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(2016) found spring and winter types to harbor similar levels of diversity, and while they found Asian winter varieties to be the most diverse, in contrast to previous studies, the varieties used were largely composed of Japanese and South Korean varieties, with a small proportion of Chinese lines.Īlthough analyses of global B. Previous examinations of diversity between growth habits have found spring types to exhibit the highest level of nucleotide diversity, followed closely by winter types, with Chinese semi-winter varieties having the lowest ( Bus et al., 2011 Delourme et al., 2013 Wang et al., 2014) and the least genetic differentiation between accessions ( Wang et al., 2014), which is likely due to the isolation of Chinese varieties since the establishment of local breeding programs ( Chen et al., 2008). 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). As breeding efforts within the last 60 years have specifically 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 1.Īdditional breeding efforts to adapt canola to local environments has further narrowed the gene pool and resulted in winter, spring, and semi-winter growth habits based on vernalization requirements, which is the primary factor affecting genetic differentiation and population structure in canola ( Delourme et al., 2013 Li et al., 2014 Gazave et al., 2016). Although swede and fodder varieties exist, it is primarily used as an oilseed crop with applications as a food source, lubricant, and biofuel. napus began relatively recently (400–500 years ago) and no truly wild populations have been recorded ( Gómez-Campo and Prakash, 1999). 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). 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.īrassica 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. 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. 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. Focusing on industry relevance, 633 varieties were initially genotyped using GBS-t to examine population structure using 61,037 SNPs. 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. 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. 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).
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As such, samples representative of global germplasm pools need to be assessed for existing population structure, diversity and linkage disequilibrium (LD).
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napus would benefit from germplasm improvement schemes that sustain diversity. Intensive breeding of Brassica napus has resulted in relatively low diversity, such that B. 2School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia.1AgriBio, Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, Australia.
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Michelle Malmberg 1,2, Fan Shi 1, German C.