ObjectiveThe study aimed to explore the factors regulating carotenoid accumulation in flesh color. MethodA loquat mutation (red-or orange-fleshed plant emerged a bud mutation of white-flesh in trunk) was used as material; HPLC analysis of β-carotene content was conducted. ResultThe β-carotene concentration in the flesh of wild and mutant types was 60.9 and 4.6 μg/g fresh weight, respectively. According to the conserved regions of genes from rose family genome, carotenogenic gene fragments in wild and mutant types were obtained. No nucleotide variation of the carotenogenic gene fragments was observed between wild and mutant genome. Real-time quantitative polymerase chain reaction (Q-PCR) was compared and one carotenogenic gene, β-ring hydroxylase (HYB) were considerably suppressed in mature mutant loquat fruits compared with that in wild. The other six carotenogenic genes were also expressed but the expression patterns appeared to be not correlated with the amount of β-carotene concentration in wild loquat flesh. ConclusionThe mutant whitish loquat lacks the ability to synthesize β-carotene because of the transcriptional down-regulation of carotenogenic gene HYB.