Genome-Wide Mapping of Loci Associated With Resistance to Clubroot in Brassica napus ssp. napobrassica (Rutabaga) Accessions From Nordic Countries

Abstract

Rutabaga [Brassica napus ssp. napobrassica (L.) Hanelt] is reported to be an excellent source of clubroot (Plasmodiophora brassicae) resistance genes. In this study, 124 rutabaga accessions from the Nordic countries (Norway, Sweden, Finland, Denmark, and Iceland) were evaluated for their reaction to five single-spore isolates representing P. brassicae pathotypes 2F, 3H, 5I, 6M, and 8N and 12 field isolates representing pathotypes 2B, 3A, 3O, 5C, 5G, 5K, 5L, 5X (two isolates, L-G2 and L-G3), 8E, 8J, and 8P. The accessions were also genotyped using a 15K Brassica SNP array and 60 PCR-based primers linked to previously identified clubroot resistance genes. Six thousand eight hundred sixty-one SNP markers were retained after filtering with TASSEL 5.0, and used to evaluate four general linear models (GLM) and four mixed linear models (MLM). The PCA + K and Q + K MLM models gave the minimal deviance of the observed from the expected distribution in quantile-quantile plots, and hence were used for SNP-clubroot association analyses. In addition, 108 alleles derived from the PCR-based markers and the phenotypic data were analyzed with the PCA + K model. Forty-five SNPs and four PCR-based markers were identified to be associated strongly with resistance to isolates representing 13 pathotypes (2F,

Identification of resistance loci against new pathotypes of Plasmodiophora brassicae in Brassica napus based on genome-wide association mapping

“…In those previous studies, the disease reaction to only a single strain of P. brassicae was assessed, and a SNP array or associative transcriptome was used rather than GBS, which might explain the difference in the number and identity of QTL detected. In a recent GWAS study, 45 QTLs were identified against 13 strains on chromosomes A01 to A10, and C02, C03 and C05 43 . In the current study, two pathotypes (3A and 2B) included in a recent study 43 were analysed using a larger and potentially more diverse germplasm collection.…”

“…In a recent GWAS study, 45 QTLs were identified against 13 strains on chromosomes A01 to A10, and C02, C03 and C05 43 . In the current study, two pathotypes (3A and 2B) included in a recent study 43 were analysed using a larger and potentially more diverse germplasm collection. The current study, however, identified different QTL from those in the previous study 43 .…”

“…In the current study, two pathotypes (3A and 2B) included in a recent study 43 were analysed using a larger and potentially more diverse germplasm collection. The current study, however, identified different QTL from those in the previous study 43 . One possible explanation for the difference between the studies could be the analysis of DSI.…”

“…One possible explanation for the difference between the studies could be the analysis of DSI. A rank-based inverse normal transformation was used to make the DSI values nearly fit the normal distribution required for parametric model-based association analysis in the current study, while highly skewed DSIs were used in the previous study 43 . In addition, different sources of B. napus collections in the current study from the previous report 43 could be an important factor contributing to the discrepancy.…”

“…A rank-based inverse normal transformation was used to make the DSI values nearly fit the normal distribution required for parametric model-based association analysis in the current study, while highly skewed DSIs were used in the previous study 43 . In addition, different sources of B. napus collections in the current study from the previous report 43 could be an important factor contributing to the discrepancy. We conclude that all 13 QTL identified in the current study are likely to be novel because they were located at different physical locations on the chromosomes from the QTL identified previously 43 .…”