Maize C-type CMS Lines and their Maintainers

DNA methylation plays an important role in gene expression regulation during biological development in plants. This study adopted methylation sensitive amplification polymorphism (MSAP) to compare the levels and patterns of cytosine methylation at CCGG sites in maize genome. The tissues assayed included seedlings and tassels of C-type cytoplasmic male sterility (C Huang Zao Si, C 48-2) and its maintainer lines. For each tissue, both C Huang Zao Si and C 48-2 were more methylated than their corresponding maintainers not only on MSAP ratios, but also on the full methylation levels. In different nuclear backgrounds, the two tissues were more methylated in Huang Zao Si than in 48-2, although the two lines shared the same cytoplasm. Full methylation of internal cytosine was the dominant type in the maize genome. In addition, four different classes of methylation patterns were identified in tassels between C-CMS lines and their maintainer lines; these were specific-methylation, demethylation, hypo-methylation, and hyper-methylation. The results obtained demonstrated the power of the MSAP technique for large-scale DNA methylation detection in the maize genome, and suggested the possible association between DNA methylation polymorphism and C-type cytoplasmic male sterility.     

Different genomic DNA methylation patterns between male and female adults of white-backed planthoppers Sogatella furcifera

DNA methylation plays a key role in gene regulation and phenotype variation in many organisms. The aim of this study was to survey the frequency and variation of cytosine methylation at CCGG sequences in adult male and female planthoppers Sogatella furcifera, a major rice pest in Asia, and to determine the occurrence of methylation changes associated with sexual dimorphism using methylation-sensitive amplification polymorphism. 1131 DNA fragments including CCGG sites were amplified using 36 pairs of selective primers: about 191 methylated bands were identified. In male planthoppers, we got a total of 581 bands, including 40 fully-methylated bands, 65 hemi-methylated bands and 476 none-methylated bands, so the fully-methylated ratio, hemi-methylated ratio and total methylated ratio were 6.88%, 11.19% and 18.07%, respectively. In the female planthopper, there were a total of 550 bands, including 44 fully-methylated bands, 42 hemi-methylated bands and 464 none-methylated bands. The fully-methylated ratio was 7.64% in female planthoppers, which was slightly higher than in the male planthoppers, however, the hemi-methylated ratio was lower (8.00%) in the female compared with the male planthopper. Altogether, 46 DNA bands displayed variable cytosine methylation patterns between male and female samples: 20 of them occurred only in male samples and 26 only in female samples. Thus, the genome methylation patterns are different between male and female adults. The results suggest that DNA methylation might be related to sexual differentiation and development in S. furcifera.     

Mitochondrial Plasmids in Sorghum: Presence of Linear Plasmids in Indian Male Sterile and Milo 296 Lines

The presence of plasm ids of sizes 5.8 kbp, 5.3 kbp, 2.3 kbp, 1.7 kbp and 1.36 kbp was detected in 3 Indian male sterile cytotypes viz. Maldandi, Guntur, Vizianagaram but not in their fertile maintainer lines. The 5.8 kbp and 5.3 kbp plasm ids do not possess any homology with the nuclear or chloroplastic DNA as also with the main mitochondrial genome of sterile and maintainer fertile lines. The detection of these plasm ids in the male sterile, maintainer fertile and fertility restored lines of 296 variety is surprising as the male sterile 296A and restored line possess a milo cytoplasm that has as yet not been shown to contain such plasmids. This observation suggests that plasm ids have no role to play in male sterility but their presence could be used as a marker for characterization/classification of certain cytoplasms especially the Indian cytoplasms.     

水稻7种不同细胞质源滇型不育系间恢保关系研究

本研究选用7种细胞质源不同的滇型不育系为母本,10个常用品种或品系为父本,得到70个杂交组合.通过分析70个杂交后代的花粉可育度和自然结实率可知,这7个细胞质源不同的滇型不育系之间的保持关系基本一致;5个滇一型恢复系对这7个不育系的恢复能力差异较大.鉴于7种不同细胞质源不育系的保持关系相同,使转育同核异质不育系成为可能,从而为实现滇型杂交水稻细胞质多样化提供了实验依据.     

