Association mapping in Brassica napus (L.) accessions identifies a major QTL for blackleg disease resistance on chromosome A01

Blackleg disease caused by the fungus Leptosphaeria maculans is one of the most devastating diseases of Brassica napus . Association mapping was used to evaluate the response of 139 B. napus accessions originated from 16 countries with 4 growth habit types to inoculation with L. maculans isolates from pathogenicity group 4. All accessions were inoculated at the seedling stage and 37,346 single nucleotide polymorphism markers based upon genotyping-by-sequencing were used for analysis. One major QTL associated with the blackleg disease was identified on chromosome A01 at 9.66 Mbp and explains about 14.7 % of phenotypic variation ( p value <2.2E−05). Orthologs of Arabidopsis thaliana hydroxyproline-rich glycoprotein family protein, acyl-CoA oxidase 1 and cysteine-/histidine-rich C1 domain family protein that are involved in plant defense mechanism were identified in this QTL region. At a lower significance ( p value <0.00139), thirty-five additional markers were identified which are located on 13 other chromosomes. Stepwise regression identified that these markers belong to ten QTL regions and together explain 51.04 % of phenotypic variations. Additional twenty orthologs of A. thaliana disease resistance genes, transcription factors, genes in phytohormone pathway and signaling in plant defense pathway have been identified to be associated with the blackleg disease. Based on the haplotype at the most significant QTL, a total of 22 genotypes were evaluated in the greenhouse. As expected with the haplotype, we had 100 % success in predicting the phenotype. These markers could further be used for identification of phenotype that can be used in the breeding program.