SSR-Based Genetic Mapping of QTLs Determining Chilling Requirements for Vegetative Budbreak in the Domesticated Apple, Malus x Domestica (Borkh.) Cultivar ‘Austin’ x ‘Anna’

The Rosaceae family contains major temperate crops such as the domesticated apple (Malus x domestica Borkh.), peach (Prunus persica L. Batsch) and European pear (Pyrus communis L.). However, despite its economic importance, it is generally poorly studied in genomic terms, relative to the other major crop groups. Genetic markers such as Simple Sequence Repeat (SSR) and Diversity Array Technology (DArT) markers are essential tools in marker-assisted selection (MAS) of high quality apples and other Rosaceous crops. SSRs are advantageous in that they are co-dominant, highly polymorphic, abundant, transferable and reliably reproducible; hence their use in this study. This research has exploited the large number of Expressed Sequence Tags (ESTs) and genome sequence data for the apple, using Tandem Repeats Finder, to design SSR primers or markers. In order for budbreak to take place in a timely and homogenous fashion, apple trees need a period of exposure to low temperatures. Within orchards the application of chemicals that induce budbreak in unsuitable environments is required to produce apples from cultivars that require high chilling levels. However, this and other practices using chemicals in orchards tend to pollute the environment. An ‘Austin’ x ‘Anna’ mapping population with 80 individuals has been used to create a genetic map in order to identify the Quantitative Trait Loci (QTLs) determining chilling requirements for vegetative budbreak. In this process, primers were designed from ESTs and genome sequence data, and used for PCR, and the resulting PCR products were then accurately sized and genotyped using the ABI 3130xl (Applied Biosystems), and the GeneMapper 4.0 software, producing 120 useable SSR genetic markers, six of which were novel and targeted the QTL region of linkage group (LG) 9. Also, a collection of 180 DArT markers was also generated for linkage map creation. Using the JoinMap 4.0 software, these markers were used to create the ‘Austin’ x ‘Anna’ genetic map consisting of markers distributed across the expected 17 LGs. Putative QTLs determining chilling requirements for budbreak were then identified on LG 9 using MapQTL 5.0, utilising vegetative budbreak phenotypic data of the cross, collected over a three-year period. These QTLs will provide the basis for marker validation on related mapping populations in the apple breeding programme, and for the future identification of candidate genes controlling the process of budbreak.