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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.


Dysregulated domains of gene expressions on different chromosomes. Log2 fold change of gene expression is performed to measure the expression deviation. Chromosomes A4, A7, A9, C1, C4, C6, and C9 harbor one domain in both comparisons, and C5 and C8 have one only in “Oro” vs. isomics comparison. The change between “Oro” and monosomics is shown in blue dot and change between “Oro” and isomics in red dot.
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Figure 4: Dysregulated domains of gene expressions on different chromosomes. Log2 fold change of gene expression is performed to measure the expression deviation. Chromosomes A4, A7, A9, C1, C4, C6, and C9 harbor one domain in both comparisons, and C5 and C8 have one only in “Oro” vs. isomics comparison. The change between “Oro” and monosomics is shown in blue dot and change between “Oro” and isomics in red dot.

Mentions: Several dysregulated domains of differential expressions between the aneuploids and euploid in which up- or downregulated genes obviously clustered captured our attentions, for these domains probably responded to the C2 loss. Totally, nine clear domains along distinct chromosomes (Figure 4) were revealed. These domains were either up- or downregulated in both pairs or only in one pair, but the upregulated domains consistently comprised the majority and the downregulated ones were mainly from the isomics. Among these domains, the minimum covered ~0.3 Mb region on C5 and the largest one located on A7 extended to ~7.2 Mb region. Remarkably, differential expressions of genes were almost up-regulated in several dysregulated domains in two aneuploids, for example, the proportion of DEGs to EGs rose to 66.67% in Oro vs. mono and 76% in Oro vs. for the upregulated domain along C1, considerably higher than the mean expression. The detailed information of all the domains was summarized in Table 4. Interestingly, the top three chromosomes (A7, C1, and C6) occupying preferential proportion of DEGs in both paired comparisons contained one large dysregulated domains, suggesting that these dysregulated domains mainly energized the boom of DEGs.


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)

Dysregulated domains of gene expressions on different chromosomes. Log2 fold change of gene expression is performed to measure the expression deviation. Chromosomes A4, A7, A9, C1, C4, C6, and C9 harbor one domain in both comparisons, and C5 and C8 have one only in “Oro” vs. isomics comparison. The change between “Oro” and monosomics is shown in blue dot and change between “Oro” and isomics in red dot.
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Related In: Results  -  Collection

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Figure 4: Dysregulated domains of gene expressions on different chromosomes. Log2 fold change of gene expression is performed to measure the expression deviation. Chromosomes A4, A7, A9, C1, C4, C6, and C9 harbor one domain in both comparisons, and C5 and C8 have one only in “Oro” vs. isomics comparison. The change between “Oro” and monosomics is shown in blue dot and change between “Oro” and isomics in red dot.
Mentions: Several dysregulated domains of differential expressions between the aneuploids and euploid in which up- or downregulated genes obviously clustered captured our attentions, for these domains probably responded to the C2 loss. Totally, nine clear domains along distinct chromosomes (Figure 4) were revealed. These domains were either up- or downregulated in both pairs or only in one pair, but the upregulated domains consistently comprised the majority and the downregulated ones were mainly from the isomics. Among these domains, the minimum covered ~0.3 Mb region on C5 and the largest one located on A7 extended to ~7.2 Mb region. Remarkably, differential expressions of genes were almost up-regulated in several dysregulated domains in two aneuploids, for example, the proportion of DEGs to EGs rose to 66.67% in Oro vs. mono and 76% in Oro vs. for the upregulated domain along C1, considerably higher than the mean expression. The detailed information of all the domains was summarized in Table 4. Interestingly, the top three chromosomes (A7, C1, and C6) occupying preferential proportion of DEGs in both paired comparisons contained one large dysregulated domains, suggesting that these dysregulated domains mainly energized the boom of DEGs.

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.