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 Al ³⁺ and Mn ²⁺ toxicities limit its production. The genetic determinants underlying acidic soil tolerance in canola are unknown and require to be uncovered for canola breeding and production. Here, through comprehensive phenotyping, whole genome resequencing, and genome-wide association analysis, we identified three QTLs for tolerance to Mn ²⁺ toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn ²⁺ tolerance in B. napus . Integrated analysis of genomic and expression QTL and Mn ²⁺ tolerance data reveals that BnMTP8.A09, in conjunction with BnMATE.C03 , BnMTP8.C04 and BnMTP8.C08 , play a central role in conferring Mn ²⁺ tolerance in B. napus . Gene expression analysis revealed a high correlation ( R ² = 0.74) between Mn ²⁺ tolerance and the BnMTP8.A09 expression. Yeast complementation assays show that BnMTP8.A09 can complement manganese-hypersensitive yeast mutant strain PMR1 Δ and restore Mn ²⁺ tolerance to wild-type levels. Inductively coupled plasma mass spectrometry revealed that Mn ²⁺ tolerant accessions accumulate less Mn in the shoots compared to Mn ²⁺ sensitives, suggesting that the BnMTP8.A09 transporter likely sequesters Mn ²⁺ into the tonoplast. Taken together, our research unveils the genetic architecture of Mn ²⁺ tolerance and identifies BnMTP8.A09 as a major gene imparting tolerance to Mn ²⁺ toxicity in B. napus .