Species-wide genome sequence and nucleotide polymorphisms from the model allopolyploid plant Brassica napus

Abstract

Brassica napus (oilseed rape, canola) is one of the world’s most important sources of vegetable oil for human nutrition and biofuel, and also a model species for studies investigating the evolutionary consequences of polyploidisation. Strong bottlenecks during its recent origin from interspecific hybridisation, and subsequently through intensive artificial selection, have severely depleted the genetic diversity available for breeding. On the other hand, high-throughput genome profiling technologies today provide unprecedented scope to identify, characterise and utilise genetic diversity in primary and secondary crop gene pools. Such methods also enable implementation of genomic selection strategies to accelerate breeding progress. The key prerequisite is availability of high-quality sequence data and identification of high-quality, genome-wide sequence polymorphisms representing relevant gene pools. We present comprehensive genome resequencing data from a panel of 52 highly diverse natural and synthetic B. napus accessions, along with a stringently selected panel of 4.3 million high-confidence, genome-wide SNPs. The data is of great interest for genomics-assisted breeding and for evolutionary studies on the origins and consequences in allopolyploidisation in plants.

Oilseed rape: learning about ancient and recent polyploid evolution from a recent crop species

“…Earlier studies also identified chromosome rearrangements within the established B. napus gene pool using molecular markers: genotype-specific translocations were detected through assessment of marker segregation patterns (Sharpe et al 1995;Osborn et al 2003). Nevertheless, it was not until next-generation sequencing technologies enabled large-scale genome resequencing that the true extent of such rearrangements in the B. napus germplasm pool and their implications for polyploid evolution, trait variation and breeding became apparent Schmutzer et al 2015). A clear example of a non-homologous chromosome exchange in B. napus directly impacting a trait was identified by Liu et al (2012): a translocation between A9 and C8 resulted in two copies of an A9 allele, affecting seed acid detergent lignin content (Fig.…”

Host–pathogen interactions in relation to management of light leaf spot disease (caused by Pyrenopeziza brassicae) on Brassica species

“…Since then, a Brassica 60k SNP array has been used in combination with large association panels by several research teams to analyse the genetic basis of traits, including resistance against pathogens Hatzig et al 2015;Wu et al 2016). Resequencing of 52 diverse natural and synthetic B. napus accessions has resulted in identification of >4 million SNPs, which are being exploited for breeding using primary and secondary gene pools (Schmutzer et al 2015).…”

Carbohydrate microarrays and their use for the identification of molecular markers for plant cell wall composition

“…Molecular markers provide the genetic tools needed for implementation, enable potentially exploitable genes to be located, and help elucidate the genetic mechanisms involved. Recent improvements in genome sequencing have enabled genome characterization, identification of structural rearrangements, and high-density linkage maps to be constructed for crop species, such as Brassica napus, which have large and complex genomes (2)(3)(4). Consequently, genome-wide association studies (GWAS) can now be conducted in crop species (5).…”