Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Cell-type specific transcriptome analysis to study germline development and reproduction in apomictic Boechera gunnisoniana- ATH1 arrays

ABSTRACT: Apomixis differs from sexual reproduction only in three major aspects: While the sexual megaspore mother cell undergoes meiosis, the apomictic initial cell omits or aborts meiosis (apomeiosis); the unreduced egg cell of apomicts forms an embryo without fertilization (parthenogenesis), and formation of functional endosperm requires specific developmental adaptations. Currently, our knowledge about the gene regulatory programs underlying apomixis is scarce. We used the apomict Boechera gunnisoniana, a close relative of Arabidopsis thaliana, to investigate the transcriptional basis underlying apomeiosis and parthenogenesis. Here, we present the first comprehensive reference transcriptome for reproductive development in an apomictic species. To compare sexual and apomictic development at the cellular level, we then used a combination of laser-assisted microdissection with microarray and RNA-Seq analysis. Our study yields important new insights into the transcriptional basis underlying apomixis. Cell-type specific transcriptome profiles were generated from the apomictic initial cell (2 biological replicates), surrounding sporophytic tissues (sporo_nucellus; 2 biological replicates), egg cell, central cell and synergid cells (one sample each) from the triploid pseudogamous obligate apomict Boechera gunnisoniana by heterologous hybridization on the Affymetrix ATH1 arrays.

ORGANISM(S): Boechera gunnisoniana

SUBMITTER: Marc Schmid

PROVIDER: E-GEOD-51996 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Some flowering plants exhibit a phenomenon called apomixis, defined as the ability to produce seeds asexually and with the same genetic constitution as the mother plant. The existence of a genetic basis for apomixis is evident, but the molecular mechanisms that underlie it remain unclear. The search for M-bM-^@M-^\the master apomixis geneM-bM-^@M-^] had led to the isolation of diverse candidate transcripts. However, neither of them could be clearly confirmed. The techniques employed so far have been based on differential-display PCR and have not allowed detecting transcripts with low levels of expression or low differential expression. For all these reasons, in this study we employed cDNA microarrays combined with subtractive libraries in order to isolate transcripts with differential expression between sexual and apomictic plants of the genus Brachiaria. We used ovaries corresponding to two developmental stages: i) stage I, appearing of initial aposporic cell in apomictic plants; and ii) stage II, degeneration of meiotic-derived tetrad and establishment of diploid embryo sac in apomictic plants. Subtractive libraries revealed some differential bands, which were spotted over glass slides together with clones from non-subtractive libraries, and with amplicons associated to apomixis obtained using degenerate PCR. A total of 26 distinct sequences showed differential expression, only 1 of them was overexpressed in apomictic plants, and the majority was related to stage I. Bioinformatic analyses confirmed meiosis-related roles for some of the genes, a result consistent with a higher level of expression in sexual ovaries. Nevertheless, for some sequences a clear function could not be assigned. Some of them appear to be related to the polyploid stage of apomictic plants, in one hand, and to putative transcription factors, on the other hand. The implications of these results under a molecular model of apomeiosis are discussed. We employed RNA from ovaries from sexual plants as a control, and RNA from ovaries of apomictic plants as experiment. Four different sexual and four apomictic genotypes were employed. A sexual genotype was compared against a given apomictic genotype, for a total of 4 comparisions. Each comparision were performed ifor two developmental stages, for a total of eight comparisions. In each comparision, a dye swap was done.

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Cell-type specific transcriptome analysis to study germline development and reproduction in apomictic Boechera gunnisoniana- ATH1 arrays

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