Determining the Genetic Differences within the QTL Associated with Chill Requirement; Between High and Low Chill Apple Varieties

With rising temperatures, it is becoming increasingly important to breed for fruit varieties that require less chill during dormancy. An important part of modern breeding is determining the markers closest to the gene or genes associated with a specific trait. In this study we use next generation sequencing technologies to determine putative candidate genes located within a QTL associated with chill requirement within apple. The QTL was verified in both “Lady Williams x Anna” and “Royal Gala x Anna” populations with both recombination and association mapping. A 2 million basepair region was selected, according to the major QTL on Linkage Group 9, for further analysis. RNA sequencing analysis was performed and the expressed genes in the area were selected and gene ontologies were ascertained. Gene expression for these genes over time intervals were plotted to discover patterns corresponding to chill requirement of individual plants. MADS-box and FLC ortholog genes were located within this region as well as high percentages membrane associated genes and transcription factors. These showed similarities to the expected expression patterns for the individual high and low chill apple varieties. The results support predictions that were made previously about the involvement and importance of transcription factors as well as role the membrane plays in response to chilling. The genetic variation in the form of SNPs and INDELs were studied, to further understand the differences in this group of genes between low and high chill varieties. Results indicate significant variation between genes that could be responsible for differences in expression patterns between apple varieties. In exploring the genetic control of chill requirement, a new variety of apple can be bred to withstand the climate change.