Analysis of ripening-related gene expression in papaya using an Arabidopsis-based microarray

Papaya transcriptome analyses resulted in the identification of 414 ripening-related genes with some having their expression validated by qPCR. The transcription profile was compared with that from ripening tomato and grape. There were many similarities between papaya and tomato especially with respect to the expression of genes encoding proteins involved in primary metabolism, regulation of transcription, biotic and abiotic stress and cell wall metabolism. XSpecies microarray data indicated that transcription factors (TFs) of the MADS-box, NAC and AP2/ERF gene families were involved in the control of papaya ripening and revealed that cell wall-related gene expression in papaya had similarities to the expression profiles seen in Arabidopsis during hypocotyl development.The cross-species array experiment identified a ripening-related set of genes in papaya allowing the comparison of transcription control between papaya and other fruit bearing taxa during the ripening process.Papaya (Carica papaya L.) is an important crop cultivated in tropical and subtropical areas and the ripe fruit has a soft and sweet pulp with high amounts of pro-vitamin A and antioxidants [1]. Papaya is a typical climacteric fruit, with striking colour changes, a rapid rise in ethylene production, and substantial pulp softening; it also responds to exogenous ethylene and 1-MCP applications [2,3]. The physico-chemical changes during papaya ripening are dependent on the expression of specific genes, and the identification of ripening-related genes involved in the activation of biochemical steps relevant for fruit quality is of both scientific and commercial interest.In order to understand the network of ripening genes in fleshy fruits, transcriptome studies are valuable tools. In the case of fruit such as tomato, microarrays have been used extensively [4,5]. However, for less well studied fruits, transcriptome analyses are based on ‘home-made’ microarrays, such as the μPEACH1.0 array [6], or class