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Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars

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Abstract

Genetic map construction and identification of quantitative trait loci (QTLs) for blackleg resistance were performed for four mapping populations derived from five different canola source cultivars. Three of the populations were generated from crosses between single genotypes from the blackleg-resistant cultivars Caiman, Camberra and AVSapphire and the blackleg-susceptible cultivar Westar10. The fourth population was derived from a cross between genotypes from two blackleg resistant varieties (Rainbow and AVSapphire). Different types of DNA-based markers were designed and characterised from a collection of 20,000 EST sequences generated from multiple Brassica species, including a new set of 445 EST-SSR markers of high value to the international community. Multiple molecular genetic marker systems were used to construct linkage maps with locus numbers varying between 219 and 468, and coverage ranging from 1173 to 1800 cM. The proportion of polymorphic markers assigned to map locations varied from 70 to 89% across the four populations. Publicly available simple sequence repeat markers were used to assign linkage groups to reference nomenclature, and a sub-set of mapped markers were also screened on the Tapidor × Ningyou (T × N) reference population to assist this process. QTL analysis was performed based on percentage survival at low and high disease pressure sites. Multiple QTLs were identified across the four mapping populations, accounting for 13–33% of phenotypic variance (V p). QTL-linked marker data are suitable for implementation in breeding for disease resistance in Australian canola cultivars. However, the likelihood of shifts in pathogen race structure across different geographical locations may have implications for the long-term durability of such associations.

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References

  • Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–560

    Article  CAS  PubMed  Google Scholar 

  • Ansun-Meleyah D, Balesdent MH, Delourme R, Pilet ML, Tanguy X, Renard M, Rouxel T (1998) Genes for race-specific resistance against blackleg disease in Brassica napus L. Plant Breed 117:373–378

    Article  Google Scholar 

  • Ayele M, Haas BJ, Kumar N, Wu H, Xiao Y, Aken SV, Utterback TR, Wortman JR, White OR, Town CD (2005) Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis. Genome 15:487–495

    Article  Google Scholar 

  • Balesdent MH, Attard A, Kühn ML, Rouxel T (2002) New avirulence genes in the phytopathogenic fungus Leptosphaeria maculans. Phytopathol 92:1122–1133

    Article  CAS  Google Scholar 

  • Batley J, Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Kaur S, Xi Li, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Walkiewicz M, Spangenberg GC, Edwards D (2007) Identification and characterization of simple sequence repeat markers Brassica napus expressed sequences. Mol Ecol Notes 7:886–889

    Article  CAS  Google Scholar 

  • Burgess B, Mountford H, Hopkins CJ, Love C, Ling AE, Spangenberg GC, Edwards D, Batley J (2006) Identification and characterization of simple sequence repeat (SSR) markers derived in silico from Brassica oleracea genome shotgun sequences. Mol Ecol Notes 6:1191–1194

    Article  CAS  Google Scholar 

  • Chèvre AM, Eber F, Jenczewski E, Darmency H, Renard M (2003) Gene flow from oilseed rape to weedy species. Acta Agric Scand B Soil Plant Sci 53:22–25

    Google Scholar 

  • Choi SR, Teakle GR, Plaha P, Kim JH, Allender CJ, Beynon E, Piao ZY, Soengas P, Han TH, King GJ, Baker GC, Hand P, Lydiate DJ, Batley J, Edwards D, Koo DH, Bang JW, Park B-S, Lim YP (2007) The reference genetic linkage map for the multinational Brassica rapa genome sequencing project. Theor Appl Genet 115:777–792

    Article  CAS  PubMed  Google Scholar 

  • Cogan NOI, Ponting RC, Vecchies AC, Drayton MC, George J, Dobrowolski MP, Sawbridge TI, Spangenberg GC, Smith KF, Forster JW (2006) Gene-associated single nucleotide polymorphism (SNP) discovery in perennial ryegrass (Lolium perenne L.). Mol Genet Genom 277:413–425

    Article  CAS  Google Scholar 

  • Crouch JH, Lewis BG, Mithen RF (1994) The effect of A genome substitution on the resistance of Brassica napus to infection by Leptosphaeria maculans. Plant Breed 112:265–278

