Genome-wide-association study and transcriptome analysis reveal the genetic basis controlling the formation of leaf wax in Brassica napus.

Cuticular wax protects plants from various biotic and abiotic stresses. However, the genetic network of wax biosynthesis and the environmental factors influencing leaf wax production in rapeseed (Brassica napus) remains unclear. Here, we showed the role of leaf wax in resisting Sclerotinia infection in rapeseed. We found that leaves treated with high light intensity had higher expression of genes involving wax biosynthesis and produced more wax on the leaf surface compared with their counterparts. Genome-wide association study (GWAS) identified 89 single nucleotide polymorphisms significantly associated with leaf wax coverage. A cross-analysis between GWAS and differentially expressed genes (DEGs) in the leaf epidermis of the accessions with contrasting differences in leaf wax content revealed 17 candidate genes that may control the variation in leaf wax coverage in rapeseed. Selective signals combined with DEG analysis unveiled 510 candidate genes with significant selective signatures. From the candidate genes, we selected BnaA02.LOX4, a putative lipoxygenase, and BnaCnn.CER1, BnaA02.CER3, BnaC02.CER3, and BnaA01.CER4 that were putatively responsible for wax biosynthesis to analyze the allelic forms and haplotypes corresponding to high or low leaf wax coverage. These data enrich our knowledge about the wax formation and provide a gene pool for breeding to achieve the ideal leaf wax content in rapeseed.