Fine mapping and candidate genes analysis for flesh thickness major locus <i>Cmqft4.1</i> of melon ( <i>Cucumis melo</i> L.)

Abstract Flesh thickness (FT) is the edible portion of melon fruit, directly affects its utilization rate with important influence on the commerciality and yield. In this study, phenotype of F2 populations derived from PI 282448 (thin-fleshed, ssp. melo, wild type) and M4-135 (thick-fleshed, ssp. melo, cultivar) showed that flesh thickness is a quantitative trait. Graded Pool-seq (GPS) combined with genetic linkage analysis identified a stable major-effect QTL (Cmqft4.1) related to flesh thickness on chromosome 4. Genetic mapping narrowed down the Cmqft4.1 locus to 222 kb interval using near-isogene line NIL_BC3F2 population, which contained 13 candidate genes. Through gene expression and sequence alignment, MELO3C012896.2 (annotated as Ethylene-responsive transcription factor 1B-like) was predicted as the key candidate gene for flesh thickness in melon. A 286 bp deletion in the promoter region of MELO3C012896.2 was existed in multiple thick-fleshed melon natural materials. These results provide a theoretical basis for further gene functional verification and breeding programs focused on flesh thickness in melon.