Weighted Gene Co-Expression Network Analysis in Chestnut Allows for the Identification of Putative Candidate Genes Linked to Adventitious Rooting

Vegetative propagation of recalcitrant woody species is a challenging task that limits biotechnological exploitation of economically relevant trees. In the case of chestnut, a severe decline in its ability to form adventitious roots is imposed during maturation. In previous reports, both juvenile-like and mature microshoots were subject to different hormonal treatments to gain deeper insights into the molecular processes driving the formation of adventitious roots while allowing us to increase our understanding of failed treatments. In the present work, RNAseq libraries from those treatments were used to develop a Weighted Gene Co-expression Network Analysis in order to identify gene modules correlated with the formation of adventitious roots. Hub genes within relevant modules were then used for promoter region analysis to identify transcription factor families that may play a role in the process by controlling the expression of the genes within those modules. bZIP and bHLH families in juvenile-like microshoots and WRKY and SBP families in mature microshoots were found to be particularly relevant for this developmental process. Specific transcription factors, like CsbHLH30 and CsbZIP44, seem to play key roles in the rooting process, while the activity of CsWRKY75 is putatively related to recalcitrant responses in mature shoots.