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Gene families encoding three enzymes of phenylpropanoid metabolism in raspberry (Rubus idaeus L) : characterization of the families, and of the cognate ripening-related fruit cDNAs Kumar, Amrita


A PCR-based homology search of the Rubus genome, led to the isolation and characterization of two PAL genes (Ripal1 and Ripal2), three 4CL genes (Ri4cl1, Ri4cl2, Ri4cl3), and ten PKS genes (Ripksl-10). These data demonstrate that such a PCR-based homology search could be extended to characterize members of the PAL, 4CL and PKS gene-family members from other crops, in a manner that is independent of their expression. To identify members of these gene-families that may be associated with fruit-ripening, a cDNA library representing partially-ripe fruits was sequentially screened at low stringency with a mixed population of each gene-family member. These hybridization-based homology screenings led to the characterization of two full-length PAL (RiPAL1 and RiPAL2), three full-length 4CL (Ri4CL1, Ri4CL2, and Ri4CL3), and three full-length PKS genes (RiPKS5, R1PKS6, and RiPKS11). Thus, the characterization of an additional 4CL (Ri4CL3) and PKS (RiPKS11) gene, suggest that a PCR-based homology search by itself may not be sufficient for isolation and characterization of all members representing these gene-families. Although phenylpropanoid-derived metabolites are important for fruit quality, the regulation of this pathway during fruit development is still poorly understood. I have therefore profiled the expression pattern of these three important phenylpropanoid gene families in ripening Rubus fruits. Quantitative RT-PCR assay with gene-specific probes, showed that the individual gene family members are differentially expressed during fruit ripening and in various Rubus tissues studied. Furthermore, some members from each of the RiPAL, Ri4CL and RiPKS gene families displayed very similar patterns of expression, which may reflect functionally-related roles in generating specific phenylpropanoid end-products in a given tissue. I have also examined the evolutionary dynamics of these three gene families. Duplication and divergence in function appears to be a common theme for evolution of all three gene families. I find that members of all three gene families from a given plant species are not necessarily more closely related to one another than they are to other genes from other species.

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