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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.


Differentially expressed genes (DEGs) between B. napus euploid and aneuploids. (A,B) DEGs among three comparisons (A) and 7370 common DEGs (B) between “Oro” vs. mono and “Oro” vs.  were shown in Venn diagram.
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Figure 2: Differentially expressed genes (DEGs) between B. napus euploid and aneuploids. (A,B) DEGs among three comparisons (A) and 7370 common DEGs (B) between “Oro” vs. mono and “Oro” vs. were shown in Venn diagram.

Mentions: The values of FPKM of genes were calculated to assess the transcript expression profiling. To analyze the impact of the loss of the chromosome C2 on the global genes expressions in leaves, the CuffDiff 2 was performed to determine the DEGs (DEGs, q < 0.05) via evaluating the value of log2(fold_change) of genes. From the comparison Oro vs. monosomics, 14,874 DEGs including 7528 (50.61%) up-regulated genes and 7436 (49.39%) down-regulated genes were identified, but the up- and down-regulated ones were comparable (χ2 test, P > 0.05). In the comparison Oro vs. isomics, 10,431 DEGs included 5038 up-regulated genes (48.30%) and 5393 (51.70%) down-regulated (Table 1), with a significant bias to the latter (χ2 test, P < 0.05). The result that more DEGs were detected in the monomsomics than the isomics (14,874 vs. 10,431) when compared with the euploid was out of expectation, for the phenotype of the monosomics was similar to that of the euploid, but isomics was much more deviated than the monosomics from the euploid. However, only 579 DEGs (3.89%) in monosomics and 858 DEGs (8.22%) in isomics were directly contributed by the missing chromosome C2, which demonstrated the dominant trans-acting effects of the zero and one copy of this chromosome on the majority of DEGs in the two aneuploidies. The comparison between monosomics and isomics (mono vs. ) found 8907 DEGs (Table 1). From the Venn diagram of DEGs for two groups (Figure 2A), 7370 common DEGs were identified, occupying 70.65% of DEGs in Oro vs. mono and 49.55% in Oro vs. , respectively. To gain deeper insights into transcriptional regulation of the common DEGs, we excluded those common DEGs that presented different expression patterns (up- or down-regulated) in Oro vs. mono and Oro vs. , while, they were accounted for only 1.85% of the common DEGs. The number of co-upregulated genes was slightly higher than that of the co-downregulated ones (Figure 2B). These numerous and well conserved DEGs implied that the response to the absence of the chromosome C2 was strong in the monosomics and isomics.


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)

Differentially expressed genes (DEGs) between B. napus euploid and aneuploids. (A,B) DEGs among three comparisons (A) and 7370 common DEGs (B) between “Oro” vs. mono and “Oro” vs.  were shown in Venn diagram.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4585227&req=5

Figure 2: Differentially expressed genes (DEGs) between B. napus euploid and aneuploids. (A,B) DEGs among three comparisons (A) and 7370 common DEGs (B) between “Oro” vs. mono and “Oro” vs. were shown in Venn diagram.
Mentions: The values of FPKM of genes were calculated to assess the transcript expression profiling. To analyze the impact of the loss of the chromosome C2 on the global genes expressions in leaves, the CuffDiff 2 was performed to determine the DEGs (DEGs, q < 0.05) via evaluating the value of log2(fold_change) of genes. From the comparison Oro vs. monosomics, 14,874 DEGs including 7528 (50.61%) up-regulated genes and 7436 (49.39%) down-regulated genes were identified, but the up- and down-regulated ones were comparable (χ2 test, P > 0.05). In the comparison Oro vs. isomics, 10,431 DEGs included 5038 up-regulated genes (48.30%) and 5393 (51.70%) down-regulated (Table 1), with a significant bias to the latter (χ2 test, P < 0.05). The result that more DEGs were detected in the monomsomics than the isomics (14,874 vs. 10,431) when compared with the euploid was out of expectation, for the phenotype of the monosomics was similar to that of the euploid, but isomics was much more deviated than the monosomics from the euploid. However, only 579 DEGs (3.89%) in monosomics and 858 DEGs (8.22%) in isomics were directly contributed by the missing chromosome C2, which demonstrated the dominant trans-acting effects of the zero and one copy of this chromosome on the majority of DEGs in the two aneuploidies. The comparison between monosomics and isomics (mono vs. ) found 8907 DEGs (Table 1). From the Venn diagram of DEGs for two groups (Figure 2A), 7370 common DEGs were identified, occupying 70.65% of DEGs in Oro vs. mono and 49.55% in Oro vs. , respectively. To gain deeper insights into transcriptional regulation of the common DEGs, we excluded those common DEGs that presented different expression patterns (up- or down-regulated) in Oro vs. mono and Oro vs. , while, they were accounted for only 1.85% of the common DEGs. The number of co-upregulated genes was slightly higher than that of the co-downregulated ones (Figure 2B). These numerous and well conserved DEGs implied that the response to the absence of the chromosome C2 was strong in the monosomics and isomics.

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.