Transcriptome-wide analysis of epitranscriptome and translational efficiency associated with heterosis in maize

Abstract

Heterosis has been extensively utilized to increase productivity in crop, yet underlying molecular mechanisms remain largely elusive. Here, we generated transcriptome-wide profiles of mRNA abundance, m 6A methylation, and translational efficiency from the maize F1 hybrid B73×Mo17 and its two parental lines to ascertain contributions of each regulatory layer to heterosis at the seedling stage.We documented that although the global abundance and distribution configuration of m 6A maintained unchanged, a greater number of genes have gained m 6A modification in hybrid. m 6A modification and translational efficiency exhibited superior variations between hybrid and parents as compared with mRNA abundance. In hybrid, the vast majority of genes with m 6A modification exhibited non-additive expression pattern, the percentage of which was exceedingly higher than that of differential genes at mRNA abundance and translational efficiency. Non-additive genes involved in different biological processes were hierarchically coordinated by discrete combinations of three regulatory layers. These findings suggest that transcriptional and post-transcriptional regulations on gene expression adopt divergent approaches to participate in the formation of heterosis in hybrid. Overall, the integrated multi-omics analysis provides a valuable portfolio for interpreting transcriptional and post-transcriptional regulation on gene expression in maize hybrid, and paves new avenues for exploring molecular mechanisms underlying hybrid vigor.

Transcriptome-Wide Analysis of RNA m6A Methylation and Gene Expression Changes Among Two Arabidopsis Ecotypes and Their Reciprocal Hybrids

“…In summary, these results implied a more general conservation pattern of m 6 A methylation in plants, which could be related to the fundamental role of m 6 A methylation in plant development (Zhong et al, 2008 ; Shen et al, 2016 ; Anderson et al, 2018 ). Nevertheless, a recently published study showed that there are much more genes with differentially m 6 A level or non-additively m 6 A variation in maize hybrid (B73 × Mo17) compared with the parents (Luo et al, 2021 ), implying that the pattern of m 6 A reprogramming in hybrid is related to species or parent lines with different degree of variation.…”

Advances in Research on the Mechanism of Heterosis in Plants

“…Gene expression in hybrids is affected by cis -acting elements, trans -acting factors, and their interaction ( Birchler and Veitia, 2010 ). Cis -regulatory elements are short DNA sequences containing trans-factor-specific binding sites that are used to control the expression of their associated genes ( Bao et al, 2019 ; Luo et al, 2021 ). It can lead to changes in gene expression, and in hybrids, different regulatory factors and transcriptional networks recombine ( Birchler et al, 2003 ; Riddle and Birchler, 2003 ; Zhang et al, 2008 ; Bougas et al, 2010 ).…”

Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling biomass heterosis in Brassica napus

“…The rapid development of sequencing technology has made it possible to explore heterosis at the molecular level [ 5 ], and it has been used in many species, such as Arabidopsis [ 6 – 8 ], rice [ 9 – 11 ], maize [ 12 , 13 ], and wheat [ 14 , 15 ]. These studies combined morphological and omics techniques to analyze the changes in the vegetative and reproductive growth phases of hybrids relative to their parents.…”