Abstract
A long-standing goal in plant breeding has been the ability to confer apomixis to agriculturally relevant species, which would require a deeper comprehension of the molecular basis of apomictic regulatory mechanisms. Eragrostis curvula (Schrad.) Nees is a perennial grass that includes both sexual and apomictic cytotypes. The availability of a reference transcriptome for this species would constitute a very important tool toward the identification of genes controlling key steps of the apomictic pathway. Here, we used Roche/454 sequencing technologies to generate reads from inflorescences of E. curvula apomictic and sexual genotypes that were de novo assembled into a reference transcriptome. Near 90% of the 49568 assembled isotigs showed sequence similarity to sequences deposited in the public databases. A gene ontology analysis categorized 27448 isotigs into at least one of the three main GO categories. We identified 11475 SSRs, and several of them were assayed in E curvula germoplasm using SSR-based primers, providing a valuable set of molecular markers that could allow direct allele selection. The differential contribution to each library of the spliced forms of several transcripts revealed the existence of several isotigs produced via alternative splicing of single genes. The reference transcriptome presented and validated in this work will be useful for the identification of a wide range of gene(s) related to agronomic traits of E. curvula, including those controlling key steps of the apomictic pathway in this species, allowing the extrapolation of the findings to other plant species.
Highlights
Apomixis, a suite of mechanisms leading to asexual seed production, is an example of a complex trait for which comparative transcriptomics is a useful approach
To investigate the apomictic/sexual pattern expression in E. curvula, total RNA was obtained from inflorescences including all the developmental reproductive stages from two genotypes with contrasting reproductive modes: the full apomictic cultivar ‘Tanganyika’, and the sexual cultivar ‘OTA-S’
Raw reads were deposited in the Sequence Reads Archive (SRA) database at NCBI as BioProject 358210 “Floral transcriptome of sexual and apomictic Eragrostis curvula” including Biosamples SAMN06167423 and SAMN06167424
Summary
A suite of mechanisms leading to asexual seed production, is an example of a complex trait for which comparative transcriptomics is a useful approach. Ar/contenidos/40/480#proyectos-grupos-deinvestigacion): PGI – TIR, CSU-142/14 and PGI 24/ A199 to V.E: Involved in study design, data collection and analysis, experiments development, decision to publish, preparation of the manuscript. Consejo Nacional de Investigaciones Cientıficas y Tecnicas (http://convocatorias.conicet.gov.ar/ proyectos-pip/): PIP 11220110100767 to V.E and 11220150100963 to I.G: Involved in study design, data collection and analysis, experiments development, decision to publish, preparation of the manuscript. Europa.eu/programmes/horizon2020/en/h2020section/marie-sklodowska-curie-actions) under the Marie Skłodowska-Curie Grant Agreement No 645674: Involved in study design, data collection and analysis, experiments development, decision to publish, preparation of the manuscript. By constructing expressed sequence tag (EST) libraries, our group has previously conducted transcriptome studies to compare near-isogenic diplosporous and sexual E. curvula genotypes [30]. This, in turn, might reveal the precise mechanisms of apomixis in this species, and allow us to extrapolate our findings to other plant species
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