Mapping of Quantitative Trait Loci (QTL) for Fruit Quality Traits in Malus Using Simple Sequence Repeats (SSRs)

A segregating mapping population of Coop 17 x Coop 16 cross was used to identify quantitative loci associated with various fruit quality traits.  Using a total of 94 seedlings and the two parents, three apples per seedling were phenotyped over two years for several fruit quality traits.  Phenotypic data were collected for fruit firmness, shape, weight, sugar content (ºBrix), and titrateable acidity (TA).  Moreover, the mapping population along with the parents were subjected to genetic screening using 502 Simple Sequence Repeats (SSRs).  These SSR markers were derived from bacterial artificial chromosome (BAC) end sequencing, expressed sequence tag (EST) sequences, and previously published markers.  These were selected based on their ability to detect polymorphism in Malus, and were also previously used in a large Malus genetic mapping project.  Depending on the trait of interest, significant differences were observed for years and genotype by environment interactions were also detected.  Data analysis yielded 20 linkage groups on a fairly high-density linkage map.  Three of the linkage groups mapped at opposite ends of chromosomes that comprise the 17 linkage groups and corresponding to the 17 chromosomes of the apple genome.  Simple interval mapping (SIM) yielded a number of QTL for fruit quality traits, which were refined using composite interval mapping (CIM) involving marker cofactors.