Tonutti et al - Genomics approaches to study fruit ripening and quality

Pietro Tonutti1*, Livio Trainotti2 e Claudio Bonghi3
1 Scuola Superiore di Studi Universitari “S. Anna”, P.za Martiri della Libertà 33, 56127 Pisa
2 Dipartimento di Biologia, Università di Padova, viale Colombo 3, 35121 Padova
3 Dipartimento di Agronomia Ambientale e Produzioni Vegetali, Università di Padova, viale dell’Università 16, 35020 Legnaro (PD)

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Key words: gene expression, transcriptome, ESTs, microarray.

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Abstract

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Genomic tools are becoming common place in many plant science laboratories including those involved in fruit physiology studies. Increased understanding of fruit ripening is feasible with highthroughput methodologies for comprehensive transcriptome analyses. This article reviews main results gained by transcript profiling methods in the identification of genes involved in the regulation of fleshy-fruit ripening, and outlines potential applications of genomic tools developed in model species and already available in some important fruit crops. Tomato has emerged as model for fleshy fruit ripening, due, in part, to simple genetics, numerous characterized mutants, cross-fertile wild germplasm and routine transformation technology. Starting from tomato, global transcript profiling methods allowed the association of newly identified genes, such as some transcription factors, with the ripening syndrome. Furthermore, they helped in the functional characterisation of genes important for quality traits, such as aroma evolution and pigmentation. Transcriptome analysis can be carried out through direct and indirect analyses. Considering direct analyses, expressed sequence tag (EST)s sequencing has been performed in several plant species and more than 350,000 fruit tissue-specific ESTs are now present in the NCBI database: apple, grapes, Prunus spp, Citrus spp and tomato are the species or genera with the highest EST number isolated starting from fruit tissues. Digital expression and cDNA-AFLP analyses performed on different species revealed the presence of up- and down-regulated genes during the transition from immature to mature stage in both climacteric and non-climacteric fruit. As far as indirect analyses are concerned and following the pioneering work on strawberry, microarray technology is now used in several fruit species. Different microarray types containing a variable number of probes corresponding to genes expressed in fruit tissues have been constructed and data concerning transcript profiles and gene clustering in relation to the ripening process and postharvest behaviour are available. Several genes associated with specific quality traits have been isolated and characterized using the microarray approach. Comparative genomics carried out by digital analysis of EST repertoires and microarray analyses indicated that groups of genes responsible for regulatory mechanisms are shared between climacteric and non-climacteric fruits. Gene sequences are important in determining fruit characteristics and can be useful in marker-assisted selection of new varieties. Further information on regulation of fruit ripening requires an extensive analysis of the proteome. Comparative proteomics is an efficient strategy that could be used to achieve this goal. The identification of differentially-expressed proteins is becoming easier as a result of the rapid growth of plant DNA databases that allow association of a protein sequence with its cognate gene.

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