Genome-wide identification and characterization of long non-coding RNAs involved in grape berry ripening

BACKGROUND: Long non-coding ribonucleic acids (lncRNAs) have been linked to many important biological processes, including fruit ripening. “Fengzao” is an early-ripening bud mutant of “Kyoho” that matures nearly 30 days earlier. However, the molecular networks controlling early ripening in Fengzao are still poorly understood in comparison to those in Kyoho. OBJECTIVE: The aim of the study was to gain a better understanding of the regulatory role of lncRNAs in the early ripening of grape berries. METHODS: The RNA-sequencing approach and quantitative real-time polymerase chain reaction validation were employed to identify lncRNAs and profile their expression patterns during berry development. RESULTS: In total, 24726 lncRNAs were identified, of which 19699 were differentially expressed (DE-lncRNAs) between developmental stages. The target genes of these lncRNAs and their regulatory relationships were predicted. The oxidoreductase activity, plant–pathogen interaction, plant hormone signal transduction, and flavanol biosynthesis pathways were enriched in the target genes of DE-lncRNAs, and six key lncRNAs (TCONS_00221683, TCONS_00684459, TCONS_00022149, TCONS_00167247, TCONS_00258125, and TCONS_00261813) were identified that may regulate the early ripening of grape berries. CONCLUSIONS: The results contribute to the understanding of the role of lncRNAs in early ripening of grape berries and will provide new insights for molecular breeding of grapes.