13 ERA-CAPS Evolution of genomes: structure-function relationships in the polyploid crop species Brassica napus

The genomes of all plants have evolved through cycles of polyploidy (during which whole genome duplication occurs) and diploidisation (during which those duplicated genomes stabilise). This cycle represents a fundamental mechanism by which the genetic control of biological processes evolve and is a key driver of diversity and performance in almost all crop species. Most of our understanding of the diploidisation process is based on analyses of its outcomes following ancient polyploidy events. Recent results, however, have suggested that the genome evolution mechanisms involved in diploidisation may be having effects on traits in important crop species now, i.e. thousands of years after the most recent polyploidy events in their ancestry.
As a model for a complex polyploid with variable rates of genome evolution we will study Brassica napus, which includes northern Europe's principal oil crop, oilseed rape. A wide range of accessions are available, of both B. napus formed in nature (an allotetraploid formed by spontaneous hybridization of B. rapa and B. oleracea species; the main source of genetic diversity for rapeseed breeding) and resynthesised B. napus (formed by induced hybridization of the same species in the laboratory), which undergoes rapid genome change.
We hypothesise that the genome evolution observed in resynthesised B. napus represents an accelerated form of the genome evolution that is ongoing in cultivated B. napus derived in nature. We aim to test this hypothesis by characterising molecular evolution on a genome-wide scale in a large panel of natural and resynthesised B. napus, including derived populations, relating the observed variation in genome structure to trait variation of relevance for rapeseed as a crop. Our specific objectives are: (1) Establish the B. napus pan-transciptome, comprising ordered unigenes (EST assemblies) representing the nascent B. napus genome. (2) Quantify the frequency of copy number variation (of transcribed sequences) and homoeologous exchanges present in B. napus formed in nature. (3) Quantify the frequency of copy number variation (of transcribed sequences) and homoeologous exchanges present in resynthesised B. napus, comparing it with the frequency observed in B. napus formed in nature. (4) Understand how genome structural evolution affects trait variation, for a range of traits of importance in this crop.
The research will be conducted by an international consortium with partners from UK, Germany and France. The partners are world-leading experts in their fields and have complementary expertise, enabling multidisciplinary investigation of shared material. The results will provide important insights into the fundamental molecular biology of plant genome evolution. Importantly, it will do this in the context of material that can be used for the improvement of one of Europe's most important crop species.

The overall approach is to use Illumina sequencing to characterise genome evolution in both resynthesised B. napus and B. napus formed in nature. Analyses will be conducted both at genome level (genotyping by sequencing; GBS) and at transcriptome level (mRNAseq), including the association of trait variation with molecular variation to identify loci quantitatively controlling traits. This approach has the advantage of producing genome-wide analyses across substantial diversity collections, enabling the identification and resolution of both structural genome changes and functional changes (including epigenetic transcriptional silencing), and producing molecular markers suitable for marker-assisted selection in subsequent breeding programs.
The research plan involves four inter-related tasks, each mapping directly onto one of the objectives of the project. Task 1 establishes a resource that enables the definition of the order of genes for which transcription has been validated (by the existence of ESTs) as they would be in a generic B. napus, formed either in nature or resynthesised, as it might have been before commencement of diploidisation. This provides a frame of reference for the definition of rearrangements and gene loss. Two tasks, running in parallel with each other and benefiting in their later stages from the outputs of the first task, aim to identify, characterise and quantify structural genome rearrangements that occur in B. napus formed in nature (Task 2) and resynthesised B. napus (Task 3). Upon the completion of these two tasks we will be in a position to compare and contrast the types of structural changes occurring in B. napus, and infer the mechanisms and factors influencing them. In Task 4, we will explore the relationships between variation for traits of importance in rapeseed as a crop and genome structural variation that we have identified and characterised.

Oilseed rape, the main vegetable oil crop in northern Europe and in several other parts of the world, is the primary crop type of the species B. napus. Across the EU-27 member states, oilseed rape is grown on nearly 7 million Ha, producing around 20 million tonnes of rapeseed. Currently valued at over 500 EUR per tonne, the rapeseed crop is therefore worth ~10 billion EUR annually to the EU-27. In addition, its inclusion in the arable rotation boosts the yield of following cereal crops, particularly wheat, making it a vital component for food security. The oil purified from rapeseed is largely used in the food industry, but is also used for biodiesel. Indeed, there are many emerging opportunities for substituting mineral oil with rapeseed oil for industrial applications.
There is a strong demand from the seed industry for the genetic improvement of rapeseed, for example in respect of disease resistance, pest resistance, tolerance of environmental variation, seed yield, oil content of seeds, seed oil composition, composition of residual meal, fertilizer input, flowering time, rate of maturity and content of co-products representing targets for "biorefining". To remain competitive in a commodity crop such as rapeseed, Europe must stay at the forefront of understanding the genetic bases of such traits in order to improve them. However, the genetic bases of traits are frequently cryptic, due partly to difficulties associated with the genetic redundancy arising from polyploidy. Only recently have the relationships between genome structural variation and trait variation been recognised, while potential epigenetic bases for trait variation (as might be revealed by changes in gene expression) remain unexplored. Thus the molecular study of genome evolution in B. napus is highly relevant for the future improvement and commercial success of the rapeseed crop. In addition, as an exemplar for other polyploids, the results are likely to be of importance for the genetic improvement of other polyploid crops, most notably (for Europe), wheat.

The very strong ties of the applicants to the plant breeding industry in France, Germany and the UK will ensure that knowledge and data gained during the project will have direct visibility, applicability and transfer into practical breeding of rapeseed/canola and other polyploid crops. In particular we expect to contribute knowledge that will assist breeders to make more efficient use of novel genetic diversity (e.g. through interspecific hybridisation) for improvement of resistance traits and exploitation of hybrid vigour. The rich resource of genomic data (genome-wide SNPs, transcriptome markers, presence-absence variants) for a broad B. napus diversity collection will be freely available for use in ongoing research in a public-private context. The populations we are investigating contain novel variation for a number of resistance and seed quality traits and have been shown to contribute to heterosis in B. napus hybrids. The data we generate will help to harness that variation in the form of new cultivars through genomic selection and predictive breeding approaches, taking genome organisation into account.