Skip to main content

Genetic and physical mapping of flowering time loci in canola (Brassica napus L.)

Abstract

We identified quantitative trait loci (QTL) underlying variation for flowering time in a doubled haploid (DH) population of vernalisation—responsive canola (Brassica napus L.) cultivars Skipton and Ag-Spectrum and aligned them with physical map positions of predicted flowering genes from the Brassica rapa genome. Significant genetic variation in flowering time and response to vernalisation were observed among the DH lines from Skipton/Ag-Spectrum. A molecular linkage map was generated comprising 674 simple sequence repeat, sequence-related amplified polymorphism, sequence characterised amplified region, Diversity Array Technology, and candidate gene based markers loci. QTL analysis indicated that flowering time is a complex trait and is controlled by at least 20 loci, localised on ten different chromosomes. These loci each accounted for between 2.4 and 28.6 % of the total genotypic variation for first flowering and response to vernalisation. However, identification of consistent QTL was found to be dependant upon growing environments. We compared the locations of QTL with the physical positions of predicted flowering time genes located on the sequenced genome of B. rapa. Some QTL associated with flowering time on A02, A03, A07, and C06 may represent homologues of known flowering time genes in Arabidopsis; VERNALISATION INSENSITIVE 3, APETALA1, CAULIFLOWER, FLOWERING LOCUS C, FLOWERING LOCUS T, CURLY LEAF, SHORT VEGETATIVE PHASE, GA3 OXIDASE, and LEAFY. Identification of the chromosomal location and effect of the genes influencing flowering time may hasten the development of canola varieties having an optimal time for flowering in target environments such as for low rainfall areas, via marker-assisted selection.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3

References

  • Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402

    PubMed  Article  CAS  Google Scholar 

  • Bastow R, Mylne JS, Lister C, Lippman Z, Martienssen RA, Dean C (2004) Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427:164–167

    PubMed  Article  CAS  Google Scholar 

  • Blackman BK, Rasmussen DA, Strasburg JL, Raduski AR, Burke JM, Knapp SJ, Michaels SD, Rieseberg LH (2011) Contributions of flowering time genes to sunflower domestication and improvement. Genetics 187:271–287

    PubMed  Article  CAS  Google Scholar 

  • Bowers JE, Chapman BA, Rong J, Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422:433–438

    PubMed  Article  CAS  Google Scholar 

  • Broman KW, Wu H, Sen Ś, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890. www.rqtl.org

    Google Scholar 

  • Butler DG, Cullis BR, Gilmour AR, Gogel BJ (2007) ASReml-R reference manual. Release 2.0. Technical report, Queensland Department of Primary Industries, Australia

  • Butruille DV, Guries RP, Osborn TC (1999) Linkage analysis of molecular markers and quantitative trait loci in populations of inbred backcross lines of Brassica napus L. Genetics 153:949–964

    PubMed  CAS  Google Scholar 

  • Choi S, Teakle G, Plaha P, Kim J, Allender C, Beynon E, Piao Z, Soengas P, Han T, King G, Barker G, Hand P, Lydiate D, Batley J, Edwards D, Koo D, Bang J, Park B-S, Lim Y (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet 115:777–792

    PubMed  Article  CAS  Google Scholar 

  • Coombes NE (2002) The reactive tabu search for efficient correlated experimental designs. PhD thesis, John Moores University, Liverpool, UK

  • Delourme R, Falentin C, Huteau V, Clouet V, Horvais R, Gandon B, Specel S, Hanneton L, Dheu JE, Deschamps M, Margale E, Vincourt P, Renard M (2006) Genetic control of oil content in oilseed rape (Brassica napus L.). Theor Appl Genet 113:1331–1345

    PubMed  Article  CAS  Google Scholar 

  • Deng W, Ying H, Helliwell CA, Taylor JM, Peacock WJ, Dennis ES (2011) FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proc Natl Acad Sci 108:6680–6685

    PubMed  Article  CAS  Google Scholar 

  • Diers BW, Osborn TC (1994) Genetic diversity of oilseed Brassica napus germplasm based on restriction fragment length polymorphisms. Theor Appl Genet 88:662–668

    Article  Google Scholar 

  • Ferreira ME, Satagopan J, Yandell BS, Williams PH, Osborn TC (1995) Mapping loci controlling vernalisation requirement and flowering time in Brassica napus. Theor Appl Genet 90:727–732

