Multiomics reveal pivotal roles of sodium translocation and compartmentation in regulating salinity resistance in allotetraploid rapeseed.

The large size and complexity of the allotetraploid rapeseed (Brassica napus) genome present huge challenges for understanding salinity resistance in this important crop. In this study, we identified two rapeseed genotypes with significantly different degrees of salinity resistance and examined the underlying mechanisms using an integrated analysis of phenomics, ionomics, genomics, and transcriptomics. Under salinity, a higher accumulation of osmoregulation substances and better root-system architecture was observed in the resistant genotype, H159, than in the sensitive one, L339. A lower shoot Na+ concentration and a higher root vacuolar Na+ concentration indicated lower root-to-shoot translocation and higher compartmentation in H159 than in L339. Whole-genome re-sequencing (WGRS) and transcriptome sequencing identified numerous DNA variants and differentially expressed genes involved in abiotic stress responses and ion transport. Combining ionomics with transcriptomics identified plasma membrane-localized BnaC2.HKT1;1 and tonoplast-localized BnaC5.NHX2 as the central factors regulating differential root xylem unloading and vacuolar sequestration of Na+ between the two genotypes. Identification of polymorphisms by WGRS and PCR revealed two polymorphic MYB-binding sites in the promoter regions that might determine the differential gene expression of BnaC2.HKT1;1 and BnaC5.NHX2. Our multiomics approach thus identified core transporters involved in Na+ translocation and compartmentation that regulate salinity resistance in rapeseed. Our results may provide elite gene resources for the improvement of salinity resistance in this crop, and our multiomics approach can be applied to other similar studies.