    Article  CAS  Google Scholar 

  • Delourme R, Pilet-Nayel ML, Archipiano M, Horvais R, Tanguy X, Rouxel T, Brun H, Renard M, Balesdent MH (2004) A cluster of major specific resistance genes to Leptosphaeria maculans in Brassica napus. Phytopathol 94:578–583

    Article  CAS  Google Scholar 

  • Delourme R, Chèvre AM, Brun H, Rouxel T, Balesdent MH, Dias JS, Salisbury, Renard M, Rimmer SR (2006) Major gene and polygenic resistance to Leptosphaeria maculans in oilseed rape (Brassica napus). Eur J Plant Pathol 114:41–52

    Article  Google Scholar 

  • Delourme R, Piel N, Horvais R, Pouilly N, Domin C, Vallée P, Falentin C, Manzanares-Dauleux M, Renard M (2008) Molecular and phenotypic characterization of near isogenic lines at QTL for quantitative resistance to Leptosphaeria maculans in oilseed rape (Brassica napus L.). Theor Appl Genet 117:1055–1067

    Article  CAS  PubMed  Google Scholar 

  • Dion Y, Gugel RK, Rakow GFW, Seguin-Swartz G, Landry BS (1995) RFLP mapping of resistance to the blackleg disease [causal agent, Leptosphaeria maculans (Desm.) Ces. et de Not.] in canola (Brassica napus L.). Theor Appl Genet 91:1190–1194

    Article  CAS  Google Scholar 

  • Erwin TA, Jewell EG, Love CG, Lim GAC, Li X, Chapman R, Batley J, Stajich J, Mongin E, Stupka E, Ross B, Spangenberg G, Edwards D (2007) BASC: an integrated bioinformatics system for Brassica research. Nucl Acids Res 35:D870–D873

    Article  CAS  PubMed  Google Scholar 

  • Ferreira ME, Rimmer SR, Williams PH, Osborn TC (1995) Mapping loci controlling Brassica napus resistance to Leptosphaeria maculans under different screening conditions. Phytopathology 85:213–217

    Article  CAS  Google Scholar 

  • Fitt BDL, Brun H, Barbetti MJ, Rimmer SR (2006) World-wide importance of phoma stem canker Leptosphaeria maculans and L. biglobosa) on Oilseed Rape (Brassica napus). Eur J Plant Pathol 114:3–15

    Article  Google Scholar 

  • Forster JW, Cogan NOI, Dobrowolski MP, Francki MG, Spangenberg GC, Smith KF (2008) Functionally-associated molecular genetic markers for temperate pasture plant improvement. In: Henry RJ (ed) Plant genotyping II: SNP technology. CABI Press, Wallingford, pp 154–187

    Chapter  Google Scholar 

  • Gilmour AR, Cullis BR, Verbyla A (1997) Accounting for natural and extraneous variation in the analysis of field experiments. J Agric Biol Environ Stat 2:269–293

    Article  Google Scholar 

  • Hopkins CJ, Cogan NOI, Hand M, Jewell E, Kaur J, Li X, Geraldine AC Lim, Ling AE, Love C, Mountford H, Todorovic M, Vardy M, Spangenberg GC, Edwards D, Batley J (2007) Sixteen new simple sequence repeat (SSR) markers from Brassica juncea expressed sequences and their cross-species amplification. Mol Ecol Notes 7:697–700

  • Howlett BJ (2004) Current knowledge of the interaction between Brassica napus and Leptosphaeria maculans. Can J Plant Pathol 26:245–252

    Google Scholar 

  • Jewell E, Robinson A, Savage D, Erwin T, Love CG, Lim GA, LiX, Batley J, Spangenberg GC, Edwards D (2006) SSR Primer and SSR Taxonomy Tree: Biome SSR discovery. Nucl Acids Res 34:W656–W659

  • Kaur S, Nicolas ME, Ford R, Norton R, Paul WJT (2006) Selection of Brassica rapa genotypes for tolerance to boron toxicity. Plant Soil 285:115–123

    Article  CAS  Google Scholar 

  • Kaur S, Ford R, Nicolas ME, Paul WJT (2008) Genetics of tolerance to high concentrations of boron in Brassica rapa. Euphytica 162:31–38

    Article  CAS  Google Scholar 

  • Ke L, Sun Y, Liu P, Yang G (2004) Identification of AFLP fragments linked to one recessive genic male sterility (RGMS) in rapeseed (Brassica napus L.) and conversion to SCAR markers for marker-aided selection. Euphytica 138:163–168

