Isolation, expression, and microRNAs analysis of genes related to carotenoid metabolism in peach fruits

The isolation and expression comparison between red and white flesh of ten genes related to carotenoid metabolism have been analyzed in two peach cultivars at six developmental stages. Furthermore, mature sequences of microRNAs (miRNAs) and targeting ranges to their targets PpCCD4, PpCHYb, PpPDS, which are the most correlated with red flesh color of fruit among ten genes according to above expression patterns, were also analyzed through bioinformatics method. The cloning results led to the isolation of 1,284, 1,716, 1,569, 1,668, 1,215, 1,644, 1,722, 933, 1,515, and 2,091 nucleotide cDNAs encoding 428, 572, 523, 556, 405, 548, 574, 311, 505, and 697 amino acids for PpCCD4, PpZDS, PpLCYe, PpCHYe, PpPSY, PpCCD1, PpPDS, PpCHYb, PpLCYb, and PpZEP genes in peach, respectively. Blast search against the NCBI database revealed the nucleotide sequences of the ten genes had high similarity to corresponding genes reported in other plants. Among the ten genes, the expression level of PpCCD1 in white flesh peach decreased as fruit developed. The expression levels of PpCCD4, PpZDS, PpPDS, and PpLCYb in red flesh peach were relatively higher than in white flesh peach at the most developmental stages of fruits. Especially, the expression level of PpCCD4 in red flesh peach significantly increased as fruit developed and was far higher than in white flesh peach. Novel mir29 and mir729, and known miR172a-5p were found to target genes PpCCD4, PpCHYb, PpPDS at nucleotide 251-270, 1270-1292, 185-205 from the 5' to the 3' end, respectively. The results obtained from this study will be useful for further functional analysis of these target genes and miRNAs in the pathway of carotenoid metabolism in peach.