    Article  Google Scholar 

  • Fowler S, Lee K, Onouchi H, Samach A, Richardson K, Coupland G, Putterill J (1999) GIGANTEA: a circadian clock-controlled gene that regulates photoperiodic flowering in Arabidopsis and encodes a protein with several possible membrane-spanning domains. EMBO J 18:4679–4688

    PubMed  Article  CAS  Google Scholar 

  • He Y, Amasino RM (2005) The role of chromatin modification in flowering-time control. Trends Plant Sci 10:30–35

    PubMed  Article  CAS  Google Scholar 

  • Helliwell CA, Wood CC, Robertson M, Peacock WJ, Dennis ES (2006) The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J 46:183–192

    PubMed  Article  CAS  Google Scholar 

  • Kardailsky I, Shukla VK, Ahn JH, Dagenais N, Christensen SK, Nguyen JT, Chory J, Harrison MJ, Weigel D (1999) Activation tagging of the floral inducer FT. Science 286:1962–1965

    PubMed  Article  CAS  Google Scholar 

  • Kennard WC, Slocum MK, Figdore SS, Osborn TC (1994) Genetic analysis of morphological variation in Brassica oleracea using molecular markers. Theor Appl Genet 87:721–732

    Article  CAS  Google Scholar 

  • Kim JS, Chung TY, King GJ, Jin M, Yang TJ, Jin YM, Kim HI, Park BS (2006) A sequence-tagged linkage map of Brassica rapa. Genetics 174:29–39

    PubMed  Article  CAS  Google Scholar 

  • Kim DH, Doyle MR, Sung S, Amasino RM (2009) Vernalization: winter and the timing of flowering in plants. Annu Rev Cell Dev Biol 25:277–299

    PubMed  Article  CAS  Google Scholar 

  • Kobayashi Y, Kaya H, Goto K, Iwabuchi M, Araki T (1999) A pair of related genes with antagonistic roles in mediating flowering signals. Science 286:1960–1962

    PubMed  Article  CAS  Google Scholar 

  • Kole C, Quijada P, Michaels SD, Amasino RM, Osborn TC (2001) Evidence for homology of flowering-time genes VFR2 from Brassica rapa and FLC from Arabidopsis thaliana. Theor Appl Genet 102:425–430

    Article  CAS  Google Scholar 

  • Koornneef M, Hanhart CJ, Veen JH (1991) A genetic and physiological analysis of late flowering mutants in Arabidopsis thaliana. Mol Gen Genet 229:57–66

    PubMed  Article  CAS  Google Scholar 

  • Koornneef M, Blankestijn-de Vries H, Hanhart C, Soppe W, Peeters T (1994) The phenotype of some late-flowering mutants is enhanced by a locus on chromosome 5 that is not effective in the Landsberg erecta wild-type. Plant J 6:911–919

    Article  CAS  Google Scholar 

  • Koornneef M, Alonso-Blanco C, Blankestijn-de Vries H, Hanhart CJ, Peeters AJM (1998) Genetic interactions among late-flowering mutants of Arabidopsis. Genetics 148:885–892

    PubMed  CAS  Google Scholar 

  • Lagercrantz U, Putterill J, Coupland G, Lydiate DJ (1996) Comparative genome mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time in Brassica. Plant J 9:13–20

    PubMed  Article  CAS  Google Scholar 

  • Levy YY, Dean C (1998a) Control of flowering time. Curr Opin Plant Biol 1:49–54

    PubMed  Article  CAS  Google Scholar 

  • Levy YY, Dean C (1998b) The transition to flowering. Plant Cell 10:1973–1989

    PubMed  CAS  Google Scholar 

  • Li F, Kitashiba H, Inaba K, Nishio T (2009) A Brassica rapa linkage map of EST-based SNP markers for identification of candidate genes controlling flowering time and leaf morphological traits. DNA Res 16:311–323

    PubMed  Article  CAS  Google Scholar 

  • Lin SI, Wang JG, Poon SY, Su CL, Wang SS, Chiou TJ (2005) Differential regulation of expression by vernalization FLOWERING LOCUS C in cabbage and Arabidopsis. Plant Physiol 137:1037–1048

    PubMed  Article  CAS  Google Scholar 

  • Long Y, Shi J, Qiu D, Li R, Zhang C, Wang J, Hou J, Zhao J, Shi L, Park B-S, Choi SR, Lim YP, Meng J (2007) Flowering time quantitative trait loci analysis of oilseed brassica in multiple environments and genome wide alignment with Arabidopsis. Genetics 177:2433–2444

