Validation of reference genes for qRT-PCR analysis in peel and flesh of six apple cultivars (Malus domestica) at diverse stages of fruit development

•We selected flesh or peel samples in fruit different development stages of six cultivars in this study.•The expression of candidate reference genes WD40, ACT and GAPDH were most stable in four peel samples.•The expression of candidate reference genes EF-1α, CKL and WD40 were most stable in two flesh samples.•The expression of candidate reference gene MDH was least stable among six flesh and peel samples.