CmWAT6.1, mined by high-density genetic map-based QTL mapping, enhances waterlogging tolerance in chrysanthemum

High-density genetic maps are a valuable tool for quantitative trait locus (QTL) mapping and gene discovery for important traits in plants. However, such work in chrysanthemum remains largely unexplored, primarily owing to its large genome and complex genetic background. In this study, a high-density map containing 11,941 SNP bins spanning a total of 2,967.76 cM in 27 linkage groups (LGs) with an average intermarker distance of 0.26 cM was developed with a genotyping by sequencing (GBS) approach. A total of 34 QTL clusters for waterlogging tolerance (WAT) were detected via multiple-QTL mapping (MQM) algorithms. A total of 186 candidate genes within these QTL clusters were mined in combination with transcriptome data. One key candidate gene within the QTL cluster cWAT6.1, which belongs to group VII ethylene response factors (CmWAT6.1), was proven to be a positive regulator of WAT in chrysanthemum. Furthermore, transcriptomic assays of transgenic and wild-type chrysanthemums under normal conditions as well as further experiments provided evidence that CmWAT6.1 regulated WAT by promoting cell wall formation and lignin biosynthesis and coordinating oligosaccharide metabolic processes. This study represents important progress in gene mining through forward genetics, provides valuable genetic resources for further WAT improvement and provides new insight into the molecular mechanism of WAT in chrysanthemum.