QTL mapping of generative bud break to promote breeding of apple cultivars resilient to climate change

Winter dormancy is a crucial phase in all deciduous trees, which is necessary for bud survival under harsh winter conditions. Onset and release of dormancy are tightly controlled by environmental cues, with ambient temperature playing a major role. Due to global warming, the increasing temperatures would negatively affect the timing of dormancy progression and bud break, resulting in irregular flowering times and a reduction of flowering quality and quantity. Loci that control dormancy and bud break need to be identified to develop genetic markers for breeding new apple cultivars that are more resilient to climate change. An F1 population derived from a cross between Malus × domestica ‘Rote Sternrenette’ (RS) and M. orientalis accession MAL0940 was used to identify quantitative trait loci (QTL) for floral bud break. In parallel, the germplasm collection (357 scion cultivars, 27 rootstocks and 63 M. spp) at PFR, New Zealand was subjected to a genome-wide association study (GWAS) on bud break and dormancy transitions. We identified four QTLs on chromosomes 9 and 15 of RS and one QTL on chromosome 15 of MAL0940. The known flowering time genes FLOWERING LOCUS C (MdFLC-like) and INDUCER OF CBF EXPRESSION 1 (MdICE1) were located within the QTL region of chromosome 9, while the genes Short Vegetative Phase b (MdSVPb), DORMANCY ASSOCIATED MADS-BOX gene 1 (DAM1) and DORMANCY ASSOCIATED MADS-BOX gene b (DAMb) were located within the QTL region on chromosome 15. Expression patterns of these candidate genes during bud development will be analyzed in both parents in a further study. This information will be very useful for developing the molecular markers for marker-assisted selection in apple breeding programs.