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

Abstract

Abstract Flesh thickness (FT) is the edible portion of melon fruit and directly affects its utilization rate, with an important influence on commerciality and yield. In this study, the 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 quantitative trait locus (Cmqft4.1) related to flesh thickness on chromosome 4. Genetic mapping narrowed down the Cmqft4.1 locus to a 222-kb interval using the 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 present 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.