Examination of apple (Malus x Domestica) fruit quality and tree morphology using molecular markers

Self-incompatibility, severe inbreeding depression, large plant size, and a long juvenile period make traditional genetic studies difficult in apple. Molecular markers have the potential to aid apple breeding by elucidating the inheritance of traits of interest and providing the means for marker-assisted selection. Genetic linkage maps were created for the parents of two half-sib apple progenies ('Wijcik McIntosh' x NY 75441-67 and 'Wijcik McIntosh' x NY 75441-58) using a double pseudotestcross mapping strategy. The maps are based primarily on 521 RAPD markers but also include isozyme markers. The 'Wijcik McIntosh' map was created using segregation data from both progenies and JOINMAP software. The 'Wijcik McIntosh' map consisted of 235 markers spanning 1206 cM and 19 linkage groups. The NY 75441-58 map has 182 markers covering 898 cM and the NY 75441-67 map has 104 markers spanning 678 cM. These maps have an average distance of 5.5 cM between markers. Molecular marker data were analyzed to find associations between markers and traits influencing tree and fruit morphology and development. Chi-square tests revealed associations between markers and categorical traits including: root suckering, burr-knot formation, columnar form, juvenile period, fruit pH, fruit bloom, and fruit color. The use of single-factor ANOVA revealed significant associations between markers and traits showing continuous variation for tree height, base diameter, branching habit, leaf break, fruit Brix, fruit weight, fruit stem length, and fruit color. On average, each quantitative trait loci (QTL) explained 7% of the phenotypic variation for a trait and combined molecular marker data explained 30 to 40% of the total phenotypic variation. A large percentage of the genotypic variation for most traits appears to be controlled by segregation at a few loci. Several traits were examined in two or three years and approximately 25% of the QTLs were detected in more than one year. Molecular markers show great promise in expanding our knowledge of apple genetics and may be important tools for selection of traits in the breeding program.