Transcriptome SNPs for Linkage Mapping and Association Genetics in B. napus

In the absence of a complete genome sequence, transcriptome sequences from polyploid crops such as Brassica napus can be utilised to construct linkage maps, enabling complex genetic analyses such as association mapping to be conducted. We sequenced the transcriptomes of 37 individuals from a B.napus mapping population enabling us to construct a cognate linkage map comprising 21,323 SNP markers, anchoring the positions of 9169 unigenes from the 95k B.napus unigene set. We then used this map to align the B.napus genome with that of Arabidopsis thaliana and genome sequence assemblies of the progenitor species B.rapa and B.oleracea, allowing us to construct a set of pseudomolecules corresponding to the 19 linkage groups of B.napus. Using this, we could then infer the hypothetical order of a further 61,613 unigenes in the A genome and 64,292 unigenes in the C genome. This framework was then used to investigate the transcriptome sequence variation in a panel of 84 B.napus accessions, which revealed 101,644 polymorphic SNPs, 26,121 of which we were able to assign to a single genome position. Using this data we were then able to precisely differentiate between crop types using cluster analysis, detect crop-specific SNP alleles and successfully perform high resolution association mapping on 53 of the accessions for a number of traits. This analysis demonstrates how next-generation transcriptome sequencing can be used to help dissect the complex genetics of polyploid crops such as B.napus, and enable high-resolution, cost-effective genetic analysis techniques to be employed.