Transcriptomic analysis reveals the mechanism underlying the anthocyanin changes in Fragaria nilgerrensis Schlecht. and its interspecific hybrids

Abstract

Background: Fragaria nilgerrensis (FN) provides a rich source of genetic variations for strawberry germplasm innovation. The color of strawberry fruits is a key factor affecting consumer preferences. However, the genetic basis of the fruit color formation in F. nilgerrensis and its interspecific hybrids has rarely been researched.

Results: In this study, the fruit transcriptomes and flavonoid contents of FN (white skin; control) and its interspecific hybrids BF1 and BF2 (pale red skin) were compared. A total of 31 flavonoids were identified. Notably, two pelargonidin derivatives (pelargonidin-3-O-glucoside and pelargonidin-3-O-rutinoside) were revealed as potential key pigments for the coloration of BF1 and BF2 fruits. Additionally, dihydroflavonol 4-reductase (DFR) (LOC101293459 and LOC101293749) and anthocyanidin 3-O-glucosyltransferase (BZ1) (LOC101300000), which are crucial structural genes in the anthocyanidin biosynthetic pathway, had significantly up-regulated expression levels in the two FN interspecific hybrids. Moreover, most of the genes encoding transcription factors (e.g., MYB, WRKY, TCP, bHLH, AP2, and WD40) related to anthocyanin accumulation were differentially expressed. We also identified two DFR genes (LOC101293749 and LOC101293459) that were significantly correlated with members in bHLH, MYB, WD40, AP2, and bZIP families. Two chalcone synthase (CHS) (LOC101298162 and LOC101298456) and a BZ1 gene (LOC101300000) were highly correlated with members in bHLH, WD40 and AP2 families.

Conclusions: Pelargonidin-3-O-glucoside and pelargonidin-3-O-rutinoside may be the key pigments contributing to the formation of pale red fruit skin. DFR and BZ1 structural genes and some bHLH, MYB, WD40, AP2, and bZIP TF family members enhance the accumulation of two pelargonidin derivatives. This study provides important insights into the regulation of anthocyanidin biosynthesis in FN and its interspecific hybrids. The presented data may be relevant for improving strawberry fruit coloration via genetic engineering.

Keywords: Anthocyanin biosynthesis; Fragaria nilgerrensis Schlecht; Interspecific hybrids; Pelargonidin derivatives; Red coloration.

Fig. 1

Fruits of F. nilgerrensis Schlecht. (FN, a and a’) and its interspecific hybrids BF1(b and b’) and BF2 (c and c’). The scale bar represents 1 cm

Fig. 2

Validation of 8 selected DEGs via qRT-PCR

Fig. 3

Venn diagram analysis of differentially expressed genes

Fig. 4

GO analysis of co-differentially expressed genes

Fig. 5

KEGG analysis of co-differentially expressed genes

Fig. 6

Expression patterns of structural DEGs related to anthocyanin biosynthesis in F. nilgerrensis and its interspecific hybrids. The level of gene expression was measured in F. nilgerrensis Schlecht. (FN) and its interspecific hybrids BF1 and BF2. Red indicatesa high level of expression at different samples. The the red dashed box represents the downstream metabolites of BZ1 gene. The abbreviations of each gene that encodes enzymes and compounds are provided in abbreviations. The levels of gene expression in these biosynthetic pathways are shown in Table S3

Fig. 7

Correlation analysis between 39 transcription factor genes with 5 anthocyanin biosynthetic related genes and 2 key anthocyanins. The color filled hexagons represent different transcription factors, the red filled spheres represent geranidin-3-o-glucoside and geranidin-3-o-rubutin, and the red filled squares represent the structural genes associated with anthocyanin biosynthetic pathways. The expression correlations are shown with colored lines, and the red line indicates a positive correlation, and the blue line indicates a negative correlation