Molecular Breeding

, Volume 28, Issue 4, pp 437–451 | Cite as

SSR-based linkage map of flax (Linum usitatissimum L.) and mapping of QTLs underlying fatty acid composition traits

  • Sylvie CloutierEmail author
  • Raja Ragupathy
  • Zhixia Niu
  • Scott Duguid


Flax (Linum usitatissimum L.) seeds contain nearly 50% oil which is high in linolenic acid (an omega-3 fatty acid). In this study, a genetic linkage map was constructed based on 114 expressed sequence tag-derived simple sequence repeat (SSR) markers in addition to five single nucleotide polymorphism markers, five genes (fad2A, fad2B, fad3A, fad3B and dgat1) and one phenotypic trait (seed coat color), using a doubled haploid (DH) population of 78 individuals generated from a cross between SP2047 (a yellow-seeded Solin™ line with 2–4% linolenic acid) and UGG5-5 (a brown-seeded flax line with 63–66% linolenic acid). This map consists of 24 linkage groups with 113 markers spanning ~833.8 cM. Quantitative trait locus (QTL) analysis detected two major QTLs each for linoleic acid (LIO, QLio.crc-LG7, QLio.crc-LG16), linolenic acid (LIN, QLin.crc-LG7, QLin.crc-LG16) and iodine value (IOD, QIod.crc-LG7, QIod.crc-LG16), and one major QTL for palmitic acid (PAL, QPal.crc-LG9). The mutant allele of fad3A, mapped to the chromosomal segment inherited from the parent SP2047, underlies the QTL on linkage group 7 and was positively associated with high LIO content but negatively associated with LIN and IOD. This fad3A locus accounted for approximately 34, 25 and 29% of the phenotypic variation observed in this DH population for these three traits, respectively. The QTL localized on linkage group 16 explained approximately 20, 25 and 13% of the phenotypic variation for these same traits, respectively. For palmitic acid, QPal.crc-LG9 accounted for ~42% of the phenotypic variation. This first SSR-based linkage map in flax will serve as a resource for mapping additional markers, genes and traits, in map-based cloning and in marker-assisted selection.


Flax Linum Linkage map SSR QTL Linolenic acid 



The authors thank Elsa Reimer, Andrzej Walichnowski, Debbie Miranda and Natasa Radovanovic for technical assistance, Mike Shillinglaw for help in the preparation of figures and Joanne Schiavoni for manuscript editing. Visiting Fellowship in a Canadian Government Laboratory for Raja Ragupathy and Zhixia Niu was supported by an AAFC A-base grant to Dr. Cloutier. This work was conducted in part under the Natural Fibres for the Green Economy (NAFGEN) and the Total Utilization Flax Genomics (TUFGEN) consortiums sponsored by Agricultural Bioproducts Innovation Program (ABIP) and Genome Canada, respectively.

Supplementary material

11032_2010_9494_MOESM1_ESM.doc (39 kb)
Supplementary material 1 (DOC 39 kb)
11032_2010_9494_MOESM2_ESM.tif (329 kb)
Supplementary Fig. 1. Phenotypic distribution of: A, palmitic acid (%); B, stearic acid (%) and C, oleic acid (%) in the flax DH population, evaluated in five environments based on overall mean data. Arrows indicate the interval corresponding to the mean phenotypic values of parents. (TIFF 329 kb)
11032_2010_9494_MOESM3_ESM.tif (966 kb)
Supplementary Fig. 2. QTL likelihood maps showing LOD scores for: A, Palmitic acid on linkage group 9; B, IOD, linoleic acid and linolenic acid on linkage group 7; C, The second QTL controlling IOD, linoleic acid and linolenic acid on linkage group 16. The horizontal line corresponds to the threshold LOD score, computed using 1,000 permutations at P = 0.05 significance level. Lower figures indicate the estimates of additive effect. (TIFF 966 kb)


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Copyright information

© Her Majesty the Queen in Right of Canada 2010

Authors and Affiliations

  • Sylvie Cloutier
    • 1
    Email author
  • Raja Ragupathy
    • 1
  • Zhixia Niu
    • 1
  • Scott Duguid
    • 2
  1. 1.Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipegCanada
  2. 2.Morden Research Station, Agriculture and Agri-Food CanadaMordenCanada

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