Connected populations for detecting quantitative resistance factors to phoma stem canker in oilseed rape (Brassica napus L.)

Molecular Breeding

Volumn 35, Issue 8, 2015, Pages

  Jestin, C ^a,c   Bardol, N ^a   Lode M ^a   Duffe P ^a   Domin, C ^a   Vallee P ^a   Mangin, B ^b   Manzanares Dauleux, M J ^a   Delourme, R ^a  

^a Universite Rennes 1   (France)

^b CEMAGREF   (France)

^c Terres Inovia   (France)

Author keywords

Brassica napus; Leptosphaeria maculans; Multi cross design; Oilseed rape; QTL; Quantitative resistance

Indexed keywords

OILSEEDS; PLANTS (BOTANY);

BRASSICA NAPUS; BRASSICA NAPUS L; GENETIC BACKGROUNDS; LEPTOSPHAERIA MACULANS; MULTI-CROSS DESIGN; OIL SEED RAPE; QTL; QUANTITATIVE RESISTANCE; RESISTANCE FACTORS; STEM CANKER;

DISEASE CONTROL;

BRASSICA NAPUS; FUNGI; LEPTOSPHAERIA MACULANS; PHOMA;

EID: 84938386199     PISSN: 13803743     EISSN: 15729788     Source Type: Journal    
DOI: 10.1007/s11032-015-0356-8     Document Type: Article

References (74)

