Transcriptome analysis of flower color reveals the correlation between SNP and differential expression genes in Phalaenopsis

Background: Phalaenopsis is an important ornamental plant, which occupies an important position in the world flower market and has great economic value due to its rich and diverse flower colors. In order to investigate the flower color formation of Phalaenopsis at transcription level, the flower color formation involved genes were identified from RNA-seq in this study. Results: White and purple petals of Phalaenopsis were collected in this study, and results were focused on two aspects: (1) the differential expression genes (DEGs) between white and purple flower color; and (2) association between SNP mutations and DEGs in transcriptome level. Results indicated that a total of 1,175 DEGs were identified, and the up- and down-regulation genes were 718 and 457, respectively. Gene Ontology (GO) and pathway enrichment showed that the biosynthesis of secondary metabolites pathway was key responsible for color formation and twelve crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase and E1.11.17) from them involved in the regulation of flower color in Phalaenopsis . Conclusion: This study firstly reported that the SNP mutations strongly associated with DEGs in color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.