Transcriptome analysis of fruit development and identification of key transcription factors related to anthocyanin pathway in cultivated octoploid strawberry

Abstract The cultivated strawberry is a vital economic crop grown extensively worldwide. Recently, there has been more focus on breeding strawberry cultivars that produce high-quality fruit. Anthocyanin is a crucial determinant of the quality of strawberries. A transcriptomes analysis of fruits at various developmental stages of the 'Yanli' cultivar was performed to examine the mechanisms of anthocyanin accumulation in the process of fruit development of cultivated strawberries. We screened 33,617 differentially expressed genes whose average expression value was more significant than 2 in at least one sample. We classified these differentially expressed genes into nine categories based on k-mean clustering analysis. Furthermore, we recognized that anthocyanin synthesis-related genes’ promoter regions had a high consistency of conserved motifs with a similar expression pattern. By conducting a correlation analysis between seven anthocyanin pathway genes and various transcription factors, we identified 560 transcription factors that might involve in the anthocyanin biosynthesis pathway. In summary, we can identify a more significant number of prospective transcription factors in the anthocyanin pathway based on the haplotype-resolved genome of ‘Yanli’.