Theoretical and Applied Genetics

, Volume 127, Issue 9, pp 2051–2064 | Cite as

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

  • Allan F. BrownEmail author
  • Gad G. Yousef
  • Kranthi K. Chebrolu
  • Robert W. Byrd
  • Koyt W. Everhart
  • Aswathy Thomas
  • Robert W. Reid
  • Isobel A. P. Parkin
  • Andrew G. Sharpe
  • Rebekah Oliver
  • Ivette Guzman
  • Eric W. Jackson
Original Paper


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 saturated Brassica 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 Brassica research.


Carotenoid Amplify Fragment Length Polymorphism Lutein Total Carotenoid Single Nucleotide Polymorphism Marker 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Conflict of interest

The authors declare that they have no conflict of interest.

Ethical standards

The experiment conducted complies with the laws of the United States and Canada.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Allan F. Brown
    • 1
    Email author
  • Gad G. Yousef
    • 1
  • Kranthi K. Chebrolu
    • 1
  • Robert W. Byrd
    • 1
  • Koyt W. Everhart
    • 1
  • Aswathy Thomas
    • 1
  • Robert W. Reid
    • 5
  • Isobel A. P. Parkin
    • 2
  • Andrew G. Sharpe
    • 3
  • Rebekah Oliver
    • 4
  • Ivette Guzman
    • 1
  • Eric W. Jackson
    • 4
  1. 1.Department of Horticultural Science, Plants for Human Health InstituteNorth Carolina State UniversityKannapolisUSA
  2. 2.Agriculture and Agri-Food CanadaSaskatoonCanada
  3. 3.National Research Council CanadaSaskatoonCanada
  4. 4.General Mills Crop BiosciencesKannapolisUSA
  5. 5.UNC Charlotte Bioinformatics Services DivisionUniversity of North Carolina-CharlotteKannapolisUSA

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