Patterns of molecular variation in a species-wide germplasm set of Brassica napus
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Rapeseed (Brassica napus L.) is the leading European oilseed crop serving as source for edible oil and renewable energy. The objectives of our study were to (i) examine the population structure of a large and diverse set of B. napus inbred lines, (ii) investigate patterns of genetic diversity within and among different germplasm types, (iii) compare the two genomes of B. napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B. napus inbred lines genotyped with 89 genome-specific SSR primer combinations. Both a principal coordinate analysis and software STRUCTURE revealed that winter types, spring types, and swedes were assigned to three major clusters. The genetic diversity of winter oilseed rape was lower than the diversity found in other germplasm types. Within winter oilseed rape types, a decay of genetic diversity with more recent release dates and reduced levels of erucic acid and glucosinolates was observed. The percentage of linked SSR loci pairs in significant (r 2 > Q 95 unlinked loci pairs) LD was 6.29% for the entire germplasm set. Furthermore, LD decayed rapidly with distance, which will allow a relatively high mapping resolution in genome-wide association studies using our germplasm set, but, on the other hand, will require a high number of markers.
KeywordsLinkage Disequilibrium Erucic Acid Amplify Fragment Length Polymorphism Restriction Fragment Length Polymorphism Germplasm Type
The authors thank Wolfgang Ecke (University of Göttingen, Germany), the Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben (Germany), Nordic Gene Bank, Alnarp (Sweden), The Centre for Genetic Resources (Netherlands), and Warwick Horticulture Research International Genetic Resources Unit (UK) for providing the seeds of the examined germplasm. Agriculture and Agri-Food Canada kindly shared the proprietary Brassica SSR markers and their map positions. We are grateful to Sarah Nele Kaul and Bent Müller for the technical assistance, as well as to the Max Planck Genome Centre Cologne for providing the genotyping facilities. The funding of this work is kindly provided by the Deutsche Forschungsgemeinschaft (DFG) and the Max Planck Society. This work was performed in the framework of the ERA-NET PG project “ASSYST”. Finally, we thank the associate editor C. Quiros and three anonymous reviewers for their valuable suggestions.
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