Journal Articles

High-density single nucleotide polymorphism (SNP) array mapping in Brassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets

August 13, 2014

High-density single nucleotide polymorphism (SNP) array mapping inBrassica oleracea: identification of QTL associated with carotenoid variation in broccoli florets Theoretical and Applied Genetics 14 Aug 2014 Allan F. Brown, Gad G. Yousef, Kranthi K. Chebrolu, Robert W. Byrd, Koyt W. Everhart, Robert W. Reid, Isobel A. P. Parkin, Andrew G. Sharpe, Rebekah Oliver, Ivette Guzman, Eric W. Jackson

Department of Horticultural Science, Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA e-mail:, UNC Charlotte Bioinformatics Services Division, University of North Carolina-Charlotte, 150 Research Campus Dr., Kannapolis, NC 28081, USA, General Mills Crop Biosciences, Kannapolis, NC 28081, USA, National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N0W9, Canada,


Key message

A high-resolution genetic linkage map of B. oleracea was developed from a B. napus SNP array. The work will facilitate genetic and evolutionary studies in Brassicaceae.


A broccoli population, VI-158 × BNC, consisting of 150 F2:3 families was used to create a saturatedBrassica oleracea (diploid: CC) linkage map using a recently developed rapeseed (Brassica napus) (tetraploid: AACC) Illumina Infinium single nucleotide polymorphism (SNP) array. The map consisted of 547 non-redundant SNP markers spanning 948.1 cM across nine chromosomes with an average interval size of 1.7 cM. As the SNPs are anchored to the genomic reference sequence of the rapid cycling B. oleracea TO1000, we were able to estimate that the map provides 96 % coverage of the diploid genome. Carotenoid analysis of 2 years data identified 3 QTLs on two chromosomes that are associated with up to half of the phenotypic variation associated with the accumulation of total or individual compounds. By searching the genome sequences of the two related diploid species (B. oleracea and B. rapa), we further identified putative carotenoid candidate genes in the region of these QTLs. This is the first description of the use of a B. napus SNP array to rapidly construct high-density genetic linkage maps of one of the constituent diploid species. The unambiguous nature of these markers with regard to genomic sequences provides evidence to the nature of genes underlying the QTL, and demonstrates the value and impact this resource will have on Brassicaresearch.




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