Defining the QTL associated with chill requirement during endodormancy in Malus × domestica Borkh

Current weather pattern predictions show the increase in winter temperatures globally. This could have a detrimental effect on fruit grown in temperate environments like the southern part of Africa. A rise in winter temperatures would lead to the non-fulfilment of chill requirements of fruit crops and subsequent losses. A need therefore arises to breed for good quality fruit varieties with a lower chill requirement. Identifying genomic regions that are associated with early flowering is the first step in breeding for such varieties. This study focuses on defining a quantitative trait locus (QTL) that is associated with budbreak in Malus × domestica Borkh. The International Rosaceae SNP consortium apple 8 K single nucleotide polymorphism (SNP) bead array v1 was used with recombination mapping and QTL analysis to identify this QTL on Linkage Group 9. A QTL was verified with association mapping and shown to be in the first 10 Mb of chromosome 9, and consisting of six clusters of SNPs, grouped together. These clusters were shown to segregate together with identical allele specification, as well as having a high linkage disequilibrium within the clusters. The haplotype blocks representing the clusters show a high correlation between them, explaining the substantial size of the QTL found with recombination mapping. Approximately 750 genes were represented by the clusters, most notably a high number of transcription factors and regulators.