Key flowering genes including FT-like genes are upregulated in the vasculature of apple dwarfing rootstocks

The Malling 9 (M.9) dwarfing rootstock is widely used in apple breeding and commercial cultivation to shorten the juvenile period, reduce vegetative growth and increase flowering of the scion. A segment of M.9 stem (interstock) or M.9 bark grafted into a compound tree can cause significant dwarfing of the scion, suggesting that the dwarfing signal may be vascular derived. To better understand how the M.9 rootstock alters the growth and development of the scion, we compared gene expression in vascular-enriched tissue from dwarfing and vigorous rootstocks. RNA sequencing indicated that key flowering genes were upregulated in M.9 relative to a vigorous rootstock, Malling 793 (M.793). An in-depth analysis of the apple FT/TFL1 gene family identified four new members: MdMFTa, MdMFTb, MdBFTa and MdBFTb. Quantitative RT-PCR analysis confirmed the higher expression of MdFT1/2, MdBFTa/b, MdCO, MdGI, and MdSOC1 in two different dwarfing rootstocks (M.9 and Malling 27 (M.27)) relative to M.793. Both MdFT1/2, and MdBFTa/b were expressed at higher levels in multiple dwarfing rootstock accessions relative to more vigorous genotypes. In perennial species, FT promotes flowering, and has additional roles in accelerating the transition from juvenility to maturity, and regulating cycles of seasonal growth and termination. Apple dwarfing rootstocks reduce the juvenile phase and promote both flowering and early shoot termination. Our work supports a role for MdFT in promoting flowering and earlier shoot termination. We suggest that upregulation of a suite of flowering genes including MdFT, and possibly MdBFT, in the vasculature is part of the underlying mechanism of apple dwarfing rootstocks. Genes involved with response to biotic and abiotic stress and disease were also upregulated in the M.9 rootstock, suggesting that stress, possibly mediated by JA and ABA signalling, also plays a role in the M.9-induced phenotype.