    PubMed  CAS  Google Scholar 

  • Lou P, Xie Q, Xu X, Edwards C, Brock M, Weinig C, McClung C (2011) Genetic architecture of the circadian clock and flowering time in Brassica rapa. Theor Appl Genet 123:397–409

    PubMed  Article  CAS  Google Scholar 

  • Lowe A, Moule C, Trick M, Edwards K (2004) Efficient large-scale development of microsatellites for marker and mapping applications in Brassica crop species. Theor Appl Genet 108:1103–1112

    PubMed  Article  CAS  Google Scholar 

  • Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290:1151–1155

    PubMed  Article  CAS  Google Scholar 

  • Lysak MA, Koch MA, Pecinka A, Schubert I (2005) Chromosome triplication found across the tribe Brassiceae. Genome Res 15:516–525

    PubMed  Article  CAS  Google Scholar 

  • Manly KF, Cudmore JRH, Meer JM (2001) Map Manager QTX, cross platform software for genetic mapping. Mamm Genome 12:930–932

    PubMed  Article  CAS  Google Scholar 

  • Michaels SD, Amasino RM (1999) FLOWERING LOCUS C encodes a novel MADS domain protein that acts as a repressor of flowering. Plant Cell 11:949–956

    PubMed  CAS  Google Scholar 

  • Nagahara U (1935) Genomic analysis in Brassica with special reference to the experimental formation of B. napus and peculiar mode of fertilisation. Jpn J Bot 7:389–452

    Google Scholar 

  • Okazaki K, Sakamoto K, Kikuchi R, Saito A, Togashi E, Kuginuki Y, Matsumoto S, Hirai M (2007) Mapping and characterization of FLC homologs and QTL analysis of flowering time in Brassica oleracea. Theor Appl Genet 114:595–608

    PubMed  Article  CAS  Google Scholar 

  • Osborn TC, Lukens L (2003) The molecular genetic basis of flowering time variation in Brassica species. The molecular genetic basis of flowering time variation in Brassica species. In: Nagata, T Tabata S (eds) Biotechnology in Agriculture and Forestry 52 Brassica and legume from genome structure to breeding. Springer, Berlin, pp 69–86

  • Osborn TC, Kole C, Parkin IAP, Sharpe AG, Kuiper M, Lydiate DJ, Trick M (1997) Comparison of flowering time enes in Brassica rapa, B. napus and Arabidopsis thaliana. Genetics 146:1123–1129

    PubMed  CAS  Google Scholar 

  • Park DH, Somers DE, Kim YS, Choy YH, Lim HK, Soh MS, Kim HJ, Kay SA, Nam HG (1999) Control of circadian rhythms and photoperiodic flowering by the Arabidopsis GIGANTEA gene. Science 285:1579–1582

    PubMed  Article  CAS  Google Scholar 

  • Parkin IA, Sharpe AG, Lydiate DJ (2003) Patterns of genome duplication within the Brassica napus genome. Genome 46:291–303

    PubMed  Article  CAS  Google Scholar 

  • Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger M, Vincourt P, Blanchard P (2005) Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet 111:1514–1523

    PubMed  Article  CAS  Google Scholar 

  • Pires JC, Zhao JW, Schranz ME, Leon EJ, Quijada PA, Lukens LN, Osborn TC (2004) Flowering time divergence and genomic rearrangements in resynthesized Brassica polyploids (Brassicaceae). Biol J Linn Soc 82:675–688

    Article  Google Scholar 

  • Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847–857

    PubMed  Article  CAS  Google Scholar 

  • Raman R, Raman H, Johnstone K, Lisle C, Smith A, Matin P, Allen H (2005) Genetic and in silico comparative mapping of the polyphenol oxidase gene in bread wheat (Triticum aestivum L.). Funct Integr Genomics 5:185–200

    PubMed  Article  CAS  Google Scholar 

  • Raman R, Allen H, Diffey S, Raman H, Martin P, McKelvie K (2009) Localisation of quantitative trait loci for quality attributes in a doubled haploid population of wheat (Triticum aestivum L.). Genome 52:701–715

    PubMed  Article  CAS  Google Scholar 

  • Raman H, Raman R, Nelson MN, Aslam MN, Rajasekaran R, Wratten N, Cowling WA, Kilian A, Sharpe AG, Schondelmaier J (2012a) Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res 19:51–65

