Development of RAPD and SCAR markers linked to the Co gene conferring columnar growth habit in apple (Malus pumila Mill.)

The columnar growth habit in apple is desirable for labour-saving cultivation, since columnar trees can be planted very close together with no staking and little pruning. Bulked segregant analysis and randomly amplified polymorphic DNA (RAPD) analysis were performed to identify DNA markers linked to the columnar growth habit (Co) using an F, progeny of standard 'Fuji' (coco) X columnar 'Tuscan' (Coco). Of the 432 10-mer or 12-mer primers examined, only one clear and repeatable polymorphic product appeared to be linked to the Co gene. The RAPD marker, designated as WB82(670), was located 1.8 cM from the Co locus, closer than markers reported previously for this gene. Based on the sequencing data of this product, two oligonucleotides of 28 bases containing the original 12-mer RAPD primer sequence (ATCCCACATTCC) were synthesized and used as sequence-specific primers for DNA amplification. All genotypes positive for WB82(670) including 'Tuscan' gave a single product of 670 bp, while all WB82(670)-negative genotypes failed to generate any product. This sequence characterized amplified region marker, designated as SCB82(670), linked to the Co gene will be useful to select for columnar growth habit at an early stage of apple breeding programmes.