Transcriptome and metabolome integrated analysis reveals the wax biosynthesis mechanism of Allium cepa L

•The primary component of onion epidermal wax was 16-Hentriacontanone.•Twenty-one key genes that may related to wax synthesis and metabolism were identified. Cuticle waxes play a crucial role in protecting plants from biotic and abiotic stresses, and their biosynthetic mechanisms are well understood in a variety of crops. However, the regulatory mechanism of cuticular wax synthesis in Allium cepa has not been fully understood. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the wax biosynthesis mechanism of A. cepa using the wild type, designated as WT1, and glossy mutant type, known as glo1, plants of A. cepa. The results revealed that the total wax content of WT1 was higher than that of glo1, with 16-Hentriacontanone identified as the main component of the wax. Transcriptomics analysis showed 384 up-regulated genes and 412 down-regulated genes in glo1 compared with WT1. Through Kyoto Encyclopedia of Genes and Genomes analysis, weighted gene co-expression network analysis, and joint analysis of transcriptome and metabolome data, we identified 21 key genes related to wax synthesis and metabolism. This research provides a comprehensive landscape of the transcriptome and metabolome, shedding light on the molecular mechanisms of cuticular wax synthesis in A. cepa. Furthermore, it lays the foundation for the development of potential breeding strategies in the future. [Display omitted]