The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.

Long non-coding RNAs (lncRNAs) play essential roles in plant growth and development. However, their expression variability and contribution to phenotypic changes during the domestication of fruit crops remain unclear. Here, we generated approximately 3.5T of strand-specific RNA sequencing data from wild, landrace, and improved pear varieties and identified 12 422 lncRNAs that exhibited higher tissue specificity and lower sequence conservation than protein-coding genes. Roughly 74% of lncRNAs overlapped with transposable elements (TEs) and significantly impacted sequence diversity, expression variation, and tissue-specific expression. DNA methylation explained approximately 32% of the expression variation of lncRNAs across accessions. Selective sweeps revealed 857 and 519 lncRNAs under domestication and improvement, respectively. These selected lncRNAs were associated with traits such as fruit size, sugar content, and stone cell content. Metabolome profiling revealed a consistent reduction in lignin-related metabolites during pear domestication and improvement. Integrating transcriptome and metabolome analyses, we established a lncRNA-mRNA co-expression network associated with lignin biosynthesis. The regulatory role of lncRNA-pys within this network was functionally validated through transgenic experiments, demonstrating that overexpressing lncRNA-pys led to an increase in lignin content in pear. This study represents the first effort to unveil the contributions of lncRNAs under human selection to the domestication traits of fruit crops.