Understanding and utilizing both genetic and epigenetic sources of crop variation is necessary to keep up with world demand of food production in the face of climate change. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. DNA methylation changes may affect the expression of genes and thus can also contribute to trait variations that can be inherited to the next generations. Such stably inherited epigenetic alleles are known as Epialleles4.

In the model plant Arabidopsis thaliana, the methylation changes at single cytosine positions can occur spontaneously across generations. Nevertheless, these spontaneous epimutations rarely form an epiallele, since they occur randomly and a majority of the methylation patterns in the A. thaliana genome are inherited faithfully during sexual reproduction. Besides naturally occurring in the population, epialleles can also be artificially induced by a wide range of experimental stimuli and treatments. They might arise from biotic or abiotic stress, chemical treatments, clonal propagations and epiRILs3.

The novel epialleles identified in progeny plants regenerated from tissue culture in maize showed partial to complete loss of p1 function indicated by pink or colourless cob glumes. DNA gel-blot analysis and genomic bisulfite sequencing revealed that silencing of the epialleles is due to hypermethylation of a region in the wild type P1-wr thereby confirming the involvement of epigenetic modifications2.

Methylation patterns at specific loci in the genome may either directly or indirectly influence an altered gene transcription. It can have a different mode of action depending on its genomic position. At promoters, methylation can repress transcription by recruiting repressive histone marks and inhibiting TF binding. Within gene bodies, it may affect alternative splicing. While, at distal regions, it can affect transcription by regulating the formation of chromatin loops. The availability of molecular tools for engineering targeted methylation changes and the creation of new epialleles is a game-changer for plant epigenetics3.

The two epialleles of the maize (Zea mays) b1 gene, B-I and B’ are tissue-specifically regulated and involved in paramutation. Chromosome conformation capture(3C) analysis revealed that the hepta-repeats physically interact with the TSS region and the involvement of chromatin looping in the transcriptional regulation of the two epialleles1. Overall, identifying the key developmental epialleles, their heritability, and their modes of action on transcription are instrumental for engineering plants with improved fitness, yields, and tolerance to stresses.

References

1 LOUWERS, M., BADER, R., HARING, M., VAN DRIEL, R., DE LAAT, W. AND STAM, M., 2009, Tissue and expression level-specific chromatin looping at maize b1 epialleles. Plant Cell, 21(3): 832–842.

2 RHEE, Y., SEKHON, R. S., CHOPRA, S. AND KAEPPLER, S., 2010, Tissue culture-induced novel epialleles of a Myb transcription factor encoded by pericarp color1 in maize. Genetics, 186(3): 843–855.

3 SRIKANT, T. AND TRI WIBOWO, A., 2021. The underlying nature of epigenetic variation: Origin, establishment and regulatory function of plant epialleles. Int. J. Mol. Sci., 22(16).

4 TONOSAKI, K., FUJIMOTO, R., DENNIS, E. S., RABOY, V. AND OSABE, K., 2022, Will epigenetics bea key player in crop breeding? Front. Plant Sci., 13.