A Major Locus for Manganese Tolerance Maps on Chromosome A09 in a Doubled Haploid Population of Brassica napus L.

Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al(3+) and Mn(2+). Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn(2+) tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn(2+) toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 μM of MnCl(2)⋅4H(2)O) and Mn treatment (125 μM of MnCl(2)⋅4H(2)O). Among parental lines, we selected Darmor-bzh and Yudal that showed significant and contrasting variation in Mn(2+) tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn(2+) tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F(1) cross, Darmor-bzh/Yudal for Mn(2+) tolerance. Mn(2+)-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn(2+)-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, BnMn(2+).A09 was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn(2+) tolerance on chromosome A09. This is the first report on the genomic localization of a Mn(2+) tolerance locus in B. napus. Additionally, an ortholog of A. thaliana encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with BnMn(2+).A09. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the BnMn(2+).A09 locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn(2+) toxic soils.