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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\u2010specific RNA sequencing data from wild, landrace, and improved pear varieties and identified 12\u00a0422 lncRNAs that exhibited higher tissue specificity and lower sequence conservation than protein\u2010coding genes. Roughly 74% of lncRNAs overlapped with transposable elements (TEs) and significantly impacted sequence diversity, expression variation, and tissue\u2010specific 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\u2010related metabolites during pear domestication and improvement. Integrating transcriptome and metabolome analyses, we established a lncRNA\u2010mRNA co\u2010expression network associated with lignin biosynthesis. The regulatory role of\n                    <jats:italic>lncRNA\u2010pys<\/jats:italic>\n                    \u00a0within this network was functionally validated through transgenic experiments, demonstrating that overexpressing\n                    <jats:italic>lncRNA\u2010pys<\/jats:italic>\n                    \u00a0led 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.\n                  <\/jats:p>","DOI":"10.1002\/advs.77091","type":"journal-article","created":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T13:42:06Z","timestamp":1787146926000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["The Landscape of Long Non\u2010Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit"],"prefix":"10.1002","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-2299-9827","authenticated-orcid":false,"given":"Bobo","family":"Song","sequence":"first","affiliation":[{"name":"College of Horticulture State Key Laboratory of Crop Genetics &amp; Germplasm Enhancement and Utilization Nanjing Agricultural University  Nanjing Jiangsu China"},{"name":"School of Horticulture Anhui Agricultural University  Hefei Anhui 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State Key Laboratory of Crop Genetics &amp; Germplasm Enhancement and Utilization Nanjing Agricultural University  Nanjing Jiangsu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lingchao","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Horticulture State Key Laboratory of Crop Genetics &amp; Germplasm Enhancement and Utilization Nanjing Agricultural University  Nanjing Jiangsu China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1566-5115","authenticated-orcid":false,"given":"Jun","family":"Wu","sequence":"additional","affiliation":[{"name":"College of Horticulture State Key Laboratory of Crop Genetics &amp; Germplasm Enhancement and Utilization Nanjing Agricultural University  Nanjing Jiangsu China"},{"name":"School of Horticulture Anhui Agricultural University  Hefei Anhui 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