Differentiation of long Non-Coding RNA expression profiles in three Fruiting stages of grape

Grapes are considered a crucial fruit crop with extensive uses globally. Cluster compactness is an undesirable trait for the productivity of Yaghooti grape, and it reduces its desirability among consumers. The RNA-Seq data were analyzed in three stages of cluster development using the FEELnc software, leading to the identification of 849 lncRNAs. 183 lncRNAs were differentially expressed during cluster development stages. The GO and KEGG enrichment analyses of these lncRNAs revealed that they target 1,814 genes, including CKX, PG, PME, NPC2, and UGT. The analysis demonstrated a relationship between these lncRNAs and key processes such as grape growth and development, secondary metabolite synthesis, and resistance to both biotic and abiotic stresses. These findings, combined with molecular experiments on lncRNA interactions with other regulatory factors, could enhance Yaghooti grape quality and decrease cluster compactness.