    Article  CAS  Google Scholar 

  • Kearsey MJ, Farquhar AGL (1998) QTL analysis in plants: where are we now? Heredity 80:137–142

    Article  PubMed  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugenet 12:172–175

    Google Scholar 

  • Ling AE, Kaur J, Burgess B, Hand M, Hopkins CJ, Li X, Love CG, Vardy M, Walkiwiecz M, Spangenberg G, Edwards D, Batley J (2007) Characterisation of simple sequence repeat markers derived in silico from Brassica rapa bacterial artificial chromosome sequences and their application in Brassica napus. Mol Ecol Notes 7:273–277

    Article  CAS  Google Scholar 

  • 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 103:491–507

    Article  CAS  Google Scholar 

  • 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 108:1103–1112

    Article  CAS  PubMed  Google Scholar 

  • Marcroft S, Bluett C (2008) Blackleg of canola. Agriculture notes, State of Victoria, Department of Primary Industries, May 2008, AG1352, ISSN 1329-8062

  • Mayerhofer R, Bansal VK, Thiagarajah GR, Stringam GR, Good AG (1997) Molecular mapping of resistance to Leptosphaeria maculans in Australian cultivars of Brassica napus. Genome 40:294–301

    Article  CAS  PubMed  Google Scholar 

  • Mayerhofer R, Wilde K, Mayerhofer M, Lydiate D, Bansal VK, Good AG, Parkin IAP (2005) Complexities of chromosome landing in a highly duplicated genome: toward map-based cloning of a gene controlling blackleg resistance in Brassica napus. Genetics 171:1977–1988

    Article  CAS  PubMed  Google Scholar 

  • McDowell JM, Simon SA (2006) Recent insights into R gene evolution. Mol Plant Pathol 7:437–448

    Article  CAS  PubMed  Google Scholar 

  • Meyers BC, Kaushik S, Nandety RS (2005) Evolving disease resistance genes. Curr Opin Plant Biol 8:129–134

    Article  CAS  PubMed  Google Scholar 

  • Mongkolporn O, Kadkol GP, Pang ECK, Taylor PWJ (2003) Identification of RAPD markers linked to recessive genes conferring siliqua shatter resistance in Brassica rapa. Plant Breed 122:1–6

    Article  Google Scholar 

  • Mukhlesur R, Mcvetty Peter BE, Li G (2007) Development of SRAP, SNP and Multiplexed SCAR molecular markers for the major seed coat color gene in Brassica rapa L. Theor Appl Genet 115:1101–1107

    Article  CAS  Google Scholar 

  • Negi MS, Devic M, Delseny M, Lakshmikumaran M (2000) Identification of AFLP fragments linked to seed coat colour in Brassica juncea and conversion to a SCAR marker for rapid selection. Theor Appl Genet 101:146–152

    Article  CAS  Google Scholar 

  • Parkin IAP, Sharpe AG, Keith DJ, Lydiate DJ (1995) Identification of the A and C genomes of amphidiploid Brassica napus (oilseed rape). Genome 38:1122–1131

    CAS  PubMed  Google Scholar 

  • Pilet ML, Delourme R, Foisset N, Renard M (1998) Identification of loci contributing to quantitative field resistance to blackleg disease, causal agent Leptosphaeria maculans (Desm.) Ces. et de Not., in Winter rapeseed (Brassica napus L.). Theor Appl Genet 96:23–30

    Article  Google Scholar 

  • Pilet ML, Duplan G, Archipiano M, Barret P, Baron C, Horvais R, Tanguy X, Lucas MO, Renard M, Delourme R (2001) Stability of QTL for field resistance to blackleg across two genetic backgrounds in oilseed rape. Crop Sci 41:197–205

    Article  CAS  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Qiu D, Morgan C, Shi J, Long Y, Liu J, Li R, Zhuang X, Wang Y, Tan X, Dietrich E, Weihmann T, Everett C, Vanstraelen S, Beckett P, Fraser F, Trick M, Barnes S, Wilmer J, Schmidt R, Li J, Li D, Meng J, Bancroft I (2006) A comparative linkage map of oilseed rape and its use for QTL analysis of seed oil and erucic acid content. Theor Appl Genet 114:67–80

