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

Abstract

BackgroundWeeping 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.ResultsAiming 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.ConclusionOur results support the hypothesis that in E. curvula the expression of apomixis leads to sexual repression.

Differential Epigenetic Marks Are Associated with Apospory Expressivity in Diploid Hybrids of Paspalum rufum

“…Otherwise, a recent work carried out in Cenchrus ciliaris showed that transcripts of Gy163, an LTR retrotransposon, are more expressed in the reproductive tissues of apomictic than of sexual plants, and this was correlated with reduced methylation level [98]. A recent study about the role of miRNA-mRNA interactions in apomixis development in E. curvula found that a transposon sequence was specifically repressed in the sexual genotype, most likely due to interactions with miRNAs [99]. Therefore, as differential expression of TE-related sequences could be assigned to differential methylation and epigenetic regulations, which would influence apospory expressivity, further specific analysis of DMCs related to LTR retrotransposons deserve to be performed in future works.…”

Controlling Apomixis: Shared Features and Distinct Characteristics of Gene Regulation

“…To gain insights into the possible involvement of small RNAs in apomixis control, their activity has been studied in different natural apomicts including Eragostris curvula [136], Paspalum notatum [29,137], Hieracium subgenus Pilosella [119], and Boechera [138,139]. Differential representation of small RNA reads in Paspalum notatum points towards their involvement in regulation of meiosis, cell cycle control, transcriptional regulation and hormonal signaling [117].…”

Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions

“…Eragrostis curvula (weeping lovegrass), an African grass with cytotypes of different ploidy levels (e.g., 2x–8x) and displaying obligate and facultative apomixis and sexual reproduction [ 46 ], has become a model for the analysis of apomixis mechanisms, due to its particular diplosporous development (meiotic diplospory maintaining the same embryo: endosperm ploidy ratio as in sexual seeds). In recent years, the reproductive mode of this grass was studied extensively, providing information about the cytoembryological aspects of its apomictic–sexual development [ 47 ], differentially expressed (DE) transcripts [ 48 , 49 , 50 , 51 ], epigenetic aspects of apomictic regulation [ 52 , 53 ], mapping of the apomixis locus [ 54 ] and a high quality genome assembly [ 55 ]. Our group also demonstrated that under different internal and external stressful situations, including a change in ploidy, water stress, in vitro culture and intraspecific hybridization, the number of sexual embryo sacs increased in facultative apomictic plants of this grass [ 40 , 56 ].…”

“…This increase in the level of sexuality was associated with genetic and epigenetic changes, like methylation and molecular markers [ 40 , 56 ]. Evidence of epigenetic mechanisms controlling apomixis was also observed since differentially expressed patterns of RNA-directed DNA methylation (RdDM) genes [ 52 ] and microRNA between sexual and apomictic genotypes [ 53 ] were recently reported in this grass.…”