Characterization of Diverse Carrot (Daucus carota L.) Genotypes Using Long Noncoding RNA Based Microsatellite Markers

In the pursuit of enhancing carrot breeding programs, our study focused on the experimental validation of selected long non-coding RNAs (lncRNAs) using end-point polymerase chain reaction (PCR). Twenty-seven carrot (Daucus carota L.) genotypes, including Asiatic and Western varieties, were grown in RCBD design and evaluated for root traits at UHS Bagalkot, Karnataka, India, during 2022-2023. These genotypes were used to validate five SSR markers developed for lncRNAs in carrots. From an initial set, five lncRNAs were chosen for further experimental validation based on their bit score and the presence of simple sequence repeat (SSR) motifs. Our novel approach involved the development of 27 imperfect SSR markers and five perfect SSR markers specifically targeting these lncRNAs. The integration of SSR markers with lncRNA studies is unprecedented in carrot breeding, opening new avenues for genetic improvement. Among the five lncRNA-derived SSR (lncSSR) markers developed, DcLNC55 and DcLNC62 exhibited polymorphisms across 27 diverse carrot genotypes. In conclusion, our study highlights the innovative use of lnc-SSR markers in carrot breeding, demonstrating their utility in genetic diversity studies and their potential role in uncovering the functional importance of lncRNAs in crop phenotypes. The findings present significant implications for future carrot breeding strategies, providing a foundation for integrating molecular markers and lncRNA research in carrot and other related horticultural crop improvement programs.