Development of near isogenic lines for the glabrous gene Cmgl by marker assisted selection and transcriptome analysis in melon

• Cmgl was introgressed into HB42 by MAS, generating NILs with a PRPG up to 98.39 %. • gl -NILs displayed a complete glabrous phenotype. • CmGL regulated melon trichome development via multiple hormonal pathways. Trichomes are hair-like structures that protect plants against biotic and abiotic stresses. CmGL encodes a HD-ZIP IV transcription factor controlling multicellular trichome development in melon, highlighting its utility in resistance breeding. However, the regulatory mechanism of CmGL in trichome development remains unclear. In this study, the glabrous donor parent M68 carrying Cmgl was crossed with the normal trichome-covered recurrent parent HB42 to generate BC 2 F 1 and BC 2 F 2 populations to develop a near isogenic line (NIL) of Cmgl . The Cmgl co-segregating marker cmgl -dCAPS was used for foreground selection and 145 polymorphic SSR markers were used for background selection. Four NILs with highest PRPG (proportion of recurrent parent genome) were obtained, with the highest reaching 98.39 %. Compared to HB42, the four NILs displayed a complete glabrous phenotype with no observable trichomes on any aboveground tissues, and CmGL transcripts were significantly decreased in both NILs and M68, indicating that Cmgl NILs have been successfully developed. Transcriptome profiling of the leaves from HB42 and gl -NIL-4 identified 520 differentially expressed genes (DEGs) with 272 up-regulated and 248 down-regulated. These DEGs were related to some well-known trichome regulators and hormonal pathways - auxin, ethylene, gibberellin and jasmonic acid - all involved in trichome development. Cell wall modification, lipid biosynthetic process, multiple phytohormone-activated signaling pathway and defense response, were significantly enriched. Quantitative RT-PCR confirmed the expression of selected DEGs. These results not only offer valuable genetic resource for resistance breeding but also facilitate further in-depth studies on the molecular mechanisms underlying trichome development in melon.