Identification of candidate genes influencing anthocyanin biosynthesis during the development and ripening of red and white strawberry fruits via comparative transcriptome analysis

Abstract

Strawberries are one of the most economically important berry fruits worldwide and exhibit colours ranging from white to dark red, providing a rich genetic resource for strawberry quality improvement. In the present study, we conducted transcriptome analyses of three strawberry cultivars, namely, ‘Benihoppe’, ‘Xiaobai’, and ‘Snow White’, and compared their gene expression profiles. Among the high-quality sequences, 5,049 and 53,200 differentially expressed genes (DEGs) were obtained when comparing the diploid and octoploid strawberry genomes and analysed to identify anthocyanin-related candidate genes. Sixty-five DEGs in the diploid genome (transcriptome data compared to the diploid strawberry genome) and 317 DEGs in the octoploid genome (transcriptome data compared to the octoploid strawberry genome) were identified among the three cultivars. Among these DEGs, 19 and 70 anthocyanin pathway genes, six and 42 sugar pathway genes, 23 and 101 hormone pathway genes, and 17 and 104 transcription factors in the diploid and octoploid genomes, respectively, correlated positively or negatively with the anthocyanin accumulation observed among the three cultivars. Real-time qPCR analysis of nine candidate genes showed a good correlation with the transcriptome data. For example, the expression of PAL was higher in ‘Benihoppe’ and ‘Xiaobai’ than in ‘Snow White’, consistent with the RNA-seq data. Thus, the RNA-seq data and candidate DEGs identified in the present study provide a sound basis for further studies of strawberry fruit colour formation.

Alterations of Phenylpropanoid Biosynthesis Lead to the Natural Formation of Pinkish-Skinned and White-Fleshed Strawberry (Fragaria × ananassa)

“…These results suggested that the FaMYB10 gene may not be directly responsible for the loss of anthocyanins in Xiaobai's flesh. Herein, we demonstrated that the inhibition of the C4H gene was the main factor responsible for the absence of anthocyanins in Xiaobai, which differed from previous reports [14,23,30]. C4H not only affects the flavonoid biosynthesis but is also necessary for the biosynthesis of osthole, hydroxycinnamic acids, dihydrochalcones, eugenol, lignin, and ubiquinone [4][5][6][7].…”

RNAseq, transcriptome analysis and identification of DEGs involved in development and ripening of Fragaria chiloensis fruit

“…RNAseq has been used to unravel intricate processes at the molecular level, such as fruit development and ripening in commercial strawberries (Sanchez-Sevilla et al, 2017 ; Gu et al, 2019 ; Zhao et al, 2021 ). The description of a massive number of genes in the Chilean strawberry is described for the first time.…”

Insights into transcription factors controlling strawberry fruit development and ripening

“…They are synthesized at the endoplasmic reticulum and later transported into the vacuole for storage mainly by glutathione S-transferases (GSTs) ( Luo et al., 2018 ; Castillejo et al., 2020 ). Among the anthocyanins, pelargonidin-3-glucoside is the major pigment in strawberry receptacles, while cyanidin-3-glucoside is present in a minor content ( Almeida et al., 2007 ; Zhao et al., 2021 ). Finally, for the biosynthesis of PAs, two main enzymes are involved, i.e., leucocyanidin reductase (LAR) and anthocyanidin reductase (ANR).…”