Identification of genes involved in almond scion tree architecture influenced by rootstock genotype using transcriptome analysis

The emergence of almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive and semi-intensive cropping systems has created a necessity for new almond cultivars with vigor and shape adapted to these new circumstances. Hence, it is important to unravel which mechanisms are behind the regulation of the tree threedimensional structure, or tree architecture, and what factors may play a role, like the choice of rootstock. In this study, we have analyzed the rootstock influence on the scion transcriptome, regarding the biological processes that control almond tree architecture. Three commercial almond cultivars were grafted onto three hybrid rootstocks known to confer different architecture to the scion, resulting in nine combinations, whose gene expression in shoot tips was analyzed via RNA-Seq. We report that differences in tree architecture phenotype are correlated with differential expression of genes involved in hormonal and molecular responses associated with the regulation of apical dominance, branch formation, plant growth, cell wall formation, or nitrogen assimilation. These results highlight the importance of the rootstock choice in selecting a desirable scion architecture and in establishing almond orchards.