Melon (Cucumis melo L.) is an economically important crop whose production is severely affected by fruit cracking, a disorder that leads to substantial post-harvest losses. While environmental factors are known contributors, the roles of long non-coding RNAs (lncRNAs), SNPs, and eQTLs in melon cracking remain poorly understood. This study aimed to characterize these molecular regulators to elucidate their functions in cracking susceptibility. Through transcriptome analysis of 112 melon recombinant inbred lines (RILs), we identified 341 high-confidence lncRNAs. Functional enrichment linked them to metabolic processes, cell wall remodeling, and stress responses. Co-expression networks revealed interactions between lncRNAs and key transcription factors (MYB, WRKY, NAC) and cell wall-related genes (EXP, XTH, AQP). eQTL analysis identified 10 lncRNAs associated with fruit cracking, with two (MSTRG.4395 and MSTRG.623) showing strong regulatory links to auxin-related (ILR1) and calcium-signaling (calmodulin) genes. SNPs in these loci significantly influenced lncRNA expression, suggesting roles in hormonal and structural pathways affecting cracking. This study provides the first genome-wide characterization of lncRNAs and eQTLs in melon fruit cracking, uncovering their regulatory roles in cell wall integrity, hormone signaling, and stress response. The identified lncRNA-mRNA networks and candidate SNPs offer potential molecular markers for breeding crack-resistant melon varieties, contributing to sustainable agriculture and reduced post-harvest losses.
Mohammadi et al. (Fri,) studied this question.