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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 SSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B are produced by primer combinations of Bfa-A+PPT20, Bfa-A+PPT8, respectively. In part A, Cap is for C. bursa-pastoris and 821 for B. napus ‘821’ and. In part B, Ory is for O. violaceus and Oro for B. napus ‘Oro’.
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pone-0056346-g003: Examples of typical SSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B are produced by primer combinations of Bfa-A+PPT20, Bfa-A+PPT8, respectively. In part A, Cap is for C. bursa-pastoris and 821 for B. napus ‘821’ and. In part B, Ory is for O. violaceus and Oro for B. napus ‘Oro’.

Mentions: Retrotransposons are the most abundant and widespread class of plant transposable element, which can rapidly increase their copy number and greatly increase plant genome size by “copy-paste” replicative mode of transposition [38]. As one of retrotransponsons, LTR (long terminal repeat) retrotransposons were commonly used to detect the mobilization of transposable elements in hybrids/allopolyploids and under stress conditions [9], [39]–[42]. Herein, to explore the alterations of retrotransposons in the two sets of lines, 11 LTR (Copia) retrotransposons detected in B. rapa were investigated in these introgressions. SSAP polymorphisms of these retrotransposons were compared across these lines and parents, and the absent and new bands were scored (Figures 2, 3). No new and absent bands were found for PPT 12, 17. For the remaining 9 retrotransposons, the frequency of loss and gain bands was generally low, with average of 3.6% and 1.3% for cross A, and 3.2% and 2.0% for cross B, respectively, while more than 90% parental bands were maintained in the progenies (Table S2, Table 2; Figure 2). The overall frequency of absent bands (3.4%) was higher than that of the new bands (1.6%), and the highest frequencies of new bands occurred for PPT 7 at 3.9% in cross A and 6.8% in cross B (Table 2). Most of lines from two crosses had both absent and novel bands, some lines had only absent bands or novel bands. The line A-5 from cross A showed only novel bands for PPT 21, 22, and the line B-6 from cross B had only novel bands for PPT 6, 7. Different lines from the same cross displayed variations in pattern and frequency of changes for each retrotransposon, except all lines from cross A with the same frequency of only absent bands for PPT 6(Table S2).


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 SSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B are produced by primer combinations of Bfa-A+PPT20, Bfa-A+PPT8, respectively. In part A, Cap is for C. bursa-pastoris and 821 for B. napus ‘821’ and. In part B, Ory is for O. violaceus and Oro for B. napus ‘Oro’.
© Copyright Policy
Related In: Results  -  Collection

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

pone-0056346-g003: Examples of typical SSAP patterns detected in 12 introgression lines and their parents.The gel profiles in parts A and B are produced by primer combinations of Bfa-A+PPT20, Bfa-A+PPT8, respectively. In part A, Cap is for C. bursa-pastoris and 821 for B. napus ‘821’ and. In part B, Ory is for O. violaceus and Oro for B. napus ‘Oro’.
Mentions: Retrotransposons are the most abundant and widespread class of plant transposable element, which can rapidly increase their copy number and greatly increase plant genome size by “copy-paste” replicative mode of transposition [38]. As one of retrotransponsons, LTR (long terminal repeat) retrotransposons were commonly used to detect the mobilization of transposable elements in hybrids/allopolyploids and under stress conditions [9], [39]–[42]. Herein, to explore the alterations of retrotransposons in the two sets of lines, 11 LTR (Copia) retrotransposons detected in B. rapa were investigated in these introgressions. SSAP polymorphisms of these retrotransposons were compared across these lines and parents, and the absent and new bands were scored (Figures 2, 3). No new and absent bands were found for PPT 12, 17. For the remaining 9 retrotransposons, the frequency of loss and gain bands was generally low, with average of 3.6% and 1.3% for cross A, and 3.2% and 2.0% for cross B, respectively, while more than 90% parental bands were maintained in the progenies (Table S2, Table 2; Figure 2). The overall frequency of absent bands (3.4%) was higher than that of the new bands (1.6%), and the highest frequencies of new bands occurred for PPT 7 at 3.9% in cross A and 6.8% in cross B (Table 2). Most of lines from two crosses had both absent and novel bands, some lines had only absent bands or novel bands. The line A-5 from cross A showed only novel bands for PPT 21, 22, and the line B-6 from cross B had only novel bands for PPT 6, 7. Different lines from the same cross displayed variations in pattern and frequency of changes for each retrotransposon, except all lines from cross A with the same frequency of only absent bands for PPT 6(Table S2).

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