Abstract
Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. napus would benefit from germplasm improvement schemes that sustain diversity. As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD). Complexity reduction genotyping-by-sequencing (GBS) methods, including GBS-transcriptomics (GBS-t), enable cost-effective screening of a large number of samples, while whole genome re-sequencing (WGR) delivers the ability to generate large numbers of unbiased genomic single nucleotide polymorphisms (SNPs), and identify structural variants (SVs). Furthermore, the development of genomic tools based on whole genomes representative of global oilseed diversity and orientated by the reference genome has substantial industry relevance and will be highly beneficial for canola breeding. As recent studies have focused on European and Chinese varieties, a global diversity panel as well as a substantial number of Australian spring types were included in this study. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. Subsequently, 149 samples representative of global diversity were selected for WGR and both data sets used for a side-by-side evaluation of diversity and LD. The WGR data was further used to develop genomic resources consisting of a list of 4,029,750 high-confidence SNPs annotated using SnpEff, and SVs in the form of 10,976 deletions and 2,556 insertions. These resources form the basis of a reliable and repeatable system allowing greater integration between canola genomics studies, with a strong focus on breeding germplasm and industry applicability.
Highlights
Brassica napus (2n = 4x = 38, AACC) is a recent allotetraploid originating from natural hybridization and genome duplication events between Brassica rapa and Brassica oleracea, sometime after B. rapa and B. oleracea diverged, between 12,500 and 7,500 years ago (Chalhoub et al, 2014) and appears to have arisen from multiple origins (Song and Osborn, 1992; Allender and King, 2010)
After genotyping all 633 GBS-t samples using the 226,855 single nucleotide polymorphisms (SNPs) list, these sites were filtered in order to only retain SNPs which were polymorphic and passed quality filtering in this sample set, resulting in 61,037 informative SNPs
Clustering revealed population structure broadly subdivided based on growth habit with spring, winter, and semi-winter groups, and was confirmed by analysis with STRUCTURE (Pritchard et al, 2000: Supplementary Methods S1 and Supplementary Figure S3)
Summary
Brassica napus (2n = 4x = 38, AACC) is a recent allotetraploid originating from natural hybridization and genome duplication events between Brassica rapa and Brassica oleracea, sometime after B. rapa and B. oleracea diverged, between 12,500 and 7,500 years ago (Chalhoub et al, 2014) and appears to have arisen from multiple origins (Song and Osborn, 1992; Allender and King, 2010). Domestication of B. napus began relatively recently (400–500 years ago) and no truly wild populations have been recorded (Gómez-Campo and Prakash, 1999). As breeding efforts within the last 60 years have targeted erucic acid and seed glucosinolate content (Walker and Booth, 2001; Wu et al, 2008), and due to high oil and protein content, canola has become the world’s second most important oilseed crop after soy bean, especially in Canada, China, India, Europe, and Australia. Within eco-geographic origins, cultivar relationships usually reflect breeding history, with some countries creating more isolation than others (Cowling, 2007; Wang et al, 2009; Qian et al, 2014)
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