Expression analysis of stem prickle formation in blackberry using cDNA-AFLP

To understand the molecular mechanism of prickle formation in blackberry, differential expression profile of cDNA between 'Boysenberry' blackberry and its thin-thorn mutant were analysed by using cDNA-AFLP. In total, 256 primer pairs were used for the cDNA-AFLP amplification to produce 45 differentially expressed fragments. The putative function of the sequenced fragments was determined using BLAST analysis. Putative functions included metabolism, signal transduction, cell skeleton and composition, transcriptional regulation and adversity defence. A 109 bp fragment was found to have an 88% sequence homology with a strawberry TRY transcription factor, which inhibits trichome development in Arabidopsis. A 124 bp fragment had a 75% homology with alfalfa cell wall hydrolase gene. This fragment was named Ruh and had higher expression in shoot apical meristem (SAM), middle and upper section of stem of thin-thorn mutant. This implied that the prickle formation was an intricate system and the sense of expression pattern of cell wall-associated hydrolase homologous gene Ruh in the thin-thorn mutant needs further investigation.