Temperate sub tropical countries for instance South Africa receive very little chill measured in Richardson Units (RU) during winter months, which causes great concern for farmers producing high chill requirement fruit crops like apples. Failure to fulfil chill requirement in apples causes prolonged dormancy symptoms for instance reduced branching and extended fruiting period in trees. The genetic mechanism of chill accumulation during endodormancy is not well understood and the aim of this study is to investigate this phenomenon. The two apple varieties, ‘Anna’ and ‘Lady Williams’ were used to compare the differentially expressed genes during chill accumulation. ‘Anna’ is a low chill apple variety that requires less than 300 hours of chill. ‘Lady Williams’ is a very high chill variety that requires more than 1500 hours of chill. QTL analysis was performed for a Lady Williams’ x ‘Anna’ mapping population using the apple 8K Infinium SNP-array. One major QTL on linkage group 9 and several minor QTLs on linkage groups, 2, 8 and 15 were detected. RNA was extracted from Lady Williams and Anna at 100h time intervals and analysed by RNA-Seq. Transcripts were investigated between time intervals to identify genes that were differentially expressed and then mapped against the QTL’s to locate the genes within the loci. A number of transcripts were highlighted as being differentially expressed between time intervals. The differentially expressed genes from Anna were compared to those from Lady Williams. Differences between the patterns of expression were identified for further analysis.
