Genomic rearrangements arising during polyploidization are an important source of genetic and phenotypic variation in the recent allopolyploid crop Brassica napus. Exchanges among homoeologous chromosomes, due to interhomoeologue pairing, and deletions without compensating homoeologous duplications are observed in both natural B.napus and synthetic B.napus. Rearrangements of large or small chromosome segments induce gene copy number variation (CNV) and can potentially cause phenotypic changes. Unfortunately, complex genome restructuring is difficult to deal with in linkage mapping studies. Here, we demonstrate how high-density genetic mapping with codominant, physically anchored SNP markers can detect segmental homoeologous exchanges (HE) as well as deletions and accurately link these to QTL. We validated rearrangements detected in genetic mapping data by whole-genome resequencing of parental lines along with cytogenetic analysis using fluorescence insitu hybridization with bacterial artificial chromosome probes (BAC-FISH) coupled with PCR using primers specific to the rearranged region. Using a well-known QTL region influencing seed quality traits as an example, we confirmed that HE underlies the trait variation in a DH population involving a synthetic B.napus trait donor, and succeeded in narrowing the QTL to a small defined interval that enables delineation of key candidate genes.

The Brassica napus 60K Illumina Infinium™ SNP array has had huge international uptake in the rapeseed community due to the revolutionary speed of acquisition and ease of analysis of this high-throughput genotyping data, particularly when coupled with the newly available reference genome sequence. However, further utilization of this valuable resource can be optimized by better understanding the promises and pitfalls of SNP arrays. We outline how best to analyze Brassica SNP marker array data for diverse applications, including linkage and association mapping, genetic diversity and genomic introgression studies. We present data on which SNPs are locus-specific in winter, semi-winter and spring B. napus germplasm pools, rather than amplifying both an A-genome and a C-genome locus or multiple loci. Common issues that arise when analyzing array data will be discussed, particularly those unique to SNP markers and how to deal with these for practical applications in Brassica breeding applications.

The development of oilseed rape or canola (Brassica napus L.) with reduced levels of antinutritive seed phenolic acid and fibre compounds would considerably improve the value of the seed meal that is used as an animal feed after oil extraction. This study describes a forward genetics approach to discover potential candidate genes for antinutritive components in seed meal from oilseed rape. Analysis of quantitative trait loci (QTL) in a doubled haploid (DH) population derived from a cross between the black-seeded winter oilseed rape inbred line ̳Express 617‘ and the yellow-seeded line ̳1012-98‘ revealed a major QTL on chromosome A09 with strong effects on phenotypic variation for seed colour, neutral detergent fibre (NDF) and acid detergent lignin (ADL), respectively (Figure 1). Comparative mapping of markers from the QTL region in other rapeseed populations confirmed the importance of the detected locus.

Seed coat phenolic compounds represent important antinutritive fibre components that cause a considerable reduction in value of seed meals from oilseed rape (Brassica napus). The nutritionally most important fibre compound is acid detergent lignin (ADL), to which a significant contribution is made by phenylpropanoid-derived lignin precursors. In this study, we used bulked-segregant analysis in a population of recombinant inbred lines (RILs) from a cross of the Chinese oilseed rape lines GH06 (yellow seed, low ADL) and P174 (black seed, high ADL) to identify markers with tight linkage to a major quantitative trait locus (QTL) for seed ADL content. Fine mapping of the QTL was performed in a backcross population comprising 872 BC1F2 plants from a cross of an F7 RIL from the above-mentioned population, which was heterozygous for this major QTL and P174. A 3:1 phenotypic segregation for seed ADL content indicated that a single, dominant, major locus causes a substantial reduction in ADL. This locus was successively narrowed to 0.75 cM using in silico markers derived from a homologous Brassica rapa sequence contig spanning the QTL. Subsequently, we located a B. rapa orthologue of the key lignin biosynthesis gene CINNAMOYL CO-A REDUCTASE 1 (CCR1) only 600 kbp (0.75 cM) upstream of the nearest linked marker. Sequencing of PCR amplicons, covering the full-length coding sequences of Bna.CCR1 homologues, revealed a locus in P174 whose sequence corresponds to the Brassica oleracea wild-type allele from chromosome C8. In GH06, however, this allele is replaced by a homologue derived from chromosome A9 that contains a loss-of-function frameshift mutation in exon 1. Genetic and physical map data infer that this loss-of-function allele has replaced a functional Bna.CCR1 locus on chromosome C8 in GH06 by homoeologous non-reciprocal translocation.

The growing resource of Brassica genome sequence data, along with the ever-improving annotation of Brassica sequences to the extremely well-characterised genome of the model crucifer Arabidopsis thaliana, represent an extremely valuable resource for molecular breeding and genetic characterisation of B. napus. In particular, the newest comparative genomics data enable a unique opportunity to navigate between and among the chromosomes of A. thaliana and B. napus, and to compare the map positions of quantitative trait loci (QTL) for complex traits of agronomic importance in the crop species with the positions of potential candidate genes in the model genome. In some cases such rough macrosynteny enables the detection of chromosome blocks in rapeseed corresponding to more or less unbroken syntenic genome regions in Arabidopsis. On the one hand this can allow orthologous Brassica sequences annotated to the corresponding Arabidopsis regions to be used for database-oriented identification of new markers for fine mapping, association studies or marker-assisted selection towards trait improvement. In some cases it is also possible to directly identify potentially relevant candidate genes for important traits in oilseed rape, based on their position in syntenic maps compared to relevant QTL. In other cases it can be feasible to navigate from potential candidate genes in Arabidopsis to homoeologous regions of the rapeseed genome, whereby not only the gene sequence itself but the complete surrounding region can be used to search for sequence polymorphisms that can be utilised as markers. In this paper we demonstrate the potential of comparative genomics data for candidate gene identification and marker development in traits related to oilseed rape seed quality. Different approaches are for dissection of traits that appear to be controlled by a relatively small number of major genes (e.g. seed colour and fibre content), and traits influenced by numerous homoeologous QTL containing an unknown number of active genes (e.g. glucosinolate content). In each case new information can be obtained that can lead to new, tightly-linked selection markers and the identification of new allelic diversity for breeding.