Identification and expression analysis of the CLC gene family in sugarcane

The chloride channel (CLC) gene family plays a crucial role in nitrate storage within plant vacuoles. However, its characteristics remain largely unexplored in the complex genome of sugarcane. In this study, we systematically identified 29 <italic>CLC</italic> genes (<italic>SsCLCs</italic>) from the <italic>Saccharum spontaneum</italic> genome. These <italic>SsCLCs</italic> were distributed across 21 chromosomes and phylogenetically classified into six subgroups (Groups a, c, d, e, f, and g). The gene family exhibited conserved structures and motif compositions. Genomic collinearity analysis indicated that the expansion of SsCLC was mainly driven by whole-genome or segmental duplication events under strong purifying selection. Promoter analysis revealed a high abundance of <italic>cis</italic>-acting elements associated with hormone responses (50.00%), growth and development (42.86%), and stress responses (7.14%). Furthermore, in a comparison between <italic>S. spontaneum</italic> Yunnan 82-1 and its three hybrid progenies, the hybrids exhibited significant improvements in key agronomic traits, including stalk diameter, leaf length, brix, fresh weight, and dry weight. Consistently, transcriptome and qRT-PCR analyses showed that 75.86% (22 out of 29) of the <italic>SsCLC</italic> genes were upregulated in the roots of the hybrids. This study presents the first comprehensive genomic characterization of the SsCLC gene family and highlights its potential role in improving nitrogen use efficiency during sugarcane nobilization through root-specific gene upregulation, thereby offering valuable genetic resources for breeding nitrogen-efficient sugarcane cultivars.