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Theoretical and Applied Genetics

, Volume 122, Issue 6, pp 1075–1090 | Cite as

The identification and mapping of candidate genes and QTL involved in the fatty acid desaturation pathway in Brassica napus

  • A. M. Smooker
  • R. Wells
  • C. Morgan
  • F. Beaudoin
  • K. Cho
  • F. Fraser
  • I. BancroftEmail author
Original Paper

Abstract

We constructed a linkage map for the population QDH, which was derived from a cross between an oilseed rape cultivar and a resynthesised Brassica napus. The linkage map included ten markers linked to loci orthologous to those encoding fatty acid biosynthesis genes in Arabidopsis thaliana. The QDH population contains a high level of allelic variation, particularly in the C genome. We conducted quantitative trait locus (QTL) analyses, using field data obtained over 3 years, for the fatty acid composition of seed oil. The population segregates for the two major loci controlling erucic acid content, on linkage groups A8 and C3, which quantitatively affect the content of other fatty acids and is a problem generally encountered when crossing “wild” germplasm with cultivated “double low” oilseed rape cultivars. We assessed three methods for QTL analysis, interval mapping, multiple QTL mapping and single marker regression analysis of the subset of lines with low erucic acid. We found the third of these methods to be most appropriate for our main purpose, which was the study of the genetic control of the desaturation of 18-carbon fatty acids. This method enabled us to decouple the effect of the segregation of the erucic acid-controlling loci and identify 34 QTL for fatty acid content of seed oil, 14 in the A genome and 20 in the C genome. The QTL indicate the presence of 13 loci with novel alleles inherited from the progenitors of the resynthesised B. napus that might be useful for modulating the content or extent of desaturation of polyunsaturated fatty acids, only one of which coincides with the anticipated position of a candidate gene, an orthologue of FAD2.

Keywords

Quantitative Trait Locus Linkage Group Simple Sequence Repeat Marker Doubled Haploid Interval Mapping 
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.

Notes

Acknowledgments

This work was supported by a PhD studentship and competitive support grant to J.I.C. from the UK Biotechnology and Biological Sciences Research Council.

Supplementary material

122_2010_1512_MOESM1_ESM.pdf (695 kb)
Supplementary material 1 (PDF 695 kb)

