Breeding for apple (Malus∈×∈domestica Borkh.) fruit quality traits in the genomics era

Abstract

Apple is one of the most widely cultivated tree fruits in the temperate regions of the world. Development of new apple cultivars is generally based on eating quality, appearance, marketability, health/wellbeing and more recently, on environmental sustainability. A range of new technologies that will both reduce unit costs and increase production are being integrated in apple breeding programmes. Also, molecular breeding is opening an opportunity to significantly reduce the time to incorporate new traits from wild relatives into established crops; enhancing nutritional value, and enabling adaptation to new environmental conditions. The availability of genome sequence along with high throughput genotyping platforms is transforming the strategies for developing new cultivars. Now a range of genome-based selection strategies are providing opportunities to accelerate cultivar breeding. Genomic selection (GS) can be used to obtain genomic breeding values for choosing next-generation parents or selections for further testing as potential commercial cultivars. An empirical study in a New Zealand apple cultivar breeding programme showed that the selection response per unit time using GS compared with the conventional selection were very high (>∈100∈%) especially for low-heritability traits. The cost for highly paralleled targeted genotyping (e.g. single nucleotide polymorphism assays) is constantly decreasing, which would make implementation of GS affordable in near future.