Rootstock genotype has been characterized as influential on the scion development. A similar process may be expected in the opposite direction. Therefore, we carried out a RNA-Seq analysis of two peach x almond hybrid roostock samples grafted with two different almond commercial cultivars in one-year ald scion/rootstock combinations, while also analyzing the effect of the rootstock genotype on scion samples.

Rootstock genotype determines multiple aspects of the scion development, including the scion three-dimensional structure, or tree architecture. Thus, rootstock choice is an important factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) planting systems, which demand cultivars whose vigor and shape adapt to these new requirements. However, if the rootstock genotype is able to alter scion development, it is likely that the scion genotype affects the rootstock performance. Here, we carried out a transcriptomic analysis of the scion/rootstock interaction in young trees, focusing on the scion effect in the rootstock molecular response. Two comercial almond cultivars were grafted onto two hybrid rootstocks, resulting in four combinations, whose gene expression in both scion and rootstock tissue was analyzed via RNA-Seq. We observed that, in fact, the scion genotype has an impact on the rootstock expression profile, affecting the expression of genes associated with hormonal regulation, root development and light signalling. Hence, scion/rootstock communication has a pivotal role in the development of both scion and rootstock, accentuating the importance of a correct choice when establishing new almond orchards.