Limits...
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.


Gene expression evidences for the loss of chromosome C2. (A) Stack column of relative number of mapping reads along all chromosomes. (B) Box plot of Log2(FPKM) of the total expressed genes (FPKM > 0) and those along all chromosomes. *Represents the outlier values. 1% extremely high or low value of gene expression were defined as outlier values in this study.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4585227&req=5

Figure 1: Gene expression evidences for the loss of chromosome C2. (A) Stack column of relative number of mapping reads along all chromosomes. (B) Box plot of Log2(FPKM) of the total expressed genes (FPKM > 0) and those along all chromosomes. *Represents the outlier values. 1% extremely high or low value of gene expression were defined as outlier values in this study.

Mentions: Then we calculated the number of reads per gigabyte along all chromosomes of three different samples to determine the origin of the missing chromosome pair (Figure 1A). Notably, compared with euploid “Oro,” the fold changes of the chromosome C2 were sharply reduced to 0.476 and 0.091 in mono/isomics, respectively, while the values of remainder chromosomes varied from 0.79 to 1.40 with the average 1.01 in monosomics and from 0.82 to 1.45 with average 1.06 in isomics. Subsequently, box plots of all expressed genes (FPKM > 0, FPKM: Fragments per Kilobase of transcript per Million mapped reads) along all chromosomes of three samples were employed to validate the expression divergence, which demonstrated that little or nothing was expressed along C2 in isomics (Figure 1B). From the gene expression specific for each chromosome, it was concluded that the chromosome pair C2 in B. napus was missing in the 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)

Gene expression evidences for the loss of chromosome C2. (A) Stack column of relative number of mapping reads along all chromosomes. (B) Box plot of Log2(FPKM) of the total expressed genes (FPKM > 0) and those along all chromosomes. *Represents the outlier values. 1% extremely high or low value of gene expression were defined as outlier values in this study.
© Copyright Policy
Related In: Results  -  Collection

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

Figure 1: Gene expression evidences for the loss of chromosome C2. (A) Stack column of relative number of mapping reads along all chromosomes. (B) Box plot of Log2(FPKM) of the total expressed genes (FPKM > 0) and those along all chromosomes. *Represents the outlier values. 1% extremely high or low value of gene expression were defined as outlier values in this study.
Mentions: Then we calculated the number of reads per gigabyte along all chromosomes of three different samples to determine the origin of the missing chromosome pair (Figure 1A). Notably, compared with euploid “Oro,” the fold changes of the chromosome C2 were sharply reduced to 0.476 and 0.091 in mono/isomics, respectively, while the values of remainder chromosomes varied from 0.79 to 1.40 with the average 1.01 in monosomics and from 0.82 to 1.45 with average 1.06 in isomics. Subsequently, box plots of all expressed genes (FPKM > 0, FPKM: Fragments per Kilobase of transcript per Million mapped reads) along all chromosomes of three samples were employed to validate the expression divergence, which demonstrated that little or nothing was expressed along C2 in isomics (Figure 1B). From the gene expression specific for each chromosome, it was concluded that the chromosome pair C2 in B. napus was missing in the 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.