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Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

Zhang X, Ge X, Shao Y, Sun G, Li Z - PLoS ONE (2013)

Bottom Line: The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets.MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation.The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China.

ABSTRACT
Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

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Examples of typical MSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B were produced by primer combinations of EcorI-ACT+H/M-TAG and EcorI-ACT+H/M-TTC, respectively. The denotations for the parents are the same as in Figure 3.
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pone-0056346-g004: Examples of typical MSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B were produced by primer combinations of EcorI-ACT+H/M-TAG and EcorI-ACT+H/M-TTC, respectively. The denotations for the parents are the same as in Figure 3.

Mentions: To reveal epigenetic alterations in these introgressions, MSAP analyses that targeted randomly sampled genomic loci were performed. By using 40 pairs of randomly selected primers, an average of 1063 and 1017 clear and reproducible bands was given by each line in cross A and B, respectively. According to the model of alteration in the introgressions, the MSAP loci could be grouped into 15 patterns in comparison with those bands in B. napus parents. These three patterns were excluded for further analysis: ++/++, ++/− and −/++, because it was difficult to decide whether there were methylated loci (++/++) or the alterations resulting from the methylation changes or sequence variation (restriction enzyme cutting site change) (++/− and −/++). The remaining 12 patterns were classified into four types (Table 4, Table S3). Type A included two patterns (A1, A2) representing the additive bands from B. napus parents, and the site number of A2 pattern was more than double of the number of A1 pattern in the two crosses. The additive bands accounted for 62.3% and 64.6% of the total bands observed in cross A and B, respectively. Among the four patterns in Type B that showed hypermethylation by gain of methylated loci at one or both CCGG sites (Figure 4), twice as many bands occurred for B2 pattern as other three types in both crosses, which presented 23.3% and 20.3% of the total loci in cross A and B, respectively, and the frequency for cross A was significantly higher than that for cross B. Other four patterns in Type C indicated hypomethylation by release of methylated loci at one or both CCGG sites (Figure 4), and C1 pattern had much fewer number than the other three which showed similar numbers. The frequencies of bands for hypomethylation were 14.0% in cross A and 14.3% in cross B, which was much lower than those for hypermethylation. Type D included two other methylation patterns which occurred at low rates, 0.3% and 0.8% in cross A and B, respectively. Overall, methylation changes were common in these lines (33.4–39.8%) and the hypermethylation was more frequent than hypomethylation. For each pattern of methylation, variation in frequencies among lines from the same or different crosses was very limited, as their genomic change and retrotransposon alteration did.


Genomic change, retrotransposon mobilization and extensive cytosine methylation alteration in Brassica napus introgressions from two intertribal hybridizations.

Zhang X, Ge X, Shao Y, Sun G, Li Z - PLoS ONE (2013)

Examples of typical MSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B were produced by primer combinations of EcorI-ACT+H/M-TAG and EcorI-ACT+H/M-TTC, respectively. The denotations for the parents are the same as in Figure 3.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3585313&req=5

pone-0056346-g004: Examples of typical MSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B were produced by primer combinations of EcorI-ACT+H/M-TAG and EcorI-ACT+H/M-TTC, respectively. The denotations for the parents are the same as in Figure 3.
Mentions: To reveal epigenetic alterations in these introgressions, MSAP analyses that targeted randomly sampled genomic loci were performed. By using 40 pairs of randomly selected primers, an average of 1063 and 1017 clear and reproducible bands was given by each line in cross A and B, respectively. According to the model of alteration in the introgressions, the MSAP loci could be grouped into 15 patterns in comparison with those bands in B. napus parents. These three patterns were excluded for further analysis: ++/++, ++/− and −/++, because it was difficult to decide whether there were methylated loci (++/++) or the alterations resulting from the methylation changes or sequence variation (restriction enzyme cutting site change) (++/− and −/++). The remaining 12 patterns were classified into four types (Table 4, Table S3). Type A included two patterns (A1, A2) representing the additive bands from B. napus parents, and the site number of A2 pattern was more than double of the number of A1 pattern in the two crosses. The additive bands accounted for 62.3% and 64.6% of the total bands observed in cross A and B, respectively. Among the four patterns in Type B that showed hypermethylation by gain of methylated loci at one or both CCGG sites (Figure 4), twice as many bands occurred for B2 pattern as other three types in both crosses, which presented 23.3% and 20.3% of the total loci in cross A and B, respectively, and the frequency for cross A was significantly higher than that for cross B. Other four patterns in Type C indicated hypomethylation by release of methylated loci at one or both CCGG sites (Figure 4), and C1 pattern had much fewer number than the other three which showed similar numbers. The frequencies of bands for hypomethylation were 14.0% in cross A and 14.3% in cross B, which was much lower than those for hypermethylation. Type D included two other methylation patterns which occurred at low rates, 0.3% and 0.8% in cross A and B, respectively. Overall, methylation changes were common in these lines (33.4–39.8%) and the hypermethylation was more frequent than hypomethylation. For each pattern of methylation, variation in frequencies among lines from the same or different crosses was very limited, as their genomic change and retrotransposon alteration did.

Bottom Line: The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets.MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation.The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

View Article: PubMed Central - PubMed

Affiliation: National Key Laboratory of Crop Genetic Improvement, National Center of Crop Molecular Breeding Technology, National Center of Oil Crop Improvement (Wuhan), College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, PR China.

ABSTRACT
Hybridization and introgression represent important means for the transfer and/or de novo origination of traits and play an important role in facilitating speciation and plant breeding. Two sets of introgression lines in Brassica napus L. were previously established by its intertribal hybridizations with two wild species and long-term selection. In this study, the methods of amplified fragment length polymorphisms (AFLP), sequence-specific amplification polymorphism (SSAP) and methylation-sensitive amplified polymorphism (MSAP) were used to determine their genomic change, retrotransposon mobilization and cytosine methylation alteration in these lines. The genomic change revealed by the loss or gain of AFLP bands occurred for ∼10% of the total bands amplified in the two sets of introgressions, while no bands specific for wild species were detected. The new and absent SSAP bands appeared for 9 out of 11 retrotransposons analyzed, with low frequency of new bands and their total percentage of about 5% in both sets. MSAP analysis indicated that methylation changes were common in these lines (33.4-39.8%) and the hypermethylation was more frequent than hypomethylation. Our results suggested that certain extents of genetic and epigenetic alterations were induced by hybridization and alien DNA introgression. The cryptic mechanism of these changes and potential application of these lines in breeding were also discussed.

Show MeSH