Genome-Wide Analysis of CSL Family Genes Involved in Petiole Elongation, Floral Petalization, and Response to Salinity Stress in Nelumbo nucifera

Lotus (<i>Nelumbo nucifera</i>), a perennial aquatic plant, endures various environmental stresses. Its diverse ornamental traits make it an ideal model for studying multigene family functional differentiation and abiotic stress responses. The <i>cellulose synthase-like</i> (<i>CSL</i>) gene family includes multiple subfamilies and holds potentially pivotal roles in plant growth, development, and stress responses. Thus, understanding this family is essential for uncovering the attributes of ancient dicotyledonous lotus species and offering new genetic resources for targeted genetic improvement. Herein, we conducted a genome-wide <i>NnCSL</i> gene identification study, integrating tissue-specific expression analysis, RNA-seq, and qRT-PCR validation. We identified candidate <i>NnCSL</i> genes linked to petiole elongation, floral petalization, salinity stress responses, and potential co-expressed TFs. 22 <i>NnCSL</i> genes were categorized into six subfamilies: NnCSLA, NnCSLB, NnCSLC, NnCSLD, NnCSLE, and NnCSLG. Promoter regions contain numerous cis-acting elements related to growth, development, stress responses, and hormone regulation. Nineteen NnCSL genes showed specific differential expression in LPA (large plant architecture) versus SPA (small plant architecture): petioles, petalized carpels (CP) and normal carpels (C), and petalized stamens (SP) and normal stamens (S). Notably, most <i>NnCSLC</i>, <i>NnCSLA</i>, and <i>NnCSLB</i> subfamily genes play diverse roles in various aspects of lotus growth and development, while <i>NnCSLE</i> and <i>NnCSLG</i> are specifically involved in carpel petalization and petiole elongation, respectively. Additionally, 11 candidate <i>NnCSL</i> genes responsive to salinity stress were identified, generally exhibiting antagonistic effects on growth and developmental processes. These findings provide an important theoretical foundation and novel insights for the functional study of <i>NnCSL</i> genes in growth, development, and stress resistance in lotus.