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Cms4:19 and at chr3-Comparing nuclear gene expression in two CMS-systems using microarray technology

ABSTRACT: ra05-11_cmsrapeseed - cms4:19 and at chr3 - -To understand how/if fertility and the mitochondrial background are interlinked. -To understand how the mitochondrial background influences the nuclear gene expression. -Compare and describe the total nuclear gene expression of CMS vs. fertile and CMS vs. Restored. -Describe and analyse genes that differ in expression (of special interest are genes that differs in both comparisons). -Group genes e.g. floral genes, highly expressed genes, transcription factors, nuclear encoded genes targeted for the mitochondrion. -Comparing two CMS-systems to elucidate differences and similarities between them. - Flower buds from four different B. napus lines (fertile cv Hanna, CMS-line 4:19, restored line 46, cv Hanna with the additon of A. thaliana chr 3) at two developmental stages (stages 0-5 and stage 8). Keywords: wt vs mutant comparison

ORGANISM(S): Arabidopsis thaliana Brassica napus

PROVIDER: GSE8819 | GEO | 2008/08/01

SECONDARY ACCESSION(S): PRJNA102139

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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Cms4:19 and at chr3-Comparing nuclear gene expression in two CMS-systems using microarray technology

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