Dwarf tree habit is a recessive phenotype independent of the dominant columnar growth in scion apples and controlled by multiple genomic loci and their epistatic interactions.

The genetic control of dwarf phenotype in scion apples is largely unknown, although quantitative trait loci (QTLs) Dw1, Dw2 and Dw3 of major dwarfing effect have been reported in apple rootstocks. To fill the knowledge gap in scion apples, we used the BSA-seq (pooled genome sequencing) approach to identify QTLs for the dwarf and (ultra-) tall phenotypes over three growth seasons in an F1 population of 365 seedlings derived from the Fuji (standard) × NYCO7-G (columnar) cross. The dwarf and tall phenotypes segregated recessively in the 140 standard progenies as well as in the 225 columnar. Data analyses revealed five QTLs (d4-d8) for dwarf and four (t1-t4) for tall each in a 1-2 Mb region on six chromosomes. However, their main effect and epistatic interactions varied markedly depending on genetic backgrounds. The top three non-linked QTLs are d4 (Chr01_20-21Mb), d5 (Chr08_4-5Mb) and t1 (Chr17_1-2Mb), and their epistatic effect explained 34.9% of phenotypic variation in the columnar background and 24.8% in the full population on average. Consequently, most seedlings with a dwarf genotype (d4d4d5d5T1T1) were dwarfs. The results demonstrated that dwarf is a recessive phenotype independent of the dominant columnar growth in scion apples and is controlled by multiple QTLs and their epistatic interactions. This study represents a step forward to enable genetic manipulation of tree height in apple scions.