Unraveling the role of MADS transcription factor complexes in apple tree dormancy using sequential DAP-seq

Abstract

Background: The effect of global warming on dormancy and flowering patterns of crop trees threatens world-wide fruit production and food security. In Rosaceous tree species, it is believed that a group of genes encoding MADS transcription factors (TFs) controls temperature-mediated dormancy cycle. These genes are similar to SHORT VEGETATIVE PHASE (SVP) from Arabidopsis thaliana and referred as DORMANCY-ASSOCIATED MADS-BOX (DAM) genes. Results: By making use of apple tree (Malus x domestica) as a model for Rosaceous species, we have investigated the function of MADS TFs during the dormancy cycle. We found that MdDAM and other dormancy related MADS TFs form multimeric complexes with MdSVPa, and that MdSVPa is essential for the transcriptional complex activity. Then, for the first time in non-model plant species, we performed sequential DNA Affinity Purification sequencing (seq-DAP-seq) to define the genome-wide binding sites of these MADS TF complexes. Target genes associated with the binding sites were identified by combining seq-DAP-seq data with transcriptomics datasets obtained by the inducible glucocorticoid receptor expression system, and reanalyzing preexisting data related to dormancy cycle in apple trees. Conclusion: We have determined a gene regulatory network formed by MdSVPa-containing complexes that regulate the dormancy cycle in apple trees in response to environmental cues. Key genes identified with our genomic approach and the elucidated regulatory relationships provide leads for breeding fruit trees better adapted to changing climate conditions. Moreover, we provide novel molecular evidence on the evolutionary functional segregation between DAM and SVP proteins in the Rosaceae family.

Bud endodormancy – a familiar but still unknown key adaptive trait in extratropical woody plants

“…In recent years, considerable progress has been made in identifying genetic components that regulate dormancy, its release, and bud burst (Figure 2; Singh et al, 2017;Singh et al, 2018;Tylewicz et al, 2018;Azeez et al, 2021;Falavigna et al, 2021;Yang et al, 2021;Yang et al, 2023). By using model trees such as Populus, apple, and pear, time-course analysis of global gene expression has been able to identify patterns of genes whose expression in the buds changes during the transition from dormancy to dormancy release and subsequent bud burst (Vimont et al, 2020).…”

“…However, on the basis of functional data using gain and loss of function approaches, the role of plant hormone ABA in dormancy regulation is now well established, with ABA response being essential for short-day-induced bud dormancy (Tylewicz et al, 2018;Yang et al, 2023). Moreover, transcription factors acting downstream of ABA, e.g., tree orthologs of SVP (SHORT VEGETATIVE PHASE), a floral repressor, have been implicated in these processes in several species (Singh et al, 2018;Falavigna et al, 2021). Downstream of ABA-SVP, considerable attention has been paid to the dynamic control of plasmodesmata (PDs), the intercellular channels, by hormonal and environmental factors.…”