References

  1. Browse J, McConn M, James D, Miquel M (1993) Mutants of Arabidopsis deficient in the synthesis of alpha-linolenate—biochemical and genetic-characterization of the endoplasmic-reticulum linoleoyl desaturase. J Biol Chem 268:16345–16351PubMedGoogle Scholar
  2. Burns MJ, Barnes SR, Bowman JG, Clarke MHE, Werner CP, Kearsey MJ (2003) QTL analysis of an intervarietal set of substitution lines in Brassica napus: (i) seed oil content and fatty acid composition. Heredity 90:39–48PubMedCrossRefGoogle Scholar
  3. Cheung WY, Champagne G, Hubert N, Landry BS (1997) Comparison of the genetic maps of Brassica napus and Brassica oleracea. Theor Appl Genet 94:569–582CrossRefGoogle Scholar
  4. Cho K, O’Neill CM, Kwon S-J, Yang T-J, Smooker A, Fraser F, Bancroft I (2010) Sequence-level comparative analysis of the Brassica napus genome around two stearoyl-ACP desaturase loci. Plant J 61:591–599PubMedCrossRefGoogle Scholar
  5. Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
  6. Foisset N, Delourme R, Barret P, Hubert N, Landry BS, Renard M (1996) Molecular-mapping analysis in Brassica napus using isozyme, RAPD and RFLP markers on a doubled-haploid progeny. Theor Appl Genet 93:1017–1025CrossRefGoogle Scholar
  7. Fourmann M, Barret P, Renard M, Pelletier G, Delourme R, Brunel D (1998) The two genes homologous to Arabidopsis FAE1 co-segregate with the two loci governing erucic acid content in Brassica napus. Theor Appl Genet 96:852–858CrossRefGoogle Scholar
  8. Hu XY, Sullivan-Gilbert M, Gupta M, Thompson SA (2006) Mapping of the loci controlling oleic and linolenic acid contents and development of FAD2 and FAD3 allele-specific markers in canola (Brassica napus L.). Theor Appl Genet 113:497–507PubMedCrossRefGoogle Scholar
  9. James DWJ, Lim E, Keller J, Plooy I, Ralston E, Dooner HK (1995) Directed tagging of the Arabidopsis fatty acid elongase-1 (FAE1) gene with the maize transposon activator. Plant Cell 7:309–319PubMedCrossRefGoogle Scholar
  10. Kachroo P, Shanklin J, Shah J, Whittle EJ, Klessig DF (2001) A fatty acid desaturase modulates the activation of defense signalling pathways in plants. Proc Natl Acad Sci USA 98:9448–9453PubMedCrossRefGoogle Scholar
  11. Kachroo A, Shanklin J, Whittle E, Lapchyk L, Hildebrand D, Kachroo P (2007) The Arabidopsis stearoyl-acyl carrier protein-desaturase family and the contribution of leaf isoforms to oleic acid synthesis. Plant Mol Biol 63:257–271PubMedCrossRefGoogle Scholar
  12. Koch MA, Haubold B, Mitchell-Olds T (2000) Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis, and related genera (Brassicaceae). Mol Biol Evol 17:1483–1498PubMedGoogle Scholar
  13. Kosambi DD (1944) The estimation of map distance from recombination values. Ann Eugen 12:172–175Google Scholar
  14. Lombard V, Delourme R (2001) A consensus linkage map for rapeseed (Brassica napus L.): construction and integration of three individual maps from DH populations. Theor Appl Genet 103:491–507CrossRefGoogle Scholar
  15. Lowe AJ, Moule C, Trick M, Edwards KJ (2004) Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor Appl Genet 108:1103–1112PubMedCrossRefGoogle Scholar
  16. Lucigen (2008) CloneSmart® cloning kitsGoogle Scholar
  17. Lühs W, Friedt W (1993) Nonfood uses of vegetable oils and fatty acids. In: Murphy DJ (ed) Designer oil crops: breeding processing and biotechnology. VCH, Cambridge, pp 73–130Google Scholar
  18. Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525PubMedCrossRefGoogle Scholar
  19. Miquel M, Browse J (1992) Arabidopsis mutants deficient in polyunsaturated fatty-acid synthesis—biochemical and genetic-characterization of a plant oleoyl-phosphatidylcholine desaturase. J Biol Chem 267:1502–1509PubMedGoogle Scholar
  20. Mithen RF, Magrath R (1992) Glucosinolates and resistance to Leptosphaeria maculans in wild and cultivated Brassica species. Plant Breed 108:60–68CrossRefGoogle Scholar
  21. O’Neill CM, Bancroft I (2000) Comparative physical mapping of segments of the genome of Brassica oleracea var. albogalabra that are homeologous to sequenced regions of chromosome 4 and 5 of Arabidopsis thaliana. Plant J 23:233–243PubMedCrossRefGoogle Scholar
  22. Parkin IAP, Gulden SM, Sharpe AG, Lukens L, Trick M, Osborn TC, Lydiate DJ (2005) Segmental structure of the Brassica napus genome based on comparative analysis with Arabidopsis thaliana. Genetics 171:765–781PubMedCrossRefGoogle Scholar
  23. Payne RW, Murray DA, Harding SA, Baird DB, Soutar DM (2009) GenStat for Windows introduction, 12th edn. VSN International, Hemel HempsteadGoogle Scholar
  24. Qiu D, Morgan CL, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E (2006) A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet 114:67–80PubMedCrossRefGoogle Scholar
  25. Rana D, Boogaart T, O’Neill CM, Hynes L, Bent E, Macpherson L, Park JY, Lim YP, Bancroft I (2004) Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J 40:725–733PubMedCrossRefGoogle Scholar
  26. Scheffler JA, Sharpe AG, Schmidt H, Sperling P, Parkin IAP, Lühs W, Lydiate DJ, Heinz E (1997) Desaturase multigene families of Brassica napus arose through genome duplication. Theor Appl Genet 94:583–591CrossRefGoogle Scholar
  27. Schierholt A, Becker HC (2001) Environmental variability and heritability of high oleic acid content in winter oilseed rape. Plant Breed 120:63–66CrossRefGoogle Scholar
  28. Schierholt A, Becker HC, Ecke WG (2000) Mapping a high oleic acid mutation in winter oilseed rape (Brassica napus L.). Theor Appl Genet 101:897–901CrossRefGoogle Scholar
  29. Simopoulos AP (2008) The importance of the omega-6/omega-3 fatty acid ratio in cardiovascular disease and other chronic diseases. Exp Biol Med 233:674–688CrossRefGoogle Scholar
  30. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J 3:739–744CrossRefGoogle Scholar
  31. Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098PubMedCrossRefGoogle Scholar
  32. Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Fujimura M, Nunome T, Fukuoka H, Matsumoto S, Hirai M (2003) Identification of two loci for resistance to clubroot (Plasmodiophora brassicae Woronin) in Brassica rapa. Theor Appl Genet 107:997–1002PubMedCrossRefGoogle Scholar
  33. Tanhuanpää P, Vilkki J, Vihinen M (1998) Mapping and cloning of FAD2 gene to develop allele-specific PCR for oleic acid in spring turnip rape (Brassica rapa ssp. oleifera). Mol Breed 4:543–550CrossRefGoogle Scholar
  34. Town CD, Cheung F, Maiti R, Crabtree J, Haas BJ, Wortman JR, Hine EE, Althoff R, Arbogast TS, Tallon LJ, Vigouroux M, Trick M, Bancroft I (2006) Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy. Plant Cell 18:1348–1359PubMedCrossRefGoogle Scholar
  35. Trick M, Bancroft I, Lim YP (2007) The Brassica rapa genome sequencing initiative. Genes Genomes Genomics 1:35–39Google Scholar
  36. Van Ooijen JW (2004) MAPQTL5, Software for the mapping of quantitative trait loci in experimental populations. Kyazma B. V., Wageningen, The NetherlandsGoogle Scholar
  37. Van Ooijen JW, Voorips RE (2001) Joinmap 3.0: software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The NetherlandsGoogle Scholar
  38. Zhao JY, Dimov Z, Becker HC, Ecke WG, Mollers C (2008) Mapping QTL controlling fatty acid composition in a doubled haploid rapeseed population segregating for oil content. Mol Breed 21:115–125CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • A. M. Smooker
    • 1
  • R. Wells
    • 1
  • C. Morgan
    • 1
  • F. Beaudoin
    • 2
  • K. Cho
    • 3
  • F. Fraser
    • 1
  • I. Bancroft
    • 1
    Email author
  1. 1.Department of Crop GeneticsJohn Innes CentreNorwichUK
  2. 2.Biological Chemistry DepartmentRothamsted ResearchHarpendenUK
  3. 3.Highland Agriculture Research Centre, Rural Development AdministrationPyeongchangKorea

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