Transcriptomic analysis reveals role of lncRNA LOC100257036 to regulate AGAMOUS during cluster compactness of Vitis vinifera cv. sistan yaghooti.

Yaghooti grape, as the earliest grape variety in Iran, is considered as more resistant to heat, drought, and salinity than other cultivars. Cluster compactness is regarded as an inappropriate feature for the productivity of Yaghooti grape as a critical commercial and nutritional product. In plants, lncRNAs play a critical role in regulating biological processes related to growth and development. However, the potential role of lncRNAs was not assessed in cluster compactness. Totally, 1549 lncRNAs were identified by RNA-Seq data analysis in three steps of cluster formation, berry formation, and final cluster size after a thorough screening process. In addition, 229 lncRNAs were differentially expressed in the cluster development steps. Based on the functional analysis, lncRNAs are related to AG and MYB, bHLH, LBD, NAC, and WRKY TFs. Further, the target genes enrichment analysis revealed a relationship between lncRNAs with grape growth and development, as well as resistance to abiotic stresses such as heat and drought, plant defense against pathogens, and early grapes ripening. The study identified four lncRNAs as precursors of miRNAs, predicting that 112 other lncRNAs could potentially be targeted by 166 miRNAs. The results provide new insights into the regulatory functions of lncRNAs in Yaghooti grape to improve overall understanding of the molecular mechanisms related to grape compactness.