1. Arcade A, Labourdette A, Falque M, Mangin B, Chardon F, Charcosset A, Joets J (2004) BioMercator: integrating genetic maps and QTL towards discovery of candidate genes. Bioinformatics 20:2324–2326
2. Aubertot JN, Schott JJ, Penaud A, Brun H, Dore T (2004) Methods for sampling and assessment in relation to the spatial pattern of phoma stem canker (Leptosphaeria maculans) in oilseed rape. Eur J Plant Pathol 110:183–192
3. Balesdent MH, Louvard K, Pinochet X, Rouxel T (2006) A large-scale survey of races of Leptosphaeria maculans occurring on oilseed rape in France. Eur J Plant Pathol 114:53–65
4. Balesdent MH, Fudal I, Ollivier B, Bally P, Grandaubert J, Eber F, Chèvre AM, Leflon M, Rouxel T (2013) The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. New Phytol 198:887–898
5. Barchi L, Lefebvre V, Sage-Palloix AM, Lanteri S, Palloix A (2009) QTL analysis of plant development and fruit traits in pepper and performance of selective phenotyping. Theor Appl Genet 118:1157–1171
6. Billotte N, Jourjon MF, Marseillac N, Berger A, Flori A, Asmady H, Adon B, Singh R, Nouy B, Potier F, Cheah SC, Rohde W, Ritter E, Courtois B, Charrier A, Mangin B (2010) QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.). Theor Appl Genet 120:1673–1687
7. Blanc G, Charcosset A, Mangin B, Gallais A, Moreau L (2006) Connected populations for detecting quantitative trait loci and testing for epistasis: an application in maize. Theor Appl Genet 113:206–224
8. Blanc G, Charcosset A, Veyrieras JB, Gallais A, Moreau L (2008) Marker-assisted selection efficiency in multiple connected populations: a simulation study based on the results of a QTL detection experiment in maize. Euphytica 161:71–84
9. Boyd LA (2006) Can the durability of resistance be predicted? J Sci Food Agric 86:2523–2526
10. Brun H, Levivier S, Somda I, Ruer D, Renard M, Chevre AM (2000) A field method for evaluating the potential durability of new resistance sources: application to the Leptosphaeria maculansBrassica napus pathosystem. Phytopathol 90:961–966
11. Brun H, Chèvre A-M, Fitt BDL, Powers S, Besnard A-L, Ermel M, Huteau V, Marquer B, Eber F, Renard M, Andrivon D (2010) Quantitative resistance increases the durability of qualitative resistance to Leptosphaeria maculans in Brassica napus. New Phytol 185:285–299
12. Chalhoub B, Denoeud F, Liu S, Parkin IAP, Tang HB, Wang XX, Chiquet J, Belcram H, Tong C, Samans B, Corréa M, Da Silva C, Just J, Falentin C, Koh CS, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger PP, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N, Le Paslier MC, Fan G, Renault V, Bayer PE, Golicz AA, Manoli S, Lee TH, Thi VHC, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom CHD, Wang XX, Canaguier A, Chauveau A, Bérard A, Deniot G, Guan M, Liu Z, Sun F, Lim YP, Lyons E, Town CD, Bancroft I, Wang XX, Meng J, Ma J, Pires JC, King GJ, Brunel D, Delourme R, Renard M, Aury JM, Adams KL, Batley J, Snowdon RJ, Tost J, Edwards D, Zhou Y, Hua W, Sharpe AG, Paterson AH, Guan C, Wincker P (2014) Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science 354:950–953
13. Charcosset A, Mangin B, Moreau L, Combes L, Jourjon MF, Gallais A (2001) Heterosis in maize investigated using connected RIL populations. Quant Genet Breed Methods Way Ahead 96:89–98
14. Cheng X, Xu J, Xia S, Gu J, Yang Y, Fu J, Qian X, Zhang S, Wu J, Liu K (2009) Development and genetic mapping of microsatellite markers from genome survey sequences in Brassica napus. Theor Appl Genet 118:1121–1131
15. Christiansen MJ, Feenstra B, Skovgaard IM, Andersen SB (2006) Genetic analysis of resistance to yellow rust in hexaploid wheat using a mixture model for multiple crosses. Theor Appl Genet 112:581–591
16. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971
17. Cuesta-Marcos A, Casas AM, Yahiaoui S, Gracia MP, Lasa JM, Igartua E (2008) Joint analysis for heading date QTL in small interconnected barley populations. Mol Breed 21:383–399
18. Danan S (2009) Diversité structurale des locus de résistance à Phytophthora infestans chez la pomme de terre et synténie chez les Solanacées. Thesis. INRA-Génétique et amélioration des plantes. Ecole doctorale Systèmes intégrés en Biologie, Agronomie, Géosciences, Hydrosciences, Environnement, Montpellier, p 230
19. Delourme R, Pilet-Nayel ML, Archipiano M, Horvais R, Tanguy X, Rouxel T, Brun H, Renard A, Balesdent AH (2004) A cluster of major specific resistance genes to Leptosphaeria maculans in Brassica napus. Phytopathology 94:578–583
