On epigenetics and epistasis: hybrids and their non-additive interactions

Abstract

EMBO J 31 2, 257–266 (2012); published online December 16 2011

Hybrid seeds have been a key component of greatly increasing the yield of many important crops, foremost of maize. If the parents are properly chosen, non-additive interactions between diverged genomes can lead to strongly superior performance of the F1 progeny, known as heterosis. While many different explanations have been advanced, a consensus for the causes of genome-wide positive epistasis in hybrids has not emerged. In this issue of The EMBO Journal, Shivaprasad and colleagues describe a new mechanism that can account for heterosis often being a genome-wide phenomenon. These authors show that small RNA (sRNA) loci of tomato can exhibit transgressive activity, which can in turn lead to epigenetic and gene expression changes within hybrid progeny. This is particularly exciting because many sRNAs are produced from non-coding regions or transposable elements (TEs), which diverge more quickly than protein-coding genes and thus provide more opportunity for unexpected genetic interactions.

Figure 1

(A–C) Three examples of transgressive effects of sRNAs (Shivaprasad et al, 2012). (A) Induction of miR395 increases salt tolerance. (B) Induction of siRNAs at the H06 locus induces local DNA methylation, leading to transcriptional gene silencing. (C) Induction of siRNAs at the PAL locus leads to post-transcriptional gene silencing. (D) Scenario for transgressive sRNA expression, through interaction between allelic or non-allelic loci that share only limited sequence identity (blue line). Small RNAs (small arrows) acting in trans. Specific features of the trans locus lead to spreading of small RNAs through a phenomenon called transitivity, and gradual amplification of sRNA production and DNA methylation over several generations.