Efficiency of one- and two-stage selection indexes for improvement of net economic merit in White Leghorns

Summary Mitochondrial (mt) and chloroplast (ct) DNAs from sugar beet lines carrying normal and introduced sources of male sterile cytoplasms have been characterized and compared on the basis of restriction enzyme analysis. Normal cytoplasm was shown to contain mt and ctDNAs which differed from those of the male sterile cytoplasms examined in the present investigation. On the other hand, four groups of male sterile cytoplasms could be differentiated by their own characteristic mtDNA digest patterns, while two were separated by ctDNA comparisons. In addition, a greater degree of variability of the mitochondrial genome is suggested. Our results also imply strict maternal inheritance of mt and ctDNAs. Thus, the organelle DNA assay provides a positive and alternative means of identifying various male sterile cytoplasms.     

用线粒体DNA鉴定玉米雄性不育细胞质的研究

参照Kemble法,通过分析玉米线粒体DNA,鉴定出我国生产上应用的玉米双型和唐徐型雄性不育细胞质属于S组。近年新获得的不育类型Y型属于T组,为玉米种子生产合理应用雄性不育细胞质提供了可靠依据,并对鉴别玉米雄性不育细胞质的方法进行了讨论。     

Concurrent Replication and Methylation at Mammalian Origins of Replication

Observations made with Escherichia coli have suggested that a lag between replication and methylation regulates initiation of replication. To address the question of whether a similar mechanism operates in mammalian cells, we have determined the temporal relationship between initiation of replication and methylation in mammalian cells both at a comprehensive level and at specific sites. First, newly synthesized DNA containing origins of replication was isolated from primate-transformed and primary cell lines (HeLa cells, primary human fibroblasts, African green monkey kidney fibroblasts [CV-1], and primary African green monkey kidney cells) by the nascent-strand extrusion method followed by sucrose gradient sedimentation. By a modified nearest-neighbor analysis, the levels of cytosine methylation residing in all four possible dinucleotide sequences of both nascent and genomic DNAs were determined. The levels of cytosine methylation observed in the nascent and genomic DNAs were equivalent, suggesting that DNA replication and methylation are concomitant events. Okazaki fragments were also demonstrated to be methylated, suggesting that the rapid kinetics of methylation is a feature of both the leading and the lagging strands of nascent DNA. However, in contrast to previous observations, neither nascent nor genomic DNA contained detectable levels of methylated cytosines at dinucleotide contexts other than CpG (i.e., CpA, CpC, and CpT are not methylated). The nearest-neighbor analysis also shows that cancer cell lines are hypermethylated in both nascent and genomic DNAs relative to the primary cell lines. The extent of methylation in nascent and genomic DNAs at specific sites was determined as well by bisulfite mapping of CpG sites at the lamin B2, c-myc, and β-globin origins of replication. The methylation patterns of genomic and nascent clones are the same, confirming the hypothesis that methylation occurs concurrently with replication. Interestingly, the c-myc origin was found to be unmethylated in all clones tested. These results show that, like genes, different origins of replication exhibit different patterns of methylation. In summary, our results demonstrate tight coordination of DNA methylation and replication, which is consistent with recent observations showing that DNA methyltransferase is associated with proliferating cell nuclear antigen in the replication fork.     

DNA methylation polymorphism and stability in Chinese indica hybrid rice

Conventional rice breeding has long focused on exploiting the DNA sequence diversity. However, epigenetic diversity, reflected particularly in DNA methylation, can also contribute to phenotypic variation and should not be overlooked in rice breeding. In this study, 20 parental lines of indica rice, which are widely used in hybrid rice breeding in China, were analyzed to investigate variations of DNA methylation and its inheritance. The results revealed a wide diversity in DNA methylation among these breeding lines. A positive correlation was seen between DNA methylation and genetic diversity. Furthermore, some of the methylated DNA was inherited in the subsequent generation, regardless of whether they were produced by selfing or hybrid-crossing. This study provides insight into the methylation patterns in rice, and suggests the importance of epigenetic diversity in rice breeding.     