    Article  CAS  PubMed  Google Scholar 

  • Rimmer SR (2006) Resistance genes to Leptosphaeria maculans in Brassica napus. Can J Plant Pathol 28:S288–S297

    CAS  Google Scholar 

  • Robinson AJ, Love CG, Batley J, Barker G, Edwards D (2004) Simple sequence repeat marker loci discovery using SSR primer. Bioinformatics 20:1475–1476

    Article  CAS  PubMed  Google Scholar 

  • Saal B, Plieske J, Hu J, Quiros CF, Struss D (2001) Microsatellite markers for genome analysis in Brassica. II. Assignment of rapeseed microsatellites to the A and C genomes and genetic mapping in Brassica oleracea L. Theor Appl Genet 102:695–699

    Article  CAS  Google Scholar 

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

  • Salisbury PA, Ballinger DJ, Wratten N, Plummer KM, Howlett BJ (1995) Blackleg disease on oilseed Brassica in Australia—a review. Aust J Exp Agric 35:665–672

    Article  Google Scholar 

  • Sebastian RL, Howell EC, King GJ, Marshall DF, Kearsey MJ (2000) An integrated AFLP and RFLP Brassica oleracea linkage map from two morphologically distinct doubled-haploid mapping populations. Theor Appl Genet 100:75–81

    Article  CAS  Google Scholar 

  • Sharpe AG, Parkin IAP, Keith DJ, Lydiate DJ (1995) Frequent nonreciprocal translocations in the amphidiploid genome of oilseed rape (Brassica napus). Genome 38:1112–1121

    CAS  PubMed  Google Scholar 

  • Sprague SJ, Balesdent M-H, Brun H, Hayden HL, Marcroft SJ, Pinochet X, Rouxel T, Howlett BJ (2006) Major gene resistance in Brassica napus (oilseed rape) is overcome by changes in virulence in populations of Leptosphaeria maculans in France and Australia. Eur J Plant Physiol 114:33–40

    Google Scholar 

  • Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterisation of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098

    Article  CAS  PubMed  Google Scholar 

  • Suwabe K, Iketani H, Nunome T, Ohyama A, Hirai M, Fukuoka H (2004) Characterisation of microsatellites in Brassica rapa genome and their potential utilization for comparative genomics in Cruciferae. Breed Sci 54:85–90

    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. Genet 173:309–319

    Article  CAS  Google Scholar 

  • Trick M, Long Y, Meng J, Bancroft I (2009) Single nucleotide polymorphism (SNP) discovery in the polyploidy Brassica napus using Solexa transcriptome sequencing. Plant Biotech J 7:334–347

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Voorips RE (2001) JOINMAP 3.0. software for the calculation of genetic linkage maps. Plant Research International, Wageningen, The Netherlands

    Google Scholar 

  • Voorrips RE, Jongerius MC, Kanne HJ (1997) Mapping of two genes for resistance to clubroot (Plasmodiophora brassicae) in a population of doubled haploid lines of Brassica oleracea by means of RFLP and AFLP markers. Theor Appl Genet 94:75–82

    Article  CAS  PubMed  Google Scholar 

  • Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: A new technique for DNA fingerprinting. Nucl Acids Res 23:4407–4414

    Article  CAS  PubMed  Google Scholar 

  • Vuylsteke M, Mank R, Antonise R, Bastiaans E, Senior ML, Stuber CW, Melchinger AE, Lübberstedt T, Xia XC, Stam P, Zabeau M, Kuiper M (1999) Two high-density AFLP® linkage maps of Zea mays L.: analysis of distribution of AFLP markers Theor Appl Genet 99:921–935

    Google Scholar 

  • Wang S, Basten CJ, Zeng Z-B (2007) Windows QTL Cartographer 2.5, Department of Statistics, North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm

  • Wu K, Burnquist W, Sorrells M, Tew T, Moore P, Tanksley S (1992) The detection and estimation of linkage in polyploidy plants using single-dose restriction fragments. Theor Appl Genet 83:294–300

    Article  Google Scholar 

  • Yu FQ, Lydiate D J, Rimmer SR (2004) Identification and mapping of a third blackleg resistance locus in Brassica napus derived from B. rapa subsp. sylvestris. Plant and Animal Genome XII, San Diego, California, USA, p 520

