Genome-Wide Association Study Elucidates the Genetic Architecture of Manganese Tolerance in Brassica napus

Brassica napus (canola) is a significant contributor to the world's oil production and is cultivated across continents, yet acidic soils with aluminium (Al³⁺) and manganese (Mn²⁺) toxicities limit its production. The genetic determinants underlying natural variation for acidic soil tolerance in canola are unknown and need to be determined. Through genome-wide association analysis of 326 canola accessions, we identified three QTLs for tolerance to Mn²⁺ toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn²⁺ tolerance in canola. Integrated analyses of genomic and expression QTL and Mn²⁺ tolerance data revealed that BnMTP8.A09, possibly in conjunction with BnMATE.C03, BnMTP8.C04 and BnMTP8.C08, play a central role in conferring Mn²⁺ tolerance in canola. Gene expression analysis showed that variation in BnMTP8.A09 expression could account for upto 74% of the variation in Mn²⁺ tolerance between individuals with extreme phenotypes. Yeast complementation assays and ectopic expression in Arabidopsis show that BnMTP8.A09 can complement manganese-hypersensitive yeast mutant strain PMR1∆ and Arabidopsis atmtp8 mutant background, respectively and restore Mn²⁺ tolerance to wild-type levels. Our multi-omics research approach unveils the genetic architecture of Mn²⁺ tolerance and identifies BnMTP8.A09 as a causal gene imparting tolerance to Mn²⁺ toxicity in canola.