Gene expression analysis of strawberry achene and receptacle maturation using DNA microarrays

Large-scale, single pass sequencing and parallel gene expression analysis using DNA microarrays were employed for the comprehensive investigation of ripening in strawberry fruit. A total of 1701 cDNA clones (comprising 1100 strawberry ESTs and 601 unsequenced cDNAs) obtained from a strawberry (Fragariaxananassa) ripe fruit cDNA library were displayed on microarrays, and used for monitoring concurrent gene expression in receptacle and achene tissues. Analysis of expression ratios identified 66 out of the 259 (25%) achene-related clones and 80 out of 182 (44%) receptacle-related clones with more than a 4-fold difference in expression between the two tissue types. Half of the achene-associated genes putatively encode proteins with unknown function, and a large number of the remainder were proteins predicted to form part of the signal and regulation cascades related to achene maturation and acquisition of stress and desiccation tolerance. These included phosphatases, protein kinases, 14-3-3 proteins, transcription factors, and others. In the receptacle, key processes and novel genes that could be associated with ripening were identified. Genes putatively encoding proteins related to stress, the cell wall, DNA/RNA/protein, and primary metabolism were highly represented. Apart from providing a global observation on gene expression programmes and metabolic pathways in the developing strawberry, this study has made available a large database and unique information for gene discovery, promoter selection and markers for molecular breeding approaches.