Apple Functional Genomics

Publicly available databases currently contain in excess of 250,000 Malus sequences (Park et al., 2006), the majority being derived from large-scale sequencing efforts of cDNA libraries from Washington University, United States and HortResearch, New Zealand (Korban et al., 2004, Newcomb et al., 2006). These Malus cDNA libraries have been sequenced to varying depths (Table 1), depending on library quality and novelty, to generate expressed sequence tags (ESTs). Malus cDNA libraries have been generated from material derived from numerous apple genotypes, many of which are cultivars of commercial significance including ‘Braeburn’, ‘Elstar’, ‘Fuji’, ‘Golden Delicious’, ‘Goldrush’, ‘Granny Smith’, ‘Holsteiner Cox’, ‘Red Delicious’, ‘Royal Gala’, ‘Pinkie’, ‘Sciros/Pacific Rose™’ and a number of dwarfing rootstocks. In addition to being derived from a range of genotypes, the Malus cDNA libraries originate from a wide variety of different tissues and developmental time points. For example, libraries have been generated from a staged series of developing and ripening ‘Royal Gala’ fruit, including flower, whole fruit, fruit cortex, skin, and seed samples (Newcomb et al., 2006). Such a series is a valuable resource of genes for experiments aimed at understanding important processes and transformations in fruit development, such as early cell proliferation, cell expansion, and ripening. This series is also of value in identification of genes encoding enzymes and transcription factors involved in the biosynthesis of health and flavor compounds from apple fruit. Other plant tissues sampled include buds, shoots, leaves, roots, phloem, and xylem. As many genes are only expressed in response to external effects, cDNA libraries have also been constructed from tissues, plants, and cell lines that were subjected to abiotic (e.g. fruit stored at high or low temperature and/or under altered atmospheric conditions), and biotic stresses, e.g. infection with the causal agents of some of the most significant bacterial and fungal diseases to affect apple cultivars including Erwinia amylovra (fire blight), Venturia inaequalis (apple scab or black spot) and Phytophthora sp. (root rot).