A combined transcriptome - miRNAome approach revealed that a kinesin gene is differentially targeted by a novel miRNA in an apomictic genotype of Eragrostis curvula.

Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass typically established in semi-arid regions, with good adaptability to dry conditions and sandy soils. This polymorphic complex includes both sexual and apomictic cytotypes, with different ploidy levels (2x-8x). Diploids are known to be sexual, while most polyploids are facultative apomicts, and full apomicts have also been reported. Plant breeding studies throughout the years have focused on achieving the introgression of apomixis into species of agricultural relevance, but, given the complexity of the trait, a deeper understanding of the molecular basis of regulatory mechanisms of apomixis is still required. Apomixis is thought to be associated with silencing or disruption of the sexual pathway, and studies have shown it is influenced by epigenetic mechanisms. In a previous study, we explored the role of miRNA-mRNA interactions using two contrasting E. curvula phenotypes. Here, the sexual OTA-S, the facultative Don Walter and the obligate apomictic Tanganyika cDNA and sRNA libraries were inquired, searching for miRNA discovery and miRNA expression regulation of genes related to the reproductive mode. This allowed for the characterization of seven miRNAs and the validation of their miRNA-target interactions. Interestingly, a kinesin gene was found to be repressed in the apomictic cultivar Tanganyika, targeted by a novel miRNA that was found to be overexpressed in this genotype, suggestive of an involvement in the reproductive mode expression. Our work provided additional evidence of the contribution of the epigenetic regulation of the apomictic pathway.

Characterization and discovery of miRNA and miRNA targets from apomictic and sexual genotypes of Eragrostis curvula.

BACKGROUND: Weeping lovegrass (Eragrostis curvula [Shrad.] Nees) is a perennial grass found in semi-arid regions that is well adapted for growth in sandy soils and drought conditions. E. curvula constitutes a polymorphic complex that includes cytotypes with different ploidy levels (from 2x to 8x), where most polyploids are facultative apomicts, although both sexual reproduction and full apomixis have been reported in this species. Apomixis is thought to be associated with silencing of the sexual pathway, which would involve epigenetic mechanisms. However, a correlation between small RNAs and apomixis has not yet been conclusively established. RESULTS: Aiming to contribute to the elucidation of their role in the expression of apomixis, we constructed small RNA libraries from sexual and apomictic E. curvula genotypes via Illumina technology, characterized the small RNA populations, and conducted differential expression analysis by comparing these small RNAs with the E. curvula reference transcriptome. We found that the expression of two genes is repressed in the sexual genotype, which is associated with specific microRNA expression. CONCLUSION: Our results support the hypothesis that in E. curvula the expression of apomixis leads to sexual repression.

De novo transcriptome sequencing and assembly from apomictic and sexual Eragrostis curvula genotypes.

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.