Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5'

ABSTRACT: 48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5' were analyzed by microarray to identify gene expression differences between the individuals to correlate gene expression patterns with phenotypic traits segregating in the population 48 individual apple trees were assayed once each using RNA isolated from a single shoot tip from each tree. There were no biological or technical replicates in the experiment. There was no control sample, since all 48 were compared to each other.

ORGANISM(S): Malus domestica

SUBMITTER: Timothy McNellis

PROVIDER: E-GEOD-43268 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Rootstock-regulated gene expression patterns associated with fire blight resistance in apple.

Jensen Philip J PJ Halbrendt Noemi N Fazio Gennaro G Makalowska Izabela I Altman Naomi N Praul Craig C Maximova Siela N SN Ngugi Henry K HK Crassweller Robert M RM Travis James W JW McNellis Timothy W TW

BMC genomics 20120109

<h4>Background</h4>Desirable apple varieties are clonally propagated by grafting vegetative scions onto rootstocks. Rootstocks influence many phenotypic traits of the scion, including resistance to pathogens such as Erwinia amylovora, which causes fire blight, the most serious bacterial disease of apple. The purpose of the present study was to quantify rootstock-mediated differences in scion fire blight susceptibility and to identify transcripts in the scion whose expression levels correlated wi ...[more]

PMID: 22229964

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Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile 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. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of 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 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes. Using a single color labeling system, a total of 24 microarray slides were utilized, one for each cortex tissue sample, for transcriptome profiling analysis. 2 cultivars x 3 developmental stages x 4 biological replicates.

Dataset Information

48 apple trees from a segregating F1 population from a cross of 'Ottawa 3' x 'Robusta 5'

Publications

Rootstock-regulated gene expression patterns associated with fire blight resistance in apple.

Similar Datasets

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