The domestic apple (Malus domestica; also known as Malus pumila Mill.) has 
become a model fruit crop in which to study commercial traits such as disease 
and pest resistance, grafting, and flavor and health compound biosynthesis. To 
speed the discovery of genes involved in these traits, develop markers to map 
genes, and breed new cultivars, we have produced a substantial expressed 
sequence tag collection from various tissues of apple, focusing on fruit tissues 
of the cultivar Royal Gala. Over 150,000 expressed sequence tags have been 
collected from 43 different cDNA libraries representing 34 different tissues and 
treatments. Clustering of these sequences results in a set of 42,938 
nonredundant sequences comprising 17,460 tentative contigs and 25,478 
singletons, together representing what we predict are approximately one-half the 
expressed genes from apple. Many potential molecular markers are abundant in the 
apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant 
sequences, mainly in the 5'-untranslated region of the gene, with a bias toward 
one repeat type (containing AG, 88%) and against another (repeats containing CG, 
0.1%). Trinucleotide repeats are most common in the predicted coding regions and 
do not show a similar degree of sequence bias in their representation. 
Bi-allelic single-nucleotide polymorphisms are highly abundant with one found, 
on average, every 706 bp of transcribed DNA. Predictions of the numbers of 
representatives from protein families indicate the presence of many genes 
involved in disease resistance and the biosynthesis of flavor and 
health-associated compounds. Comparisons of some of these gene families with 
Arabidopsis (Arabidopsis thaliana) suggest instances where there have been 
duplications in the lineages leading to apple of biosynthetic and regulatory 
genes that are expressed in fruit. This resource paves the way for a concerted 
functional genomics effort in this important temperate fruit crop.