Brassica genome and transcriptome sequencing

We have been involved in several projects that generate sequence data from Brassica species. These data are being used to help us understand the structural consequences of plant genome evolution and for the development of molecular markers for the analysis of the genetic control of important traits in Brassica crops. A key collaborator on this work is Martin Trick, JIC.

Why transcriptome sequencing?

The polyploid nature of oilseed rape (Brassica napus) leads to complexities when trying to sequence its genome, and as yet, there is no publicly available genomic sequence. However, sequencing projects working on the diploid progenitors B.rapa and B.oleracea which come together to form the B.napus genome, have been completed.

Nagaharu U.(1935) "Genome analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilization". Japan. J. Bot 7: 389–452

The absence of a Brassica reference sequence has necessitated the use of collinearity with A.thaliana gene models and established a reference sequence based on the unigene assemblies used for the community Brassica microarray.

BrGSP : Brassica rapa Genome Sequencing Project

The MBGP selected the 'A' genome Brassica rapa line Chiifu-401 as the first species to be sequenced. The multinational BrGSP made significant progress with this, based on a conventional end-sequenced anchor-BAC and chromosome-specific BAC by BAC sequencing to Phase II. The strategy has been modified with the availability of high throughput sequencing (primarily 454 and Illumina), and so a project initiated by CAAS/BGI in China has incorporated the existing data into a shotgun approach.

The B.rapa genome sequence has now been published : The Brassica rapa Genome Sequencing Project Consortium (2011) The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43, 1035-1039

Information about Brassica sequencing projects and access to sequence resources (including the 1015 sequenced and annotated B.rapa BACs) can be found at the Brassica Genome Gateway.

Transcriptome sequencing

Sequencing from the transcriptome (RNA) rather than the genome (DNA) provides us with data about expressed genes; both their genetic sequence and the level of expression, and we can exploit this extra level of information in many ways -

SNP Identification

Single Nucleotide Polymorphisms (SNPs) are individual base changes in the genetic code. Comparing the variation at this level between species allows us to understand how the genome structure has changed as the species have evolved and hybridised (Trick et al. 2009).

Looking at the variety of SNPs across a wide-ranging panel of diverse germplasm enables us to conduct phylogenetic studies and move into the use of association genetics tools for crop models.

Linkage mapping – using the SNP variations as genetic markers on lines within a B.napus mapping population TNDH (Bancroft et al. 2011).

Network and systems analysis – integrating gene expression data for B.napus populations with phenotypic and metabolic data.

Relevant References:

Bancroft I, Morgan C, Fraser F, Higgins J, Wells R, Clissold L, Baker D, Long Y, Meng J, Wang X, Liu S, and Trick M.(2011)
Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing. Nature Biotechnology 29: 762-766.