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Little is known of the precise physiological or genetic basis of the phenomenon of rootstock-induced dwarfing in apple (Malus x domestica Borkh.). Phenotypic assessment and genetic marker analysis of a segregating population of apple rootstocks derived from a cross between the dwarfing rootstock 'Malling 9' ('M.9') and the vigorous rootstock 'Robusta 5' ('R5') was undertaken over a 5-year growth period. Clear segregation of the appearance of the 'Braeburn' scions permitted expert visual classification of each tree into four growth habit classes: dwarfed, semidwarfed, intermediate, or vigorous. Measurements of the cross-sectional area of the trunk of each tree correlated clearly with the expert-assigned phenotypic class. This clear segregation facilitated bulked segregant analysis (BSA) of the 'M.9' x 'R5' population, and the Dwarfing 1 (Dw1) gene was located in a 2.5-cM region at the top of the linkage group 5 of 'M.9'. The gene Dw1 was mapped between the random amplified polymorphic DNA marker NZraAM18_700 and the microsatellite marker CH03a09, identified by BSA and the genome scanning approach, respectively. Dw1 is the first reported mapped locus controlling the dwarfing ability of the apple rootstock and maps to a chromosome region not previously known to contain quantitative trait loci or major genes that contribute to tree architecture and development. The identification of a group of trees in the 'M.9' x 'R5' population exhibiting a vigorous phenotype although their rootstocks possess alleles from the Dw1 region of 'M.9' suggests that more loci may be involved in conditioning the dwarfing phenotype. Dw1 is a major component of dwarfing, as most of the dwarfing and semidwarfing rootstocks carried the dwarfing allele of this locus. Genetically mapping Dw1 is a major step in unraveling the mechanism behind the dwarfing ability of apple rootstocks. [ABSTRACT FROM AUTHOR]