Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture

Abstract

DNA methylation can contribute to the maintenance of genome integrity and regulation of gene expression. In most situations, DNA methylation patterns are inherited quite stably. However, changes in DNA methylation can occur at some loci as a result of tissue culture resulting in somaclonal variation. To investigate heritable epigenetic changes as a consequence of tissue culture, a sequence-capture bisulfite sequencing approach was implemented to monitor context-specific DNA methylation patterns in ∼15 Mb of the maize genome for a population of plants that had been regenerated from tissue culture. Plants that have been regenerated from tissue culture exhibit gains and losses of DNA methylation at a subset of genomic regions. There was evidence for a high rate of homozygous changes to DNA methylation levels that occur consistently in multiple independent tissue culture lines, suggesting that some loci are either targeted or hotspots for epigenetic variation. The consistent changes inherited following tissue culture include both gains and losses of DNA methylation and can affect CG, CHG, or both contexts within a region. Only a subset of the tissue culture changes observed in callus plants are observed in the primary regenerants, but the majority of DNA methylation changes present in primary regenerants are passed onto offspring. This study provides insights into the susceptibility of some loci and potential mechanisms that could contribute to altered DNA methylation and epigenetic state that occur during tissue culture in plant species.

Precise evaluation of tissue culture-induced variation during optimisation of in vitro regeneration regime in barley

“…Protocols have been developed for the regeneration of crop and model plant species that speed up the time of obtaining plants (Patial et al 2019), eliminate disease (García-Gonzáles et al 2010) and continually produce hundreds of thousands of regenerants. Although plant regeneration via tissue culture has many advantages, it triggers tissue culture-induced variation that is shared among regenerants (Bednarek et al 2007;Fiuk et al 2010;Machczyńska et al 2015) and subsequently transmitted to the progeny (Han et al 2018). The level of induced variation may significantly impact the homogeneity of regenerants (Coronel et al 2018), which may adversely affect evaluated materials.…”

“…Plants regenerated via tissue culture methods of androgenesis or somatic embryogenesis are not completely uniform at morphological (Al Hattab et al 2017), genetic (Hazubska-Przybył and Dering 2017) and epigenetic (Han et al 2018) levels. In vitro plant regeneration from anthers or isolated microspores in barley (Bednarek et al 2007), triticale (Machczyńska et al 2015) and many other species (Fiuk et al 2010) induce numerous changes that affect genome sequences and DNA methylation patterns.…”

Regeneration of Solanum tuberosum Plants from Protoplasts Induces Widespread Genome Instability

“…Somaclonal variation, i.e. genotypic and phenotypic differences from the source plant (Landsmann and Uhrig, 1985;Lee and Phillips, 1988;Bao et al, 1996), has been associated with epigenetic changes (Stroud et al, 2013;Ong-Abdullah et al, 2015;Han et al, 2018), single nucleotide mutations (Miyao et al, 2012), chromosomal structure changes, and aneuploidy (Lee and Phillips, 1988). Notwithstanding the high likelihood of large phenotypic impact, chromosomal mutation, such as aneuploidy and structural changes, remain poorly documented.…”

Widespread genome instability inSolanum tuberosumplants regenerated from protoplasts

“…Collapse of genome maintenance in the defective micronuclear environment is thought to result in chromosome-specific shattering (Crasta et al, 2012;Zhang et al, 2015;Ly et al, 2017) . The frequent and often stereotypical chromosomal breaks could result from epigenetic upheaval and transposon activation, which have been well documented (Hirochika et al, 1996;Stroud et al, 2013;Ong-Abdullah et al, 2015;Han et al, 2018) . Whatever the causes, confirmation of this syndrome in other species will affect the prospects for protoplast utilization.…”

“…Somaclonal variation, i.e. genotypic and phenotypic differences from the source plant (Landsmann and Uhrig, 1985;Lee and Phillips, 1988;Bao et al, 1996) , has been associated to epigenetic changes (Stroud et al, 2013;Ong-Abdullah et al, 2015;Han et al, 2018) , single nucleotide mutations (Miyao et al, 2012) , structural changes, and aneuploidy (Lee and Phillips, 1988) . Notwithstanding the high likelihood of large phenotypic impact, chromosomal alterations remain poorly documented.…”