Abstract To identify Insertion-deletion (Indel) markers tightly linked to the fruit bitterness (Bt) gene in cucumber (cucumis sativus L.), a F2 population including 184 individuals derived from two cucumber inbred lines 931(btbt) and 46GBt (BtBt) was used in this study. Results showed that the inheritance of fruit bitterness in cucumber was controlled by one dominant gene Bt. Based on primary mapping of Bt gene and re-sequence of two parental lines, Bioinformatics was employed to analyze the sequence difference between the two parental lines in the primary mapping region of Bt gene. Then seven Indel markers were developed. The InDel marker Bt-InDel-1 tightly linked to Bt gene with 0.8 cM was identified after analysis on F2 population with 184 individuals using the seven Indel markers. The veracity of Bt-InDel-1 was tested using another F2 population with 58 individuals, and the accuracy rate for this marker was 94.8%. The results indicated that the Bt-InDel-1 marker can be used in non-bitter MAS cucumber breeding and fine-mapping of Bt gene.
