Decipherment of transcriptional aneuploidy response patterns of monosomic alien addition lines (MAALs) in a restituted Brassica rapa
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ABSTRACT:
PROVIDER: PRJNA437247 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6813780_1.fastq.gz | Fastqsanger.gz | |||
| SRR6813780_2.fastq.gz | Fastqsanger.gz | |||
| SRR6813790_1.fastq.gz | Fastqsanger.gz | |||
| SRR6813790_2.fastq.gz | Fastqsanger.gz | |||
| SRR6813800_1.fastq.gz | Fastqsanger.gz |
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Project description:Herein, we performed high-throughput technology to detect gene expression alterations of a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) in comparison of parental restituted B. rapa (RBR). Both MAALs and RBR obtained previously are in the background of natural B. napus genotype “Oro”. We found that, compared to diploid RBR, all the MAALs showed various degree of dysregulated expression genes resulting from cis-effect and more prevailing trans-effect. And trans-effect on gene expression in MAALs likely was increasing with the homology between recipient A genome and additional C chromosome instead of genes content of extra C chromosome. Totally, 10 trans-effect dysregulated expression genes mainly involved in the function of transporter activity were observed in all pairwise comparisons. Strikingly, highly expressed gene was more prone to down-regulated and opposite situation was observed for low expressed genes in all pairwise comparisons, suggesting this is a common character in transcriptional patterns response to aneuploidy.
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Project description:Alien chromosome substitution lines are vital germplasm for breeding and genetic mapping. Previously, a whole set of nine Brassica rapa-oleracea monosonic alien addition lines (MAALs, C1-C9) was established in the background of natural B. napus genotype “Oro”, after the restituted B. rapa (RBR) for Oro was realized. Herein, a monosomic substitution line with one alien C1 chromosome (Cs1) in the RBR complement was selected in the progenies of MAAL C1 and RBR, by the PCR amplification of specific gene markers and fluorescence in situ hybridization. Cs1 exhibited the whole plant morphology similar to RBR except for the defective stamens without fertile pollen grains, but it produced some seeds and progeny plants carrying the C1 chromosome at high rate besides those without the alien chromosome after pollination by RBR. The viability of the substitution and its progeny for the restituted B. rapa diploid further elucidated the functional compensation between the chromosome pairs with high homoeology. To reveal the impact of such aneuploidy on genome-wide gene expression, the transcriptomes of MAAL C1, Cs1 and euploid RBR were analyzed. Compared to RBR, Cs1 had sharply reduced gene expression level across chromosome A1, demonstrating the loss of one copy of A1 chromosome. Both additional chromosome C1 in MAAL and substitutional chromosome C1 in Cs1 caused not only cis-effect but also prevalent trans-effect differentially expressed genes. A dominant gene dosage effects prevailed among low expressed genes across chromosome A1 in Cs1, and moreover, dosage effects for some genes potentially contributed to the phenotype deviations. Our results provided novel insights into the transcriptomic perturbation and gene dosage effects on phenotype in chromosome substitution related to one naturally evolved allopolyploid.
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Project description:Gossypium hirsutum/Gossypium australe alien addition line Raw sequence reads
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Project description:Establishing the whole set of aneuploids, for one naturally evolved allopolyploid species, provides a unique opportunity to elucidate the transcriptomic response of the constituent subgenomes to serial aneuploidy. Previously, the whole set of monosomic alien addition lines (MAALs, C1-C9) with each of the nine C subgenome chromosomes, added to the extracted A subgenome, was developed in the context of the allotetraploid Brassica napus donor "Oro," after the restitution of the ancestral B. rapa (RBR Oro) was realized. Herein, transcriptomic analysis using high-throughput technology was conducted to detect gene expression alterations in these MAALs and RBR. Compared to diploid RBR, the genes of all of the MAALs showed various degrees of dysregulated expressions that resulted from cis effects and more prevailing trans effects. In addition, the trans-effect on gene expression in MAALs increased with higher levels of homology between the recipient A subgenome and additional C subgenome chromosomes, instead of gene numbers of extra chromosomes. A total of 10 trans-effect dysregulated genes, among all pairwise comparisons, were mainly involved in the function of transporter activity. Furthermore, highly expressed genes were more prone to downregulation and vice-versa, suggesting a common trend for transcriptional pattern responses to aneuploidy. These results provided a comprehensive insight of the impact of gene expression of individual chromosomes, in one subgenome, on another intact subgenome for one allopolyploid with a long evolutionary history.
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