Construction of an integrated consensus map of the apple genome based on four mapping populations

An integrated consensus genetic map for apple was constructed on the basis of segregation data from four genetically connected crosses (C1=Discovery × TN10-8, C2=Fiesta × Discovery, C3=Discovery × Prima, C4= Durello di Forli × Fiesta) with a total of 676 individuals using CarthaGene® software. First, integrated female–male maps were built for each population using common female– male simple sequence repeat markers (SSRs). Then, common SSRs over populations were used for the consensus map integration. The integrated consensus map consists of 1,046 markers, of which 159 are SSR markers, distributed over 17 linkage groups reflecting the basic chromosome number of apple. The total length of the integrated consensus map was 1,032 cM with a mean distance between adjacent loci of 1.1 cM. Markers were proportionally distributed over the 17 linkage groups (χ2= 16.53, df=16, p=0.41). A non-uniform marker distribution was observed within all of the linkage groups (LGs). Clustering of markers at the same position (within a 1-cM window) was observed throughout LGs and consisted predominantly of only two to three linked markers. The four integrated female–male maps showed a very good colinearity in marker order for their common markers, except for only two (CH01h01, CH05g03) and three (CH05a02z, NZ02b01, Lap-1) markers on LG17 and LG15, respectively. This integrated consensus map provides a framework for performing quantitative trait locus (QTL) detection in a multi-population design and evaluating the genetic background effect on QTL expression.