Genetic Analysis of Apple Autumn Canopy Senescence in a Nordic Climate

Autumn phenology traits are likely to be essential for the adaptation of apple to boreal climate. However, the genetic control of these traits is not well understood, and, for example, growth cessation does not appear to be controlled by day length as in many other boreal tree species. Here, I combine a quantitative genetic and population genomic approach to study autumn senescence in apple. I phenotyped a diverse germplasm collection for the timing of autumn senescence, performed quantitative trait loci (QTL) mapping in a multiparental population (MPP), and investigated genomic signals of selection to identify candidate genes. The timing of 50% autumn senescence was negatively correlated with adaptation to higher (boreal) climate zones. Two QTL were found to control the timing of autumn senescence in the MPP, exhibiting both dominance and epistatic interactions. The QTL on linkage group (LG) 17 was also variable in the diversity germplasm, while the QTL on LG11 was not. Cultivars adapted to boreal climate showed weak signals of selection at two loci within the genomic region of chromosome 17 corresponding to the LG17 QTL interval, consistent with a recent expansion to northern Sweden. These loci coincide with two predicted UGT85 genes and a possible copy number variation in PHYC, respectively. Thus, this study provides valuable information for further research and breeding of apple in light of the ongoing climate change.