Abstract：The sex differentiation of melon is a complex system-regulation network, which is effected by different environment factors and level of hormone. In this study, a set of recombinant inbred lines of melon(Cucumis melo L.) was derived by crossing WI 998 with TopMark. The transcript profiles of monoecious lines and gynoecious lines in F2S6 group were acquired using the second-generation high throughput sequencing method, and genes associated with plant hormone biosynthesis pathways were analyzed by comparison of differentially expressed genes, Solexa sequencing and sequence-assembling, the results showed that 77 376 Unigenes were acquired from transcripts of monoecious lines with an average length of 435 bp, and 80 825 Unigenes were acquired from transcripts of gynoecious lines with an average length of 509 bp. Comparing the transcript profiles between monoecious and gynoecious lines, 8 966 genes were deemed as differentially expressed. In these genes, 4 296 genes were down-regulated while 4 670 genes were up-regulated. These genes were classified by gene ontology(GO)-ranking method, 2 352 Unigenes were related to biological process, 4 107 Unigenes were related to cellular process, and 2 507 Unigenes were related to molecular functions. The differential expressed genes participated in 121 pathways, gibberellin biosynthesis pathway, gibberellin3- oxidase(GA3-ox)(MU3674), GA7-ox(MU36987), GA2-ox(MU13098/MU13099), GA20-ox and GA2-ox (MU33020) were differentially expressed. Thirty eight genes expressed differentially involved in abscisic acid biosynthesis pathway, which 19 genes were up-regulated and 19 genes were down-regulated. In brassinolide biosynthesis, MU22012 (cytochrome P450) and MU26893 (cytochrome P450) were up-regulated, and MU56098 (cytochrome P450, CYP724B3) and MU76596 (CYP724A1) were down-regulated. In this study, the sex differentiation was also associated with the biosynthesis and signal transduction pathways of gibberellin, abscisic acid, brassinolide and zeatin. The results provide strong and important basis for the analysis of the possible mechanism of sex differentiation of melon, and for the further research on melon sex-modification genes cloning
