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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.


The trends of fold change (FC) for mean genes expression along individual chromosome between “Oro” and aneuploidies. The fold change between “Oro” and monosomics [FC(mono/Oro)] is shown in blue solid line and the fold change between “Oro” and isomics [FC(/Oro)] in red solid line. Both of modified fold change (MFC) of A2 are shown in dotted line.
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Figure 5: The trends of fold change (FC) for mean genes expression along individual chromosome between “Oro” and aneuploidies. The fold change between “Oro” and monosomics [FC(mono/Oro)] is shown in blue solid line and the fold change between “Oro” and isomics [FC(/Oro)] in red solid line. Both of modified fold change (MFC) of A2 are shown in dotted line.

Mentions: As the chromosomes A2 and C2 in B. napus were highly homoeologous chromosome pairs and were syntenic along their entire length (Parkin et al., 2005), it was fascinating how the gene expression for A2 was affected by the loss of C2, reduced or enhanced for dosage compensation? To reveal the expression differences among chromosomes, the fold changes of mean gene expression (MGE) of individual chromosomes except the absent C2 were compared between two aneuploids and euploid. The tendency of fold changes between two pairs (Figure 5) was comparatively similar (Correlation test, R = 0.91), consistent with above result of distributions of gene expressions, which implied a similar mechanism responding to the absence of C2 in both mon-/isomics again. But contrary to the expectation, the fold change of A2 turned out to be the lowest one in both pairs (1.16 in Oro vs. mono and 0.85 in Oro vs. ), and was significantly different from others of remainder chromosomes in both pairs (Po/m = 1.17E-05, Po/n = 1.68E-07). So the gene expression from A2 was reduced, not improved in the two aneuploids.


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)

The trends of fold change (FC) for mean genes expression along individual chromosome between “Oro” and aneuploidies. The fold change between “Oro” and monosomics [FC(mono/Oro)] is shown in blue solid line and the fold change between “Oro” and isomics [FC(/Oro)] in red solid line. Both of modified fold change (MFC) of A2 are shown in dotted line.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 5: The trends of fold change (FC) for mean genes expression along individual chromosome between “Oro” and aneuploidies. The fold change between “Oro” and monosomics [FC(mono/Oro)] is shown in blue solid line and the fold change between “Oro” and isomics [FC(/Oro)] in red solid line. Both of modified fold change (MFC) of A2 are shown in dotted line.
Mentions: As the chromosomes A2 and C2 in B. napus were highly homoeologous chromosome pairs and were syntenic along their entire length (Parkin et al., 2005), it was fascinating how the gene expression for A2 was affected by the loss of C2, reduced or enhanced for dosage compensation? To reveal the expression differences among chromosomes, the fold changes of mean gene expression (MGE) of individual chromosomes except the absent C2 were compared between two aneuploids and euploid. The tendency of fold changes between two pairs (Figure 5) was comparatively similar (Correlation test, R = 0.91), consistent with above result of distributions of gene expressions, which implied a similar mechanism responding to the absence of C2 in both mon-/isomics again. But contrary to the expectation, the fold change of A2 turned out to be the lowest one in both pairs (1.16 in Oro vs. mono and 0.85 in Oro vs. ), and was significantly different from others of remainder chromosomes in both pairs (Po/m = 1.17E-05, Po/n = 1.68E-07). So the gene expression from A2 was reduced, not improved in the two aneuploids.

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.