Toward Deciphering of Mechanisms Underlying White Drupelet and Reversion Disorders of Blackberry

White drupelet disorder and reversion are both aesthetic and economic problems in ripening blackberries (Rubus spp). The commercial industry has low tolerance for either disorder and growers can suffer significant loss of revenue due to rejected fruit. In order to identify genes that are differentially expressed in fruit with these disorders, drupelets displaying different colors were harvested from the fruit of the cultivar, Apache. White, brown, and black drupelets were dissected from fully ripe berries, representing severe, moderate and no symptoms of the white drupelet disorder respectively. One hour after fruit was harvested and reversion of drupelets from black to red was occurring, red and black drupelets were also harvested. Total RNA was extracted from multiple drupelets of the same color of the same berry and subjected to RNA-Seq analysis. A total of 245.7 Million 125bp Illumina HiSeq reads were generated. After trimming and removing low quality reads, 241.3M reads were retained. The CLC Genomic Workbench was used to assemble 57.9 M nucleotides in 74,870 contigs (N50 = 935). Pairwise differential expression analysis was carried out between each group. We found there were 12,437 and 11,351 genes differentially expressed between black-white and red-white drupelets. A smaller set of genes (537) were differentially expressed between black and red drupelets, from which 329 were common with black-white group. These genes were subjected to functional annotation and KEGG pathways were generated.