AbstractBACKGROUNDThe levels and ratios of sugar and acid are important contributors to fruit taste. Kumquat is one of the most economically important citrus crops, but information on the soluble sugar and organic acid metabolism in kumquat is limited. Here, two kumquat varieties – ‘Rongan’ (RA) and its mutant ‘Huapi’ (HP) – were used to assess soluble sugar and organic acid accumulation and the related genes.RESULTSSoluble sugars include sucrose, glucose and fructose, while malate, quinic acid and citrate are the dominant organic acids in the fruits of both kumquat varieties. HP accumulated more sugars but fewer organic acids than did RA. Transcriptome analysis revealed 63 and 40 differentially expressed genes involved in soluble sugar and organic acid accumulation, respectively. The genes associated with sugar synthesis and transport, including SUS, SPS, TST, STP and ERD6L, were up‐regulated, whereas INVs, FRK and HXK genes related to sugar degradation were down‐regulated in HP kumquat. For organic acids, the up‐regulation of PEPC and NAD‐MDH could accelerate malate accumulation. In contrast, high expression of NAD‐IDH and GS resulted in citric acid degradation during HP fruit development. Additionally, the PK, PDH, PEPCK and FBPase genes responsible for the interconversion of soluble sugars and organic acids were also significantly altered in the early development stages in HP.CONCLUSIONThe high sugar accumulation in HP fruit was associated with up‐regulation of SUS, SPS, TST, STP and ERD6L genes. The PEPCK, PEPC, NAD‐MDH, NADP‐IDH, GS and FBPase genes played important roles in acid synthesis and degradation in HP kumquat. These findings provide further insight into understanding the mechanisms underlying metabolism of sugars and organic acids in citrus. © 2021 Society of Chemical Industry