Data from: QTL analysis of soft scald in two apple populations

The apple (Malus×domestica Borkh.) is one of the world’s most widely grown
and valuable fruit crops. With demand for apples year round, storability
has emerged as an important consideration for apple breeding programs.
Soft scald is a cold storage-related disorder that results in sunken,
darkened tissue on the fruit surface. Apple breeders are keen to generate
new cultivars that do not suffer from soft scald and can thus be marketed
year round. Traditional breeding approaches are protracted and labor
intensive, and therefore marker-assisted selection (MAS) is a valuable
tool for breeders. To advance MAS for storage disorders in apple, we used
genotyping-by-sequencing (GBS) to generate high-density genetic maps in
two F1 apple populations, which were then used for quantitative trait
locus (QTL) mapping of soft scald. In total, 900 million DNA sequence
reads were generated, but after several data filtering steps, only 2% of
reads were ultimately used to create two genetic maps that included 1918
and 2818 single-nucleotide polymorphisms. Two QTL associated with soft
scald were identified in one of the bi-parental populations originating
from parent 11W-12-11, an advanced breeding line. This study demonstrates
the utility of next-generation DNA sequencing technologies for QTL mapping
in F1 populations, and provides a basis for the advancement of MAS to
improve storability of apples.