Global transcriptional regulation during apple fruit maturation and associated texture changes were assessed by transcriptome profiling and systematic characterization of maturation progression of two cultivars, ‘Honeycrisp’ (HC) and ‘Cripps Pink’ (CP). A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50–70-mer isothermal probes, representing 23,997 unigenes, was designed for and manufactured on a NimbleGen array platform. Cortex tissues from both HC and CP at three maturation stages, i.e., 4, 2, and 0 week(s) before physiological maturity, were utilized for transcriptome profiling. A total of 1,793 and 1,209 differentially expressed unigenes, 7.47 % and 5.04 % of all unigenes deposited on the array, were identified from HC and CP, respectively. Unigenes associated with ethylene biosynthesis and response, auxin homeostasis and transport, gibberellin reception and metabolism as well as degradation of hemicelluloses may contribute to the observed phenotypic variations in apple maturation patterns and texture attributes such as fruit firmness and crispness. Microarray data validation indicated that more than 85 % of randomly selected unigenes showed consistent expression patterns with qRT-PCR results. Physiological characterization demonstrated substantial differences in maturation progression between these two cultivars, and a remarkable transformation in fruit texture occurred from week −4 to week 0.
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