Proteomic changes during two stages of pomegranate (Punica granatum L.) seed development identified using the isobaric mass tags for relative and absolute quantitation method

In pomegranates, the seed hardness directly affects the taste and edibility. However, the morphological traits of pomegranate seeds are not yet known. This study aimed to elucidate the molecular mechanism underlying the seed hardness of pomegranates by comparing the protein expression profiles between soft- and hard-seeded pomegranate varieties by using the isobaric mass tags for relative and absolute quantitation technology. Of the 1940 proteins identified, 571 were differentially expressed. Among these differentially expressed proteins, many were involved in lignin, cellulose, and hemicellulose biosynthesis, and proteins associated with the depolymerisation pathway were down-regulated during the maturation period of soft-seeded pomegranates. These findings suggested the importance of these metabolic pathways in determining the extent of seed hardness. In addition, the transcript and protein levels of several proteins/genes were inconsistent, indicating the existence of post-transcriptional regulation. We identified several proteins related to cell wall formation and degradation that are activated during pomegranate ripening. Our findings might form the basis for conducting further studies to analyse the molecular mechanisms underlying the determination of seed hardness level in pomegranate.