    PubMed  Article  CAS  Google Scholar 

  • Raman R, Taylor B, Marcroft S, Stiller J, Eckermann P, Coombes N, Rehman A, Lindbeck K, Luckett D, Wratten N, Batley J, Edwards D, Wang X, Raman H (2012b) Molecular mapping of qualitative and quantitative loci for resistance to Leptosphaeria maculans; causing blackleg disease in canola (Brassica napus L.). Theor Appl Genet 125:405–418

    PubMed  Article  CAS  Google Scholar 

  • Rana D, Boogaart T, O’Neill CM, Hynes L, Bent E, Macpherson L, Young Park J, Lim YP, Bancroft I (2004) Conservation of the microstructure of genome segments in Brassica napus and its diploid relatives. Plant J 40:725–733

    PubMed  Article  CAS  Google Scholar 

  • Razi H, Howell E, Newbury H, Kearsey M (2008) Does sequence polymorphism of FLC paralogues underlie flowering time QTL in Brassica oleracea? Theor Appl Genet 116:179–192

    PubMed  Article  CAS  Google Scholar 

  • Rouse DT, Sheldon CC, Bagnall DJ, Peacock WJ, Dennis ES (2002) FLC, a repressor of flowering, is regulated by genes in different inductive pathways. Plant J 29:183–191

    PubMed  Article  CAS  Google Scholar 

  • Salisbury PA, Wratten N (1999) Brassica napus breeding. In: Salisbury PA, Potter TD, McDonald G, Green AG (eds) Canola in Australia: the first 30 years, pp 29–36

  • Samach A, Onouchi H, Gold SE, Ditta GS, Schwarz-Sommer Z, Yanofsky MF, Coupland G (2000) Distinct roles of CONSTANS target genes in reproductive development of Arabidopsis. Science 288:1613–1616

    PubMed  Article  CAS  Google Scholar 

  • Schmitz RJ, Amasino RM (2007) Vernalization: a model for investigating epigenetics and eukaryotic gene regulation in plants. Biochimica et Biophysica Acta (BBA) Gene Struct Expr 1769:269–275

    Google Scholar 

  • Schranz ME, Quijada P, Sung S-B, Lukens L, Amasino R, Osborn TC (2002) Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 162:1457–1468

    PubMed  CAS  Google Scholar 

  • Schranz ME, Lysak MA, Mitchell-Olds T (2006) The ABC’s of comparative genomics in the Brassicaceae: building blocks of crucifer genomes. Trends Plant Sci 11:535–542

    PubMed  Article  CAS  Google Scholar 

  • Sheldon CC, Burn JE, Perez PP, Metzger J, Edwards JA, Peacock WJ, Dennis ES (1999) The FLF MADS box gene: a repressor of flowering in Arabidopsis regulated by vernalization and methylation. Plant Cell 11:445–458

    PubMed  CAS  Google Scholar 

  • Sheldon CC, Rouse DT, Finnegan EJ, Peacock WJ, Dennis ES (2000) The molecular basis of vernalization: the central role of FLOWERING LOCUS C (FLC). Proc Natl Acad Sci USA 97:3753–3758

    PubMed  Article  CAS  Google Scholar 

  • Sung S, Amasino RM (2005) Remembering winter: towards a molecular understanding of vernalization. Ann Rev Plant Biol 56:491–508

    Article  CAS  Google Scholar 

  • Suwabe K, Tsukazaki H, Iketani H, Hatakeyama K, Kondo M, Fujimura M, Nunome T, Fukuoka H, Hirai M, Matsumoto S (2006) Simple sequence repeat-based comparative genomics between Brassica rapa and Arabidopsis thaliana: the genetic origin of clubroot resistance. Genetics 173:309–319

    PubMed  Article  CAS  Google Scholar 

  • Suwabe K, Morgan C, Bancroft I (2008) Integration of Brassica A genome genetic linkage map between Brassica napus and B. rapa. Genome 41:169–176

    Google Scholar 

  • Tadege M, Sheldon C, Helliwell C, Stoutjesdijk P, Dennis E, Peacock W (2001) Control of flowering time by FLC orthologues in Brassica napus. Plant J 28:545–553

    PubMed  Article  CAS  Google Scholar 

  • Teutonico RA, Osborn TC (1994) Mapping of RFLP and quantitative trait loci in Brassica rapa and comparison to the linkage maps of B. napus, B. oleracea and Arabidopsis thaliana. Theor Appl Genet 89:885–894

