DNA methylation and small interference RNAs participate in the regulation of MADS-box genes involved in dormancy in sweet cherry (Prunus avium L.)

Abstract

Epigenetic modifications can yield information about connections between genotype, phenotype variation and environmental conditions. Bud dormancy release in temperate perennial fruit trees depends on internal and environmental signals such as cold accumulation and photoperiod. Previous investigations have noted the participation of epigenetic mechanisms in the control of this physiological process. We examined whether epigenetic modifications were modulated in MADS-box genes, potential candidates for the regulation of bud dormancy and flowering in sweet cherry (Prunus avium L.). We identified and cloned two MADS-box genes homologous to the already-characterized dormancy regulators DORMANCY-ASSOCIATED MADS-box (DAM3 and DAM5) from Prunus persica (L.) Batsch. Bisulfite sequencing of the identified genes (PavMADS1 and PavMADS2), Methylated DNA Immunoprecipitation and small RNA deep sequencing were performed to analyze the presence of DNA methylations that could be guided by non-coding RNAs in the floral buds exposed to differential chilling hours. The results obtained reveal an increase in the level of DNA methylation and abundance of matching small interference RNAs (siRNAs) in the promoter of PavMADS1 when the chilling requirement is complete. For the first intron and 5' UTR of PavMADS1, de novo DNA methylation could be associated with the increase in the abundance of 24-nt siRNA matching the promoter area. Also, in the second large intron of PavMADS1, maintenance DNA methylation in all cytosine contexts is associated with the presence of homologous siRNAs in that zone. For PavMADS2, only maintenance methylation was present in the CG context, and no matching siRNAs were detected. Silencing of PavMADS1 and PavMADS2 coincided with an increase in Flowering Locus T expression during dormancy. In conclusion, DNA methylations and siRNAs appear to be involved in the silencing of PavMADS1 during cold accumulation and dormancy release in sweet cherry.

Modulation of Dormancy and Growth Responses in Reproductive Buds of Temperate Trees

“…In effect, global and specific levels of genomic DNA cytosine methylation change during bud development in chestnut ( Santamaría et al, 2009 ) and apple ( Kumar et al, 2016 ), and recent functional studies reveal the important role of DNA methylation enzymes in seasonal dormancy regulation: overexpression of a chestnut DEMETER-like ( CsDML ) DNA demethylase accelerates photoperiodic-dependent bud formation ( Conde et al, 2017b ), whereas down-regulation of poplar DEMETER-like ( PtaDML10 ) delays bud break ( Conde et al, 2017a ) in poplar. In sweet cherry ( Prunus avium ), specific DNA methylations and siRNAs are associated with silencing of the DAM -like gene PavMADS1 during dormancy release ( Rothkegel et al, 2017 ). Modification of transcript stability by microRNA action has been also hypothesized to participate in bud dormancy regulation.…”

Structure and Expression of Bud Dormancy-Associated MADS-Box Genes (DAM) in European Plum

“…Several studies have been focused on a group of genes, called DORMANCY-ASSOCIATED MADS-BOX (DAM) and other orthologs of SHORT VEGETATIVE PHASE (SVP) genes, which recently have emerged as potential regulators of dormancy in several species such as almond (Prunus dulcis; Prudencio et al, 2018), apple (Malus x domestica; Falavigna et al, 2014;Wu et al, 2017), apricot (Prunus armeniaca; Balogh et al, 2019), Chinese cherry (Prunus pseudocerasus; Zhu et al, 2015), hybrid aspen (Populus tremula x tremuloides; Singh et al, 2018), Japanese apricot (Prunus mume; Sasaki et al, 2011), kiwifruit (Actinidia chinensis; Wu et al, 2019;Actinidia deliciosa;Wu et al, 2012), leafy spurge (Euphorbia esula; Horvath et al, 2008), pear (Pyrus pyrifolia; Saito et al, 2015), and sweet cherry (Prunus avium; Rothkegel et al, 2017). These genes were firstly identified in an evergrowing mutant (evg) of peach (Prunus persica) that shows a non-dormant phenotype, maintaining apical growth and persistent leaves in response to dormancy inducing conditions (Bielenberg et al, 2004).…”

Evolution of SHORT VEGETATIVE PHASE (SVP) genes in Rosaceae: Implications of lineage‐specific gene duplication events and function diversifications with respect to their roles in processes other than bud dormancy

“…In Mei (Prunus mume), all PmDAM genes (PmDAM1-PmDAM6) were strongly repressed during prolonged cold exposure in winter and maintained at low levels till the release of endodormancy, and overexpression of PmDAM6 in poplar (Populus tremula × Populus tremuloides) led to growth cessation and terminal bud set and bud endodormancy, even under favorable conditions (Sasaki et al, 2011). Interestingly, similar to the functional profiles of FLC genes and their homologs in Brassicaceae, some of the DAM genes, such as DAM5 and DAM6 in peach, could be suppressed by chilling temperatures and are inversely correlated with bud break rate (Jimenez et al, 2010), and those processes are also regulated by histone modifications and DNA methylation (de la Fuente, Conesa, Lloret, Badenes, & Rios, 2015;Leida et al, 2012;Rothkegel et al, 2017;Saito et al, 2015), as well as day length (Li, Reighard, Abbott, & Bielenberg, 2009) and plant hormones (Falavigna et al, 2019;Kurokura et al, 2013;Rinne et al, 2011;Tuan et al, 2017;Tylewicz et al, 2018), similar to FLC in Brassicaceae (Rios, Leida, Conejero, & Badenes, 2014). These results suggested that the biological functions of SVP genes, rather than FLC genes, might have been evolutionarily enhanced for bud dormancy in Rosaceae (Falavigna et al, 2019. Bud dormancy is an adaptive process that allows perennial plants to survive the winter conditions of temperate climates (Falavigna et al, 2019;Paul, Rinne, & van der Schoot, 2014).…”