Seed size is an important agronomic trait in melons that directly affects the seed germination and subsequent seedling growth. However, the genetic mechanism underlying seed size in melon has remained unclear. In the present study, we employed Bulked-Segregant Analysis sequencing (BSA-seq) to identify a candidate region (∼1.35 Mb) on chromosome 6 that corresponds to seed size. This interval was confirmed by QTL mapping of three seed size-related traits from an F₂ population across three environments. This mapping represented nine QTLs that shared an overlapping region on chromosome 6, collectively referred to as qSS6.1. New InDel markers were developed in the qSS6.1 region, narrowing it down to a 68.35-kb interval that contains eight annotated genes. Sequence variation analysis of the eight genes identified a SNP with a C to T transition mutation in the promoter region of MELO3C014002, a leucine-rich repeat receptor-like kinase (LRR-RLK) gene. This mutation affected promoter activity of the MELO3C014002 gene and was successfully used to differentiate the large-seeded accessions (C-allele) from the small-seeded accessions (T-allele). qRT-PCR revealed differential expression of MELO3C014002 between the two parental lines. Its predicted protein has typical domains of LRR-RLK family, and phylogenetic analyses reveled its similarity with the homologs in several plant species. Altogether, these findings suggest MELO3C014002 as the most likely candidate gene involved in melon seed size regulation. Our results will be helpful for better understanding the genetic mechanism regulating seed size in melons and for genetically improving this important trait through molecular breeding pathways.

Melon (Cucumis melo) includes more than ten botanical groups, many of which feature netting ornamentation on the surface of mature fruit. Ripe melons display a netted skin that signifies their ripeness and readiness for consumption. Previously, we identified SKIN NETTING (CmSN), which encodes an EamA-like transporter family protein, as the candidate gene controlling fruit skin netting formation in melon, while its biological functions remain unclear. In this study, we demonstrated that the expression of the CmSN gene was considerably lower in netted melons compared to smooth-skinned melons, indicating a negative correlation between CmSN expression and netting formation. Subsequently, we employed transient overexpression and virus-induced gene silencing (VIGS) experiments to explore the role of CmSN gene during fruit development. Overexpression of the CmSN gene inhibited netting development, whereas silencing it promoted netting formation. Using heterologous transformation in tomato, we further confirmed the effect of the CmSN gene on rind texture and toughness, as these tomatoes exhibited rougher and tougher skins. Analysis with near-isogenic lines (NILs) revealed that CmSN gene-bearing fruits (NIL_CmSN) possessed significantly harder rinds than the control smooth-skinned variety HB42, underscoring the role of CmSN in enhancing rind protection. Together, our research offers essential insights into the netting formation and genetic improvement of melon fruits.