    Article  CAS  Google Scholar 

  • Udall J, Quijada P, Lambert B, Osborn T (2006) Quantitative trait analysis of seed yield and other complex traits in hybrid spring rapeseed (Brassica napus L.): 2. Identification of alleles from unadapted germplasm. Theor Appl Genet 113:597–609

    PubMed  Article  CAS  Google Scholar 

  • Verbyla AP, Cullis BR, Thompson R (2006) The analysis of QTL by simultaneous use of the full linkage map. Theor Appl Genet 116:95–111

    Article  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93(1):77–78

    PubMed  Article  CAS  Google Scholar 

  • Wang J, Long Y, Wu BD, Liu J, Jiang CC, Shi L, Zhao JW, King GJ, Meng JL (2009) The evolution of Brassica napus FLOWERING LOCUS T paralogues in the context of inverted chromosomal duplication blocks. BMC Evol Biol 9:271

    PubMed  Article  Google Scholar 

  • Wang N, Qian W, Suppanz I, Wei L, Mao B, Long Y, Meng J, Müller AE, Jung C (2011a) Flowering time variation in oilseed rape (Brassica napus L.) is associated with allelic variation in the FRIGIDA homologue BnaA.FRI.a. J Exp Bot 62:5641–5658

    PubMed  Article  CAS  Google Scholar 

  • Wang X, Wang H, Wang J, Sun R, Wu J, Liu S, Bai Y, Mun J-H, Bancroft I, Cheng F, Huang S, Li X, Hua W, Wang J, Wang X, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park B-S, Weisshaar B, Liu B, Li B, Liu B, Tong C, Song C, Duran C, Peng C, Geng C, Koh C, Lin C, Edwards D, Mu D, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang H, Wang H, Belcram H, Zhou H, Hirakawa H, Abe H, Guo H, Wang H, Jin H, Parkin IA, Batley J, Kim J-S, Just J, Li J, Xu J, Deng J, Kim JA, Li J, Yu J, Meng J, Wang J, Min J, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao M, Jin M, Ramchiary N, Drou N, Berkman PJ, Cai Q, Huang Q, Li R, Tabata S, Cheng S, Zhang S, Zhang S, Huang S, Sato S, Sun S, Kwon S-J, Choi S-R, Lee T-H, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li Y, Du Y, Liao Y, Lim Y, Narusaka Y, Wang Y, Wang Z, Li Z, Wang Z, Xiong Z, Zhang Z (2011b) The genome of the mesopolyploid crop species Brassica rapa. Nature Genetics 43:1035–1039

  • Yamamoto T, Lin H, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics 154:885–891

    PubMed  CAS  Google Scholar 

  • Yang TJ, Kim JS, Kwon SJ, Lim KB, Choi BS, Kim JA, Jin M, Park JY, Lim MH, Kim HI, Lim YP, Kang JJ, Hong JH, Kim CB, Bhak J, Bancroft I, Parka BS (2006) Sequence-level analysis of the diploidization process in the triplicated FLOWERING LOCUS C region of Brassica rapa. Plant Cell 18:1339–1347

    PubMed  Article  CAS  Google Scholar 

  • Yuan Y-X, Wu J, Sun R-F, Zhang X-W, Xu D-H, Bonnema G, Wang X-W (2009) A naturally occurring splicing site mutation in the Brassica rapa FLC1 gene is associated with variation in flowering time. J Exp Bot 60:1299–1308

    PubMed  Article  CAS  Google Scholar 

  • Zhao JJ, Kulkarni V, Liu NN, Del Carpio DP, Bucher J, Bonnema G (2010) BrFLC2 (FLOWERING LOCUS C) as a candidate gene for a vernalization response QTL in Brassica rapa. J Exp Bot 61:1817–1825

    PubMed  Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the BioFirst Initiative (NSW Agricultural Genomic Centre) grant of NSW Government to H. Raman. We would like to thank Dr Jun Zou (HAU, China) and Mr. Pradeep Ruperao (UQ) for PCR analysis of FLC3 gene and preparing figures for physical maps, respectively.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Harsh Raman.

Additional information

Communicated by R. Visser.

Electronic supplementary material

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Raman, H., Raman, R., Eckermann, P. et al. Genetic and physical mapping of flowering time loci in canola (Brassica napus L.). Theor Appl Genet 126, 119–132 (2013). https://doi.org/10.1007/s00122-012-1966-8

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-012-1966-8

Keywords

  • Quantitative Trait Locus
  • Simple Sequence Repeat Marker
  • Doubled Haploid
  • Doubled Haploid Line
  • Quantitative Trait Locus Region