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 F 1 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 F 1 populations, and provides a basis for the advancement of MAS to improve storability of apples. Fruit storage: Getting under the skin of apple damage Identifying the genes underlying the apple disorder 'soft scald' could lead to more storable varieties that can be eaten all year round. When apples are stored at low temperatures, fruits may suffer from sunken, darkened patches known as 'soft scald.' Sean Myles of Dalhousie University, Truro, Canada, and colleagues used modern genomic sequencing methods to map the genome of two hybrid apple populations. This enabled them to 'quantitative trait loci' (QTLs), with small effects on susceptibility to soft scald. Together, multiple QTLs can have a large, additive effect. They may provide starting points for 'marker assisted selection', in which genes are selected at the seedling stage before the trees show mature characteristics. The hope is to generate apples that can be cold stored for many months without deleterious effects.