Transcriptome profiling by RNA-Seq reveals differentially expressed genes related to fruit development and ripening characteristics in strawberries (Fragaria×ananassa)

Abstract

Strawberry (Fragaria × ananassa) is an ideal plant for fruit development and ripening research due to the rapid substantial changes in fruit color, aroma, taste, and softening. To gain deeper insights into the genes that play a central regulatory role in strawberry fruit development and ripening characteristics, transcriptome profiling was performed for the large green fruit, white fruit, turning fruit, and red fruit stages of strawberry. A total of 6,608 differentially expressed genes (DEGs) with 2,643 up-regulated and 3,965 down-regulated genes were identified in the fruit development and ripening process. The DEGs related to fruit flavonoid biosynthesis, starch and sucrose biosynthesis, the citrate cycle, and cell-wall modification enzymes played important roles in the fruit development and ripening process. Particularly, some candidate genes related to the ubiquitin mediated proteolysis pathway and MADS-box were confirmed to be involved in fruit development and ripening according to their possible regulatory functions. A total of five ubiquitin-conjugating enzymes and 10 MADS-box transcription factors were differentially expressed between the four fruit ripening stages. The expression levels of DEGs relating to color, aroma, taste, and softening of fruit were confirmed by quantitative real-time polymerase chain reaction. Our study provides important insights into the complicated regulatory mechanism underlying the fruit ripening characteristics in Fragaria × ananassa.

Developmental Variation in Fruit Polyphenol Content and Related Gene Expression of a Red-Fruited versus a White-Fruited Fragaria vesca Genotype

“…The expression profiles of the transcription factors (TFs) revealed that the anthocyanin production promoter MYB10 and repressor MYB1 were both significantly lower at the R stage in white PC than in red BS (Figure 3). The transcript levels of the anthocyanin production repressor MYB1 in this study differ from those for FaMYB1 in red F. x ananassa [47], and in red F. vesca [28], seeming to increase at R rather than declining, indicating that it was not functioning as a repressor. In a white F. chiloensis, FcMYB1 was also high at T and R, suppressing anthocyanin accumulation [19].…”

“…Medina-Puche et al [29] suggested that MYB10 may regulate most or all of the flavonoid pathway genes in the early and late stages of fruit development in F. x ananassa. There was no apparent expression of MYB10 at G1 and more expression in red than white at G2 in our study, as with FaMYB10 in F. x ananassa [29,47], but MYB10 was lower in white PC at stage R in comparison to BS. Overexpression of FvMYB10 in F. vesca greatly increased anthocyanin concentration [26], but other flavonoid levels were not affected except for p-coumaroyl glucose, suggesting MYB10 may only act on the final anthocyanin-related branch.…”

Motif analysis in co-expression networks reveals regulatory elements in plants: The peach as a model

“…Our results are supported by previous studies reporting that bZip were induced by various environmental cues. Indeed it was revealed that they play a pivotal role in responses to cold stress in peach and enhance water use efficiency in almond-peach rootstocks (Hu et al, 2018). WRKYs putative motifs were restricted to M6 and were exclusively activated in leaf tissue under hyper-hydricity (HH) stress.…”

Comparative transcriptome analysis reveals the response mechanism of Cf-16-mediated resistance to Cladosporium fulvum infection in tomato

“…Transcriptome sequencing (RNA-Seq) has strongly accelerated research on host-pathogen interactions in plants such as rice [31], maize [32], cucumber [33], watermelon [34] and strawberry [35]. Avr4/Cf-4and Avr9/Cf-9-dependent defense gene expression has been confirmed by cDNA-AFLP (cDNA-amplified fragment length polymorphism) analysis [36].…”