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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

ORGANISM(S): Malus domestica

PROVIDER: GSE43268 | GEO | 2013/11/04

SECONDARY ACCESSION(S): PRJNA185338

REPOSITORIES: GEO

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

Project description: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.

2013-11-04 | E-GEOD-43268 | biostudies-arrayexpress

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Malus domestica

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

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Project description:miRNAs are key players in multiple biological processes, therefore analysis and characterization of these small regulatory RNAs is a critical step towards better understanding of animal and plant biology. In apple (Malus domestica) two hundred microRNAs are known, which most probably represents only a fraction of miRNAome diversity. As a result, more effort is required to better annotate miRNAs and their functions in this economically important species. We performed deep sequencing of twelve small RNA libraries obtained for fire blight resistant and fire blight sensitive trees. In the sequencing results we identified 116 novel microRNAs and confirmed a majority of previously reported apple miRNAs. We then experimentally verified selected candidates with RT-PCR and stem-loop qPCR and performed differential expression analysis. Finally, we identified and characterized putative targets of all known apple miRNAs. In this study we considerably expand the apple miRNAome by identifying and characterizing dozens of novel microRNAs. Moreover, our data suggests that apple microRNAs might be considered as regulators and markers of fire blight resistance. Actively-growing shoot tip tissue samples were collected from twelve apple trees, which includes three biological replicates of each following scion-rootstock combinations: B.9, G.30, M.111 and M.27.

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