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The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra.

Ghani MA, Li J, Rao L, Raza MA, Cao L, Yu N, Zou X, Chen L - BMC Plant Biol. (2014)

Bottom Line: The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid.The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid.The small RNAs results showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively.

View Article: PubMed Central - PubMed

ABSTRACT

Background: An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome "shock" and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid and its allotetraploid between Brassica rapa and Brassica nigra in the present study.

Results: The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The small RNAs results showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, qRT-PCR analysis showed that the expression levels of the target genes were negatively corrected with the expressed miRNAs.

Conclusions: The study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids.

No MeSH data available.


Related in: MedlinePlus

DNA methylation in the parents and their allodiploid and allotetraploid.
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Fig3: DNA methylation in the parents and their allodiploid and allotetraploid.

Mentions: In this study, 1449 reproducible and clear loci were obtained using 36 primer pairs (Additional file 2). These 1449 loci were classified into four major groups (a-d), including 60 categories according to the variation model between the parents and their allodiploids and allotetraploids (Additional file 1). Group A consisted of 12.22% and 12.08% of the monomorphic loci in AB and AABB, respectively. In Group B, 11.94% of the polymorphic loci were specifically found in AB and AABB. Of the loci in Group C, 18.91% and 28.64% of the polymorphic loci were specifically found in AB and AABB, respectively. Compared with the parents, the Group D loci displayed alterations in DNA methylation only in 56.94% and 48.10% of those found in AB and AABB, respectively. There was a significant difference in the methylation patterns between AB and AABB. With respect to the DNA methylation status, the ratios between the allodiploids, the allotetraploids, and their parents demonstrated significant differences (Additional file 1). In addition, the CG methylation was high (24.50%) in AB compared with AABB (Figure 3 and Additional file 1). Thus, the DNA methylation alteration in AB was significantly higher compared with that in AABB. Moreover, the genetic study revealed that two types of the fragments can be used to estimate the genomic changes in the allodiploids and allotetraploids, which have a loss of fragments compared with the parents in addition to novel fragments. The percentages of genetic changes were 10.32% in AB and 21.41% in AABB (Figure 4 and Additional file 3). Thus, the percentage of genetic changes was significantly higher in AABB compared with AB.Figure 3


The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra.

Ghani MA, Li J, Rao L, Raza MA, Cao L, Yu N, Zou X, Chen L - BMC Plant Biol. (2014)

DNA methylation in the parents and their allodiploid and allotetraploid.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4209033&req=5

Fig3: DNA methylation in the parents and their allodiploid and allotetraploid.
Mentions: In this study, 1449 reproducible and clear loci were obtained using 36 primer pairs (Additional file 2). These 1449 loci were classified into four major groups (a-d), including 60 categories according to the variation model between the parents and their allodiploids and allotetraploids (Additional file 1). Group A consisted of 12.22% and 12.08% of the monomorphic loci in AB and AABB, respectively. In Group B, 11.94% of the polymorphic loci were specifically found in AB and AABB. Of the loci in Group C, 18.91% and 28.64% of the polymorphic loci were specifically found in AB and AABB, respectively. Compared with the parents, the Group D loci displayed alterations in DNA methylation only in 56.94% and 48.10% of those found in AB and AABB, respectively. There was a significant difference in the methylation patterns between AB and AABB. With respect to the DNA methylation status, the ratios between the allodiploids, the allotetraploids, and their parents demonstrated significant differences (Additional file 1). In addition, the CG methylation was high (24.50%) in AB compared with AABB (Figure 3 and Additional file 1). Thus, the DNA methylation alteration in AB was significantly higher compared with that in AABB. Moreover, the genetic study revealed that two types of the fragments can be used to estimate the genomic changes in the allodiploids and allotetraploids, which have a loss of fragments compared with the parents in addition to novel fragments. The percentages of genetic changes were 10.32% in AB and 21.41% in AABB (Figure 4 and Additional file 3). Thus, the percentage of genetic changes was significantly higher in AABB compared with AB.Figure 3

Bottom Line: The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid.The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid.The small RNAs results showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively.

View Article: PubMed Central - PubMed

ABSTRACT

Background: An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome "shock" and instability occur during this process, whereas chromosome doubling results in doubling and reconstructing the genome dosage. Recent studies have demonstrated that small RNAs, play an important role in maintaining the genome reconstruction and stability. However, to date, little is known regarding the role of small RNAs during the process of wide hybridisation and chromosome doubling, which is essential to elucidate the mechanism of polyploidisation. Therefore, the genetic and DNA methylation alterations and changes in the siRNA and miRNA were assessed during the formation of an allodiploid and its allotetraploid between Brassica rapa and Brassica nigra in the present study.

Results: The phenotypic analysis exhibited that the allotetraploid had high heterosis compared with their parents and the allodiploid. The methylation-sensitive amplification polymorphism (MSAP) analysis indicated that the proportion of changes in the methylation pattern of the allodiploid was significantly higher than that found in the allotetraploid, while the DNA methylation ratio was higher in the parents than the allodiploid and allotetraploid. The small RNAs results showed that the expression levels of miRNAs increased in the allodiploid and allotetraploid compared with the parents, and the expression levels of siRNAs increased and decreased compared with the parents B. rapa and B. nigra, respectively. Moreover, the percentages of miRNAs increased with an increase in the polyploidy levels, but the percentages of siRNAs and DNA methylation alterations decreased with an increase in the polyploidy levels. Furthermore, qRT-PCR analysis showed that the expression levels of the target genes were negatively corrected with the expressed miRNAs.

Conclusions: The study showed that siRNAs and DNA methylation play an important role in maintaining the genome stability in the formation of an allotetraploid. The miRNAs regulate gene expression and induce the phenotype variation, which may play an important role in the occurrence of heterosis in the allotetraploid. The findings of this study may provide new information for elucidating that the allotetraploids have a growth advantage over the parents and the allodiploids.

No MeSH data available.


Related in: MedlinePlus