The columnar-specific Gypsy-44 integration leads to gross changes in gene expression in leaves of McIntosh Wijcik compared with McIntosh

The columnar growth habit of apple trees (Malus x domestica Borkh.) is a unique and economically valuable plant architecture phenotype that arose as a bud sport mutation of a McIntosh tree in the 1960s. The mutation, later called “Co-gene”, lead to trees (McIntosh Wijcik) that have thick, upright main stems with short internodes and that generate short fruit spurs instead of long lateral branches. Although Co has been localized to chromosome 10 between 18.71 – 19.09 megabases according to the apple genome annotation (Velasco R, et al. (2010) Nat Genet 42:833-839), the molecular nature of Co was not known up to now. In a classical positional cloning approach in combination with the analysis of NGS data we cloned and analyzed the Co-region. Our results show that the insertion of a Ty3/Gypsy retrotransposon into a non-coding region at position 18.8 Mb on chromosome 10 is most likely the molecular basis of columnar growth. This insertion is the only detectable genomic difference between McIntosh and McIntosh Wijcik and is found in all columnar cultivars. The genetic effect of the retrotransposon insertion is unclear; however, Illumina® RNA-seq data sets of McIntosh and McIntosh Wijcik suggest that the columnar growth habit is the consequence of the differential expression of the retrotransposon transcript, causing changes of the expression levels of a large number of protein coding genes.