Genetic diversity and relationships in Malus sp germplasm collections as determined by randomly amplified polymorphic DNA

Four subsets of apple (Malus Mill.) germplasm representing modern and old c ultivars from the repository and apple genetics population of the Horticult ure and Food Research Institute of New Zealand Limited were used in this st udy. A total of 155 genotypes randomly chosen from the four subsets were an alyzed for random amplified polymorphic DNA (RAPD) variation. Nine decamer primers generated a total of 43 fragments, 42 of which were polymorphic acr oss the 155 genotypes, Pair,vise distances were calculated between germplas m subsets using the distance metric algorithm in S-PLUS, and used to examin e intra-and inter-subset variance components by analysis of molecular varia tion (AMOVAR), A phenogram based on unweighted pair group method with arith metic average (UPGMA) cluster analysis was constructed from the pairwise di stances and a scatter plot was generated from principal coordinate analysis . The AMOVAR showed that most of the variation in the germplasm (94.6%) was found,within subsets, suggesting that there is significant variation among the germplasm, The grouping of genotypes based on the phenogram and scatte r plot generally did not reflect the pedigree or provenance of the genotype s. It is possible that more RAPD markers are needed for determining genetic relationships in apple germplasm, Nevertheless, the variation observed in the study suggests that the current practice of sublining populations in th e first generation to control inbreeding may not be necessary in subsequent generations. If these results are confirmed by fully informative molecular markers, germplasm managers should reassess the structure of their genetic s populations, There may be a need to combine sublines in order to capture the maximum genetic diversity available and to streamline breeding efforts.