Stem canker caused by the fungus Leptosphaeria maculans is a major disease of Brassica napus. Quantitative resistance factors appear to be important components for effective and durable control of this pathogen. Quantitative trait loci (QTL) for stem canker resistance have previously been identified in the Darmor variety. However, before these QTL can be used in marker-assisted selection (MAS) to breed resistant varieties, they must be validated in a wide range of genetic backgrounds. We used an association mapping approach to confirm the markers located within the QTL previously identified in Darmor and establish their usefulness in MAS. For this, we characterized the molecular diversity of an oilseed rape collection of 128 lines showing a large spectrum of responses to infection by L. maculans, using 72 pairs of primers for simple sequence repeat and other markers. We used different association mapping models which either do or do not take into account the population structure and/or family relatedness. In all, 61 marker alleles were found to be associated with resistance to stem canker. Some of these markers were associated with previously identified QTL, which confirms their usefulness in MAS. Markers located in regions not harbouring previously identified QTL were also associated with resistance, suggesting that new QTL or allelic variants are present in the collection. All of these markers associated with stem canker resistance will help identify accessions carrying desirable alleles and facilitate QTL introgression

Key messageSix stable QTL for resistance againstL. maculans(phoma stem canker) have been identified by QTL × environment interaction analysis using data from five winter oilseed rape field experiments.AbstractPhoma stem canker, caused by Leptosphaeria maculans, is a disease of worldwide importance on oilseed rape (Brassica napus). Quantitative trait loci (QTL)-mediated resistance against L. maculans in B. napus is considered to be race non-specific and potentially durable. Identification and evaluation of QTL for resistance to L. maculans is important for breeding oilseed rape cultivars with durable resistance. An oilseed rape mapping population was used to detect QTL for resistance against L. maculans in five winter oilseed rape field experiments under different environments. A total of 17 QTL involved in ‘field’ quantitative resistance against L. maculans were detected and collectively explained 51 % of the phenotypic variation. The number of QTL detected in each experiment ranged from two to nine and individual QTL explained 2–25 % of the phenotypic variation. QTL × environment interaction analysis suggested that six of these QTL were less sensitive to environmental factors, so they were considered to be stable QTL. Markers linked to these stable QTL will be valuable for selection to breed for effective resistance against L. maculans in different environments, which will contribute to sustainable management of the disease.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-015-2620-z) contains supplementary material, which is available to authorized users.

SummaryEvolutionary processes during plant polyploidization and speciation have led to extensive presence–absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high‐resolution genetic analysis in major crops frequently implements simple, cost‐effective, high‐throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population‐based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures. We reveal that including SNaPs in genetic analyses elucidate segregation of small to large‐scale structural variants in nested association mapping populations of oilseed rape (Brassica napus), a recent polyploid crop with widespread structural variation. Including SNaP markers in genomewide association studies identified numerous quantitative trait loci, invisible using SNP markers alone, for resistance to two major fungal diseases of oilseed rape, Sclerotinia stem rot and blackleg disease. Our results indicate that PAV has a strong influence on quantitative disease resistance in B. napus and that SNaP analysis using cost‐effective SNP array data can provide extensive added value from ‘missing data’. This strategy might also be applicable for improving the precision of genetic mapping in many important crop species.

Improvement of effectiveness and durability of disease resistance in crops most often relies on the use of quantitative resistance, with the hypothesis that a wide range of quantitative resistance factors (QTL) makes the overcoming of the resistance by the pathogen more difficult. For an optimum use of these QTL in effective and durable strategies of resistance deployment, there is a need to precisely know their localization but also their stability/specificity and their allelic effects in various genetic backgrounds. Stem canker caused by the fungus Leptosphaeria maculans is one of the most important diseases in oilseed rape. In this Brassica napus-L. maculans pathosystem, QTL were previously identified by linkage analysis using populations derived from biparental crosses that were analyzed separately. In this study, we explored new quantitative resistance factors using a multi-cross connected design derived from four resistant lines crossed with a single susceptible line. Independent and connected mapping analyses revealed to be complementary to get an overview of QTL organization. We validated different QTL across different years and genetic backgrounds and identified novel QTL which had not yet been mapped. Population-common and population-specific QTL were identified. Knowledge of QTL organization and effects should help in the rational choice of relevant factors in breeding resistant genotypes to be integrated with other control means such as cultural practices and rotations for durable management of the disease.