A de novo sequencing catalogue B, Oleracea
Brassica oleracea is a species that includes many diverse economically important crops with extreme phenotypes, like cabbages, kohlrabi, cauliflower, broccoli and kales. In 2014 the first reference genomes were published, of a white cabbage and a rapid cycling kale like plant, which was recently followed by a broccoli genome. The availability of these reference genomes, plus resequencing data generated in a previously funded 1000 genome TKI project, illustrated that the genomes of these morphotypes vary considerably. In addition, introgression breeding to transfer traits across crops is often hampered by reduced recombination. One hypothesis is that structural variations between the genomes of these different crops influence recombination behaviour. The aim of this project is to generate five de novo reference genomes (cabbage, cauliflower, kale, kohlrabi and broccoli) and analyse structural variations (SVs) between these genomes. To reveal whether these SVs affect both the rate and the positions of recombination we will develop five four-way-crosse populations and assess recombination in their progeny.
Microscopic analyses of directly study the effect that structural differences between the genomes may have on suppression of meiotic recombination in the intermorphotypic F1s. The approach in which we combine de novo sequencing, bioinformatics, genetics and cytological analyses is novel, with a potentially large scientific impact as well as an immediate practical impact on breeding strategies and thus crop improvement.
Here we describe how this project contributes to ST2, Priority 44,
ST2 Key technologies, biotechnology and breeding
Of the different sub-programs that are featured under ST2, this project contributes to:
Genome technology (genomics and transcriptomics): The de novo reference genomes will be created using sequence data from several platforms, Illumina, PacBio, Oxford nanopore. Combining this information with Bionano optical maps provides the opportunity to create chromosome-scale genomes. For annotation purposes expression data will be generated of diverse tissues, developmental stages and conditions (stresses) using Illumina Novaseq 6000 platform.
Bioinformatics and big data: Currently available approaches on comparative genomics are adjusted to be able to locate and annotate genomic variations such as small and large scale genomic variations. Four-way-cross populations of all different combinations of the five genotypes will be resequenced and tools developed to map recombination events between all pairwise combinations. These recombination maps will be compared to the structural sariation maps to reveal whether these are associated.
Priority 44: Biotech and Breeding.
The proposed project clearly fits this priority as it develops insights and biotechnology tools to facilitate breeding of Brassica oleracea crops. The type of innovation we propose is highly multi-disciplinary and covers the connection from genotype to meiotic behavior. Interaction between academic researchers and the staff involved from the participating breeding companies is highly relevant.
Contribution of this project is the delivery of data (de novo genomes of 5 B. oleracea crops, segregating populations and recombination maps between all pairwise combinations) and knowledge on effect of SVs on recombination. This is of great importance on the intelligent design of breeding strategies.
The generation of de novo genomes becomes feasible these days, as overall costs of sequencing decreases and the sequencing technologies improve. Despite this, it is still a major effort, and a too high investment for most single companies. In addition, such project fits better in an academic setting, in order to profit from scientific innovations and share this with breeding in practice. This specific project is unique in that it combines the generation of de novo genomes with in depth investigation of recombination in B. oleracea. For this the collaboration between academics and companies was essential, as companies could both deliver homozygous materials as starting point and generate the segregating populations. The final outcome will not only be scientific publications on the effect of SVs on recombination, but also improved breeding strategies in B. oleracea crops.
• 5 high quality de novo genomes (broccoli, cauliflower, cabbage, kale and kohlrabi) with annotation: delivered month 31 (july 2020)
• RNA seq data of the 5 genotypes (combined tissues, developmental stages and stresses) Delivered month 24 (December 2019)
• Catalogue of variations (SNPs, SVs (insertions deletions inversions translocations) delivered month 36 (December 2020)
• 5 four-way-cross populations with resequence data (will be delivered around month 44 (august 2021)
• Pairwise recombination maps (tranfer info ongoing, updated in progress reports/presentations). Final results will be delivered month 48 (december 2021)
• Twice a year academic partners and company partners meet. Both parties present progress (company partners present their in kind contributions). The presentations are shared on the portal. Also progress reports are shared.