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

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.Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.Z. Y. Dong and Y. M. Wang have equally contributed to the work.     

粘类非1BL/1RS小麦CMS基因定向选择及其育性特性的研究

对携有不同不育基因的4个粘类小麦雄性不育系进行了定向选择与鉴定,并对其育性特性进行研究,以选育更具应用价值的粘类非1BL/1RS小麦雄性不育系,推动三系杂交小麦的实际应用.结果表明:(1)根尖体细胞随体鉴定和A-PAGE技术分析筛选出的SP4、莫迦小麦为非1BL/1RS类型,其它供试不育系均属于1BL/1RS类型;(2)减数分裂及成熟花粉粒形态观察,粘类非1BL/1RS小麦雄性不育系其不育性是在整个配子发育过程中连续产生的,且在B型不育细胞质背景下,SP4和莫迦小麦的花粉细胞学形态与在K、Ven型2种不育细胞质背景下的不同,B型不育细胞质背景下SP4和莫迦不育系的花粉萌发率比K、Ven型不育细胞质背景下的花粉萌发率高;(3)以不同来源不育基因培育成的粘类K、Ven型非1BL/1RS不育系育性恢复性测定发现,SP4、莫迦小麦2种雄性不育系育性恢复性有一定差异,莫迦小麦不育类型育性恢复性高于SP4.     

Differential DNA methylation between two wing phenotypes adults of Sogatella furcifera

Sogatella furcifera is a major rice pest with wing dimorphism . DNA methylation is an important epigenetic modification that plays a role in gene regulation and phenotype variation in most organisms. The objective of the current research was to survey the frequencies and variation of cytosine methylation at CCGG sequences in macropterous female adults (MFA) and brachypterous female adults (BFA) of S. furcifera, and to determine the occurrence of methylation changes associated with wing phenotypes by using methylation‐sensitive amplification polymorphism (MSAP). No differences were found in the average proportions of methylated CCGG sites between MFA and BFA, but there were significant differences for methylation patterns between MFA and BFA. The fully methylated ratio was 5.81% in BFA, much higher than 2.40% in MFA; while the hemi‐methylated ratio was 4.35% in BFA, much lower than 8.35% in MFA. These results provide circumstantial evidence that DNA methylation might be related to wing phenotype variation in S. furcifera. We also cloned and got 14 satisfactory sequences, which displayed variable cytosine methylation patterns between MFA and BFA. All these data will facilitate the researches on the epigenetic mechanisms of insect wing polymorphism. genesis 51:819–826. © 2013 Wiley Periodicals, Inc.     

Small mitochondrial DNA molecules of wild abortive cytoplasm in rice are not necessarily associated with CMS

Summary Mitochondrial DNA was isolated from leaf tissue of both the cytoplasmic male sterile line of Indica rice variety V41, which carries wild abortive (WA) cytoplasm, and from the corresponding maintainer line. In addition to the main mitochondrial DNA, four small plasmid-like DNA molecules were detected in both the male sterile and fertile lines. Restriction analysis of total mitochondrial DNA from the male sterile and fertile lines showed DNA fragments unique to each. Our findings suggest that the four small mitochondrial DNA (mtDNA) molecules are conserved when WA cytoplasm is transferred into different nuclear backgrounds. However, there is no simple correlation between the presence/ absence of small mitochondrial DNA molecules and the expression of WA cytoplasmic male sterility (CMS).     

Mitochondrial plasmid-like molecules in fertile and male sterileVicia faba L

Biochemical analysis and electron microscopy showed that mitochondria of both the fertile and the male sterile 350 and 447 cytoplasms ofVicia faba. L. contain two small supercoiled DNA molecules of mean length of 1 700 and 1 420 base pairs in addition to the main mitochondrial DNA of high molecular weight. By agarose gel electrophoresis, the male sterile cytoplasm 350 is distinguished from the fertile cytoplasm and from the male sterile cytoplasm 447 by the presence of an additional supercoiled DNA molecule of approximately 1 540 bp.