PreBreed-Yield: Population Genomics Resources for Nested Association Mapping and Precision Breeding in Winter Oilseed Rape

The allopolyploid species Brassica napus (genome AACC) is a major international oilseed crop (canola, oilseed rape), however breeding progress suffers from low genetic diversity caused by severe selection bottlenecks in recent decades. To overcome this problem, the public-private consortium "PreBreed-Yield" is generating, genotyping and characterizing extensive nested association mapping (NAM) populations, incorporating novel genetic diversity, as a resource for B. napus genome analysis and future breeding. The consortium, coordinated by the German Seed Alliance GmbH, includes 7 commercial breeding companies and 7 scientific institutes covering all relevant fields: genomics, genetics, bioinformatics and statistics, complex trait phenotyping/phenomics and breeding. Fifty genetically diverse founder accessions, including 30 novel resynthesised B. napus lines derived from interspecific hybrids between diverse A and C genome donors, were crossed to an elite winter oilseed rape breeding line as a basis for production of NAM populations. From each of these 50 F1 combinations, half-sib subpopulations of 50 to 100 doubled haploids (DH: from natural B. napus parents) or single-seed descent inbred lines (SSD: from resynthesised B. napus parents) are currently being completed. More than 3000 BnNAM lines are being genotyped in 2012 and 2013 with the 60kSNP Infinium Brassica consortium array. At the same time, the 51 founder lines are being resequenced to around 15x coverage by Illumina 100bp paired-end sequencing. In combination with the recombination break points extrapolated from the genome-wide SNPs, knowledge of the parental genome sequences will enable reconstruction of the whole-genome sequences for the entire segregating meta-population. This comprehensive haplotype data, in combination with deep phenotyping, transcriptome analyses and metabolite profiling, will provide a powerful resource for association genetics, systems biology and predictive breeding during the coming decades. Furthermore, the resequencing data will facilitate a comprehensive survey of genome-wide SNP variation and structural chromosome rearrangements, resulting from ancient and de novo polyploidy in the complex B. napus genome, and the effects of genome-scale variation on agronomic traits.