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Decipherment of transcriptional aneuploidy response patterns of monosomic alien addition lines (MAALs) in a restituted Brassica rapa

ABSTRACT: 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.

ORGANISM(S): Brassica rapa

PROVIDER: GSE111510 | GEO | 2019/03/06

REPOSITORIES: GEO

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Project description:Background: The fertile and sterile plants are derived from the self-pollinated offspring of the F1 hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus, which possess the identical cytoplasmic genetic material arising from Nsa CMS line. As far as the nuclear genetic background is concerned, both fertile and sterile plants have the complete set of chromosomes from Brassica napus, except one or two members of the added Sinapis arvensis chromosome pair in the fertile plant. To elucidate gene expression and regulation caused by the A and C subgenomes, the alien chromosome and cytoplasm from S. arvensis during the development of young floral buds, we performed genome-widely high-throughput transcriptomic sequencing between young floral buds of sterile and fertile plants. Results: In this study, equal amount of RNA taken from young floral buds of sterile and fertile plants were sequenced using Illumina/Solexa platform. A total of 4,415,866 and 4,244,140 raw tags were obtained in sterile plant (Ste) and fertile plant (Fer) libraries, respectively. After filtering out low quality data, a total of 2,760,574 and 2,714,441 clean tags remained from the two libraries, from which 242,163 (Ste) and 253,507 (Fer) distinct tags were obtained. To identify the genes corresponding to the distinct tags in each library, all distinct sequencing tags were annotated using all possible CATG+17-nt sequences of the genome and transcriptome of Brassica rapa and those of Brassica oleracea as the reference sequences, respectively. Many genes showed substantial differences in expression between the two libraries. In total, there were 3231 genes of B. rapa and 3371 genes of B. oleracea which were detected with significant differential expression levels. GO and pathway-based analyses were performed to determine and further understand the biological functions of differentially expressed genes (DEGs). In addition, there were 1089 specially expressed unknown tags in Fer, which were neither mapped to B. oleracea nor mapped to B. rapa, and these unique tags were presumed to arise basically from the added alien chromosome of S. arvensis. Fifteen genes were randomly selected and confirmed their expression levels by quantitative RT-PCR, fourteen of the fifteen genes showed expression patterns consistent with the digital gene expression (DGE) data. Conclusions: A number of genes were differentially expressed between the young floral buds of sterile and fertile plants. Some of these genes may be candidates for future research on CMS in Nsa line, fertility restoration and improved agronomic traits in NR1 line. Further study of the unknown tags which were specially expressed in Fer will help to dig those genes with desirable agronomic traits from wild species. mRNA profiles of fertile buds (Fer) and sterile buds (Ste) were generated by deep sequencing.

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Decipherment of transcriptional aneuploidy response patterns of monosomic alien addition lines (MAALs) in a restituted Brassica rapa

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