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Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L.

Zhu B, Shao Y, Pan Q, Ge X, Li Z - Front Plant Sci (2015)

Bottom Line: In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome.But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss.These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

View Article: PubMed Central - PubMed

Affiliation: National Key Lab 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, China.

ABSTRACT
Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the isomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than isomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

No MeSH data available.


More severe dynamic variation of gene expression in monosomics. Coefficient of Variation (COV) of gene expression per chromosome is calculated to measure the gene expression deviation. Red panel represents for “Oro,” blue panel for monosomics, and green panel for isomics.
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Figure 3: More severe dynamic variation of gene expression in monosomics. Coefficient of Variation (COV) of gene expression per chromosome is calculated to measure the gene expression deviation. Red panel represents for “Oro,” blue panel for monosomics, and green panel for isomics.

Mentions: Another intriguing phenomenon was that substantially more DEGs were detected in monosomics than isomics. We have demonstrated that it was not the certain chromosomes which preferentially responded to the burst of DEGs in Oro vs. mono. Possibly, the whole gene expression of monosomics was more severely perturbed than in isomics. Then the genome-wide differential expression between the aneuploids and euploid was assessed, with a view to the distribution of the fold changes of gene expression along all chromosomes (see Figure S3). For each remainder chromosome, except some regions of certain ones, the high fold changes (/FC/> 2) of gene expressions were manifested more obviously in Oro vs. mono than Oro vs. . Subsequently, the Coefficient of Variation (COV) of gene expression per chromosome was analyzed to compare the dynamic variation of gene expression among three types. The COV was always higher in both aneuploids, except for the chromosomes A2, C3, and A5 which showed slightly lower COV in isomics. Compared to isomics, a tendency of higher COV was observed in monosomics, except for the chromosomes A3, A4, A10, C3, C4, and the missing C2, however, the difference between them was negligible for A4 (14.493 vs. 14.496) and C3 (11.445 vs. 11.496) (Figure 3).


Genome-wide gene expression perturbation induced by loss of C2 chromosome in allotetraploid Brassica napus L.

Zhu B, Shao Y, Pan Q, Ge X, Li Z - Front Plant Sci (2015)

More severe dynamic variation of gene expression in monosomics. Coefficient of Variation (COV) of gene expression per chromosome is calculated to measure the gene expression deviation. Red panel represents for “Oro,” blue panel for monosomics, and green panel for isomics.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4585227&req=5

Figure 3: More severe dynamic variation of gene expression in monosomics. Coefficient of Variation (COV) of gene expression per chromosome is calculated to measure the gene expression deviation. Red panel represents for “Oro,” blue panel for monosomics, and green panel for isomics.
Mentions: Another intriguing phenomenon was that substantially more DEGs were detected in monosomics than isomics. We have demonstrated that it was not the certain chromosomes which preferentially responded to the burst of DEGs in Oro vs. mono. Possibly, the whole gene expression of monosomics was more severely perturbed than in isomics. Then the genome-wide differential expression between the aneuploids and euploid was assessed, with a view to the distribution of the fold changes of gene expression along all chromosomes (see Figure S3). For each remainder chromosome, except some regions of certain ones, the high fold changes (/FC/> 2) of gene expressions were manifested more obviously in Oro vs. mono than Oro vs. . Subsequently, the Coefficient of Variation (COV) of gene expression per chromosome was analyzed to compare the dynamic variation of gene expression among three types. The COV was always higher in both aneuploids, except for the chromosomes A2, C3, and A5 which showed slightly lower COV in isomics. Compared to isomics, a tendency of higher COV was observed in monosomics, except for the chromosomes A3, A4, A10, C3, C4, and the missing C2, however, the difference between them was negligible for A4 (14.493 vs. 14.496) and C3 (11.445 vs. 11.496) (Figure 3).

Bottom Line: In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome.But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss.These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

View Article: PubMed Central - PubMed

Affiliation: National Key Lab 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, China.

ABSTRACT
Aneuploidy with loss of entire chromosomes from normal complement disrupts the balanced genome and is tolerable only by polyploidy plants. In this study, the monosomic and isomic plants losing one or two copies of C2 chromosome from allotetraploid Brassica napus L. (2n = 38, AACC) were produced and compared for their phenotype and transcriptome. The monosomics gave a plant phenotype very similar to the original donor, but the isomics had much smaller stature and also shorter growth period. By the comparative analyses on the global transcript profiles with the euploid donor, genome-wide alterations in gene expression were revealed in two aneuploids, and their majority of differentially expressed genes (DEGs) resulted from the trans-acting effects of the zero and one copy of C2 chromosome. The higher number of up-regulated genes than down-regulated genes on other chromosomes suggested that the genome responded to the C2 loss via enhancing the expression of certain genes. Particularly, more DEGs were detected in the monosomics than isomics, contrasting with their phenotypes. The gene expression of the other chromosomes was differently affected, and several dysregulated domains in which up- or downregulated genes obviously clustered were identifiable. But the mean gene expression (MGE) for homoeologous chromosome A2 reduced with the C2 loss. Some genes and their expressions on C2 were correlated with the phenotype deviations in the aneuploids. These results provided new insights into the transcriptomic perturbation of the allopolyploid genome elicited by the loss of individual chromosome.

No MeSH data available.