  • Yu F, Lydiate DJ, Rimmer SR (2005) Identification of two novel genes for blackleg resistance in Brassica napus. Theor Appl Genet 110:969–979

    Article  CAS  PubMed  Google Scholar 

  • Yu F, Lydiate DJ, Rimmer SR (2008) Identification and mapping of a third blackleg resistance locus in Brassica napus derived from B. rapa subsp. sylvestris. Genome 51:64–72

    Article  CAS  PubMed  Google Scholar 

  • Zhao J, Wang X, Deng Bo, Lou P, Wu J, Sun R, Xu Z, Jaap V, Maarten K, Guusje B (2005) Genetic relationships within Brassica rapa as inferred from AFLP fingerprints. Theor Appl Genet 110:1301–1314

    Article  PubMed  Google Scholar 

  • Zhu B, Rimmer SR (2003) Inheritance of resistance to Leptosphaeria maculans in two accessions of Brassica napus. Can J Plant Path 25:98–103

    Google Scholar 

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Acknowledgments

This work was supported by funding from the Grains Research and Development Corporation.

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Correspondence to G. C. Spangenberg.

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Communicated by C. Gebhardt.

Electronic supplementary material

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Supplementary material 1 (XLS 126 kb) SSR marker primer pair summary data

Supplementary material 2 (XLS 28 kb) SNP marker amplification and interrogation primer summary data

122_2009_1160_MOESM3_ESM.xls

Supplementary material 3 (XLS 409 kb) Genotypic scoring matrices for the Caiman3 × Westar10, Camberra4 × Westar10, AVSapphire5 × Westar10 and Rainbow4 × AVSapphire5 mapping populations, incorporating information on informative, high quality scaffold reference markers used in QTL map analyses

122_2009_1160_MOESM4_ESM.xls

Supplementary material 4 (XLS 361 kb) Genotypic scoring matrices for the Caiman3 × Westar10, Camberra4 × Westar10, AVSapphire5 × Westar10 and Rainbow4 × AVSapphire5 mapping populations, incorporating information on informative, high quality scaffold reference markers used in QTL map analyses

122_2009_1160_MOESM5_ESM.xls

Supplementary material 5 (XLS 579 kb) Genotypic scoring matrices for the Caiman3 × Westar10, Camberra4 × Westar10, AVSapphire5 × Westar10 and Rainbow4 × AVSapphire5 mapping populations, incorporating information on informative, high quality scaffold reference markers used in QTL map analyses

122_2009_1160_MOESM6_ESM.xls

Supplementary material 6 (XLS 250 kb) Genotypic scoring matrices for the Caiman3 × Westar10, Camberra4 × Westar10, AVSapphire5 × Westar10 and Rainbow4 × AVSapphire5 mapping populations, incorporating information on informative, high quality scaffold reference markers used in QTL map analyses

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Supplementary material 7 (PPT 356 kb) Schematic depicting genetic map structure for the Caiman3 × Westar10 mapping population

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Supplementary material 8 (PPT 381 kb) Schematic depicting genetic map structure for the Camberra4 × Westar10 mapping population

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Supplementary material 9 (PPT 303 kb) Schematic depicting genetic map structure for the AVSapphire5 × Westar10 mapping population

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Supplementary material 10 (PPT 208 kb) Schematic depicting genetic map structure for the Rainbow4 × AVSapphire5 mapping population

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Supplementary material 11 (DOC 35 kb) Summary information on genetic map locations and flanking markers in the T × N population, as described in ESM1

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Supplementary material 12 (PPT 1197 kb) Frequency histograms for the phenotypic data generated from trials performed at the Dahlen and Lake Bolac blackleg infection nurseries. Common scales for percentage survival are used for all populations apart from Sapphire5 × Westar10, because of higher variation for recorded data

122_2009_1160_MOESM13_ESM.txt

Supplementary material 13 (TXT 12117 kb) All Brassica EST DNA sequences analysed for SSR and SNP discovery in this study, in a single concatenated FASTA format text file. Heading line includes details of source material and species of origin and cDNA synthesis method used

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Kaur, S., Cogan, N.O.I., Ye, G. et al. Genetic map construction and QTL mapping of resistance to blackleg (Leptosphaeria maculans) disease in Australian canola (Brassica napus L.) cultivars. Theor Appl Genet 120, 71–83 (2009). https://doi.org/10.1007/s00122-009-1160-9

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