Identification and functional characterization of lncRNAs and mRNAs in response to salt stress in mulberry

Long non-coding RNAs (lncRNAs) have been recognized as significant contributors to the mechanisms underlying abiotic stress tolerance in various organisms. Nevertheless, the specific mechanisms through which they contribute to this tolerance remain ambiguous. This study identified salt-response genes and characterized the functions of lncRNAs in mulberry roots. RNA-seq identified 6,330 mRNAs and 1,201 lncRNAs as responsive to salt treatment. We identified the function of mulberry salt in response to lncRNA (lnc15780). Transgenic hairy root plants of mulberry overexpressing lnc15780 were generated. lnc15780 reduces the salt tolerance of plants by inhibiting antioxidant activity. LUC combined with RNA sequencing showed that lnc15780 inhibited the expression of <italic>MnIAA27</italic> by binding to its promoter. The hairy root plants of mulberry with <italic>MnIAA27</italic> overexpression were produced. The overexpression of <italic>MnIAA27</italic> gives it salt tolerance. In addition, <italic>MnIAA27</italic> reduces ROS accumulation. In summary, lnc15780 acts as a negative regulator of <italic>MnIAA27</italic>, leading to a reduction in the expression of lnc15780 during periods of salt stress. This decrease activates the expression of <italic>MnIAA27</italic>, which subsequently promotes both plant growth and enhances salt tolerance. Consequently, lnc15780 emerges as a promising candidate gene for molecular breeding efforts aimed at developing plant varieties that exhibit higher growth rates alongside improved resilience to salt stress. Our findings indicate that lncRNA is integral to the salt response mechanisms in mulberry, highlighting its significance in the plant's adaptation to saline environments.