Transcriptome analysis of colouration-related genes in two white-fleshed nectarine varieties and their yellow-fleshed mutants

Nectarine, a variety of peach is rich in bioactive and antioxidant compounds, and both white- and yellow-fleshed nectarine fruits are commercially popular. However, although anthocyanin (flavonoid) and carotenoid biosynthetic pathways play important roles in plant colouration, the molecular basis of fruit flesh colouration remains largely unknown. Accordingly, we performed an RNA sequencing-based transcriptome analysis of two white-fleshed nectarines, Zhongyou9 (ZY9) and Zhongyou13 (ZY13-W), and their yellow-fleshed mutants, Hongyu (HY) and Zhongyou13-Y (ZY13-Y). To differentiate the impact of ripening on gene expression, we also compared ZY9 and HY at two different time points, namely, before and after fruit ripening. We found that the yellow-fleshed HY may accumulate flavonoids through the generation of more flavonoid biosynthesis precursors, as well as through the overexpression of flavonoid synthase genes. In addition, we also found that HY could impede carotenoid degradation <i>via</i> beta-carotene 3-hydroxylase and carotenoid cleavage dioxygenase genes. Meanwhile, ZY13-Y may regulate its yellow colouration through overexpression of chalcone synthase genes, in order to accumulate flavonoids, as well as through the underexpression of flavonol 3-O-methyltransferase and carotenoid cleavage dioxygenase genes, in order to slow flavonoid and carotenoid degradation. As demonstrated by the multiple transcription factors that were differentially expressed in the yellow- and white-fleshed varieties, it is clear that the regulation of peach and nectarine colouration is a complex process. Furthermore, we also identified several other genes that are potentially related to fruit colouration. Thus, our results provide a valuable advancement in the elucidation of the molecular basis of flesh colouration in nectarine.