Abstract
Small RNAs (sRNAs) are epigenetic regulators of eukaryotic genes and transposable elements (TEs). Diverse sRNA expression patterns exist within a species, but how this diversity arises is not well understood. To provide a window into the dynamics of maize sRNA patterning, sRNA and mRNA transcriptomes were examined in two related Zea mays recombinant inbred lines (RILs) and their inbred parents. Analysis of these RILs revealed that most clusters of sRNA expression retained the parental sRNA expression level. However, expression states that differ from the parental allele were also observed, predominantly reflecting decreases in sRNA expression. When RIL sRNA expression differed from the parental allele, the new state was frequently similar between the two RILs, and similar to the expression state found at the allele in the other parent. Novel sRNA expression patterns, distinct from those of either parent, were rare. Additionally, examination of sRNA expression over TEs revealed one TE family, Gyma, which showed consistent enrichment for RIL sRNA expression differences compared to those found in parental alleles. These findings provide insights into how sRNA silencing might evolve over generations and suggest that further investigation into the molecular nature of sRNA trans regulators is warranted.
Highlights
Small RNAs are diverse gene regulators that can repress complementary loci. This repression occurs through epigenetic transcriptional gene silencing (TGS) via RNA-directed DNA methylation (RdDM) or post-transcriptional gene silencing (PTGS), which are typically mediated by 24 nucleotide and 21-22nt sRNA, respectively (Reviewed in Borges and Martienssen, 2015)
Transcriptomic analysis showed that sRNA expression differed between two recombinant inbred lines (RILs) and their inbred parents (Figure 1). sRNA and mRNA root expression data from maize inbred parents AC7643 and AC7729/TZSRW, and two derived RILs, RIL64 and RIL208, were retrieved from the Sequence Read
RIL sRNA expression is prevalent over low copy number transposable elements (TEs) with other-parental sRNA expression preferentially targeting Gyma elements
Summary
Small RNAs (sRNAs) are diverse gene regulators that can repress complementary loci. In plants, this repression occurs through epigenetic transcriptional gene silencing (TGS) via RNA-directed DNA methylation (RdDM) or post-transcriptional gene silencing (PTGS), which are typically mediated by 24 nucleotide (nt) and 21-22nt sRNA, respectively (Reviewed in Borges and Martienssen, 2015). Much progress has been made in understanding the molecular mechanisms that elicit sRNA expression changes in genetically homogenous lab strains (Cuerda-Gil and Slotkin 2016; Hung and Slotkin 2021). Extrapolating these molecular mechanisms to diverse plant populations, it appears likely that changes in both genetic and epigenetic factors drive inheritance in sRNA expression patterns. How these mechanisms orchestrate the evolution of sRNA expression diversity in plant populations remains poorly understood
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
