Molecular-marker analysis of quantitative traits for growth and development in juvenile apple trees

Random, amplified polymorphic DNAs (RAPDs) were used in combination with a double pseudo-testcross mapping strategy to estimate the position and effects of quantitative trait loci (QTLs) for traits influencing juvenile tree growth and development in two apple cultivars. The mapping population consisted of 172 Fl trees from a cross between the columnar mutant 'Wijcik McIntosh' and a standard form disease-resistant selection NY 75441-58. Significant associations were found between markers and height increment, internode number, internode length, base diameter increment? base diameter after 9 years of growth, branch number, and leaf break. The number of genomic regions associated with each trait varied from one to eight. The amount of variation explained by linear regression on individual marker loci (R(2)) ranged from 3.9 to 24.3%, with an average of 7%. Multiple regression using markers for each putative QTL explained from 6.6 to 41.6% of the phenotypic variation. with an average value of 24.3%. A large number of traits had significant variation associated with the map position of the dominant columnar gene, Co. QTL stability over years was estimated by comparing the locations of putative QTLs for traits measured in multiple years. The majority of genomic regions were, associated with a trait in only a single year, although regions associated with a trait in more than 1 year were also detected. The limitations of dominant markers and an outbred mapping pedigree for QTL analysis are discussed.