Heterosis and inbreeding depression of epigenetic Arabidopsis hybrids

Abstract

We have addressed the possible epigenetic contribution to heterosis using epigenetic inbred lines (epiRILs) with varying levels and distributions of DNA methylation. One line consistently displayed parent-of-origin heterosis for growth-related traits. Genome-wide transcription profiling followed by a candidate gene approach revealed 33 genes with altered regulation in crosses of this line that could contribute to the observed heterosis. Although none of the candidate genes could explain hybrid vigour, we detected intriguing, hybrid-specific transcriptional regulation of the RPP5 gene, encoding a growth suppressor. RPP5 displayed intermediate transcript levels in heterotic hybrids; surprisingly however, with global loss of fitness of their F2 progeny, we observed striking under-representation of the hybrid-like intermediate levels. Thus, in addition to genetic factors contributing to heterosis, our results strongly suggest that epigenetic diversity and epigenetic regulation of transcription play a role in hybrid vigour and inbreeding depression, and also in the absence of parental genetic diversity.

Integrated analysis of phenome, genome, and transcriptome of hybrid rice uncovered multiple heterosis-related loci for yield increase

“…Of note, genes involved in flowering time and circadian clock control were found to be linked to heterosis by mediating physiological and metabolic pathways (21)(22)(23)(24)(25). Recent studies further confirm the role of epigenetic regulation of transcription in hybrid vigor in Arabidopsis (25)(26)(27). Although Arabidopsis is not a staple crop, these advanced studies gave deep insight into the molecular mechanism of heterosis and highlighted the importance of integrating molecular approaches with phenomics methods for the study of crop heterosis.…”

Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids

“…Recently, epiHybrids have been generated by crossing a met1-derived epiRIL with Col-wt, and heterosis for biomass was reported for one of the epiHybrids (Dapp et al, 2015). The effect was observed only with the epiRIL as maternal parent, suggesting a strong maternal effect (Dapp et al, 2015).…”

“…The effect was observed only with the epiRIL as maternal parent, suggesting a strong maternal effect (Dapp et al, 2015). In this study, we created epiHybrids by crossing Col-wt as a maternal parent to 19 different near-isogenic but epigenetically divergent ddm1-derived epiRILs, allowing the assessment of epigenetic variation in identical maternal backgrounds.…”

“…There is growing evidence that epigenetic factors also play a role in heterosis (Groszmann et al, 2013;Springer, 2013;Dapp et al, 2015;Zhu et al, 2017). For example, it has been shown that altered epigenetic profiles at genes regulating circadian rhythm play an important role in heterotic Arabidopsis (Arabidopsis thaliana) hybrids (Ni et al, 2009).…”

“…To specifically address the contribution of parental epigenetic variation to F1 heterosis, we made use of the same epiRILs (Johannes et al, 2009;Reinders et al, 2009) to generate F1 epigenetic hybrids, hereafter called epiHybrids (Dapp et al, 2015). EpiRILs are near isogenic but display mosaic patterns in terms of their epigenomes.…”