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ARS Home » Pacific West Area » Wenatchee, Washington » Physiology and Pathology of Tree Fruits Research » Research » Publications at this Location » Publication #257491

Research Project: Genetic, Metabolic, and Physiological Factors Regulating Deciduous Tree Fruit Quality

Location: Physiology and Pathology of Tree Fruits Research

Title: Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes

Author
item Zhu, Yanmin
item Zheng, Ping - Washington State University
item Varanasi, Vijaya - Washington State University Extension Service
item Main, Dorrie - Washington State University
item Curry, Eric
item Mattheis, James

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/16/2010
Publication Date: 11/17/2010
Citation: Zhu, Y., Zheng, P., Varanasi, V., Main, D., Curry, E.A., Mattheis, J.P. 2010. Transcriptome profiling of cultivar-specific apple fruit ripening and texture attributes. Meeting Abstract. N/A.

Interpretive Summary:

Technical Abstract: Transcriptome analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, ‘Honeycrisp’ (HC) and ‘Cripps Pink’ (CP), which have distinct ripening features and texture attributes. Based on weekly maturity data at comparable ripening stages, substantial differences of fruit firmness and crispness were observed between these two cultivars. SEM images of fruit cortex tissues showed distinguishable cell wall thickness, which may contribute to the phenotypic variations of cultivar-specific fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and 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, 4, 2 and 0 week(s) before harvest, were utilized for transcriptome profiling and each sample is represented by 4 biological repeats. A total of 1793 and 1209 differentially expressed unigenes were identified from HC and CP, respectively, based on ANOVA analyses with a cutoff value of 2-fold change of normalized signal intensity and a non-adaptive false discovery rate (FDR) of 0.01. Unigenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the major transcriptomic changes during ripening. Between two cultivars, most of the identified unigenes were similarly regulated during fruit ripening. A short list of gene families or specific family members exhibited distinct expression patterns, which may represent the candidates controlling cultivar-specific fruit ripening patterns and quality attributes. Our data suggested that a deficiency of auxin transport and homeostasis occurred in late-ripening CP with extreme firm fruit; while the elevated expression patterns for a number of unigenes related to auxin and JA functions as well as for hemicelluloses-degrading XTHs were observed in early-ripening HC with outstanding crispness. For 12 randomly selected unigenes, more than 85% of values showed consistent expression patterns between microarray data and RT-qPCR results. Selected candidate genes are being further investigated in wider selections of apple germplasm, including a cross population of 150 siblings between HC and CP, to validate their specific associations with apple fruit ripening and texture attributes.