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

Abstract

Abstract Background: Fragaria nilgerrensis (FN) provides a rich source of genetic variations for strawberry germplasm innovation. The coloration of strawberry fruits is a critical 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, DFR (LOC101293459 and LOC101293749) and 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 bHLH, MYB, WD40, AP2, and bZIP transcription factors. Two CHS genes (LOC101298162 and LOC101298456) and a BZ1 gene (LOC101300000) were highly correlated with bHLH, WD40, and AP2 transcription factors. 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 inFN and its interspecific hybrids. The presented data may be relevant for improving strawberry fruit coloration via genetic engineering.