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

Abstract

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.

Asexual reproduction through seeds: the complex case of diplosporous apomixis

“…For instance, EcAGO104 and EcDMT102, genes implicated in the RNA-dependent DNA methylation, were found to be differentially expressed in apomictic vs sexual genotypes, even though functional studies on mutants have not been carried out yet (Selva et al, 2017). Moreover, the latest findings support the idea of a micro-RNA involvement in the regulation of apomixis in E. curvula (Garbus et al, 2019;Pasten et al, 2022).…”

From tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula

“…These three processes are defined as apomeiosis, parthenogenesis, and pseudogamy, respectively. Even though many studies of the group at transcriptomic, genomic, and epigenomic levels were taken and several advances were made to elucidate the apomixis mechanisms in E. curvula , the key molecular components regulating this pathway have not yet been resolved ( Cervigni et al., 2008a ; Cervigni et al., 2008b ; Garbus et al., 2017 ; Selva et al., 2017 ; Carballo et al., 2019 ; Garbus et al., 2019 ; Zappacosta et al., 2019 ; Selva et al., 2020 ; Carballo et al., 2021a ; Pasten et al., 2022 ).…”

Differentially methylated genes involved in reproduction and ploidy levels in recent diploidized and tetraploidized Eragrostis curvula genotypes

“…Using genomics and transcriptomics approaches over sexual and apomictic genotypes, different candidate genes and regulatory pathways were found to be differentially enriched (Garbus et al 2017 ; Carballo et al 2019 , 2023 ; Zappacosta et al 2019 ; Selva et al 2020 ). In addition, analyses of methylation patterns and microRNA representation in different genotypes shed light on the epigenetic regulation of apomixis (Rodrigo et al 2017 ; Garbus et al 2019 ; Carballo et al 2021a ; Pasten et al 2022 ). Methylation studies using the MSAP technique were used in tetraploidized and diploidized lines, showing lower methylation levels in the diploid genotypes and methylation recovery after tetraploidization (Ochogavia et al 2009 ).…”