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.苹果（Malus×domestica Borkh.）是全球种植范围最广、经济价值最高的果树作物之一。随着苹果周年市场需求的不断提升，果实耐贮性已成为苹果育种项目的重要考量指标。软疤病是一类与冷贮相关的生理病害，会导致果实表面形成凹陷发黑的病组织。苹果育种工作者亟需培育出不会发生软疤病的新品种，以实现苹果的全年市场化供应。传统育种方法耗时漫长且劳动强度大，因此标记辅助选择（marker-assisted selection, MAS）成为育种者的重要辅助工具。为推进苹果贮运相关病害的标记辅助选择研究，本研究利用测序分型（genotyping-by-sequencing, GBS）技术，在两个F1苹果群体中构建了高密度遗传图谱，并以此开展软疤病的数量性状位点（quantitative trait locus, QTL）定位分析。本研究共生成9亿条DNA序列读段，但经多轮数据过滤流程后，最终仅保留2%的读段，用于构建两张分别包含1918和2818个单核苷酸多态性（single-nucleotide polymorphisms）标记的遗传图谱。在其中一个双亲杂交群体中，我们鉴定到两个与软疤病相关的QTL，该群体的亲本为先进育种品系11W-12-11。本研究证实了新一代DNA测序技术在F1群体QTL定位中的应用价值，并为通过标记辅助选择改良苹果耐贮性提供了坚实的理论基础。