20. Delourme R, Chèvre AM, Brun H, Rouxel T, Balesdent MH, Dias JS, Salisbury P, Renard M, Rimmer SR (2006a) Major gene and polygenic resistance to Leptosphaeria maculans in oilseed rape (Brassica napus). Eur J Plant Pathol 114:41–52
21. 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 (2006b) Genetic control of oil content in oilseed rape (Brassica napus L.). Theor Appl Genet 113:1331–1345
22. Delourme R, Piel N, Horvais R, Pouilly N, Domin C, Vallee P, Falentin C, Manzanares-Dauleux MJ, 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
23. Delourme R, Bousset L, Ermel M, Duffé P, Besnard AL, Marquer B, Fudal Linglin J, Chadoeuf J, Brun H (2014) Quantitative resistance affects the speed of frequency increase but not the diversity of the virulence alleles overcoming a major resistance gene to Leptosphaeria maculans in oilseed rape. Infect Genet Evol 27:490–499
24. Doyle J, Doyle J (1990) Isolation of plant DNA from fresh tissue. Focus 12:13–15
25. Evans N, Baierl A, Semenov MA, Gladders P, Fitt BDL (2008) Range and severity of a plant disease increased by global warming. J R Soc Interface 5:525–531
26. 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
27. Fitt BDL, Hu BC, Li ZQ, Liu SY, Lange RM, Kharbanda PD, Butterworth MH, White RP (2008) Strategies to prevent spread of Leptosphaeria maculans (phoma stem canker) onto oilseed rape crops in China; costs and benefits. Plant Pathol 57:652–664
28. Fopa Fomeju B, Falentin C, Lassalle G, Manzanares-Dauleux MJ, Delourme R (2014) Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker. BMC Genomic 15:498
29. Haldane JBS (1919) The combination of linkage values, and the calculation of distances between the loci of linked factors. J Genet 8:299–309
30. Hayward A, McLanders J, Campbell E, Edwards D, Batley J (2012) Genomic advances will herald new insights into the Brassica: Leptosphaeria maculans pathosystem. Plant Biol 14:1–10
31. Iniguez-Luy F, Voort A, Osborn T (2008) Development of a set of public SSR markers derived from genomic sequence of a rapid cycling Brassica oleracea L. genotype. Theor Appl Genet 117:977–985
32. Jestin C, Lodé M, Domin C, Falentin C, Horvais R, Coedel S, Manzanares-Dauleux MJ, Delourme R (2011) Association mapping of quantitative resistance for Leptosphaeria maculans in oilseed rape (Brassica napus L.). Mol Breed 27:190–201
33. Jestin C, Vallée P, Domin C, Manzanares-Dauleux MJ, Delourme R (2012) Assessment of a new strategy for selective phenotyping applied to complex traits in Brassica napus. Open J Genet 2:190–201
34. Jourjon M-F, Jasson S, Marcel J, Ngom B, Mangin B (2005) MCQTL: multi-allelic QTL mapping in multi-cross design. Bioinformatics 21:128–130
35. Kaur S, Cogan N, Ye G, Baillie R, Hand M, Ling A, McGearey A, Kaur J, Hopkins C, Todorovic M, Mountford H, Edwards D, Batley J, Burton W, Salisbury P, Gororo N, Marcroft S, Kearney G, Smith K, Forster J, Spangenberg G (2009) 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
36. Kim H, Choi S, Bae J, Hong C, Lee S, Hossain MJ, Van Dan N, Jin M, Park B, Bang J, Bancroft I, Lim Y (2009) Sequenced BAC anchored reference genetic map that reconciles the ten individual chromosomes of Brassica rapa. BMC Genom 10:15
37. Lander ES, Botstein D (1989) Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121:185–199
38. Larièpe A, Mangin B, Jasson S, Combes V, Dumas F, Jamin P, Lariagon C, Jolivot D, Madur D, Fiévet J, Gallais A, Dubreuil P, Charcosset A, Moreau L (2012) The genetic basis of heterosis: multiparental quantitative trait loci mapping reveals contrasted levels of apparent overdominance among traits of agronomical interest in maize (Zea mays L.). Genetics 190:795–811
39. Lee S, Rouf Mian MA, Sneller CH, Wang H, Dorrance AE, McHale LK (2014) Joint linkage QTL analyses for partial resistance to Phytophthora soja in soybean using six nested inbred populations with heterogeneous conditions. Theor Appl Genet 127:429–444
40. Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor Appl Genet 103:455–461
41. Li H, Sivasithamparam K, Barbetti MJ (2003) Breakdown of a Brassica rapa subsp sylvestris single dominant blackleg resistance gene in B. napus rapeseed by Leptosphaeria maculans field isolates in Australia. Plant Dis 87:752
42. Lincoln S, Daly M, Lander E (1992) Constructing genetic linkage maps with Mapmaker/Exp 3.0: a tutorial and reference manual. Whitehead Institute technical report 3rd edn
43. 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
44. Lynch M, Walsh B (1998) Mapping QTLs: inbred line crosses—precision of ML estimates of QTL position. In: Associates Sinauer (ed) Genetics and analysis of quantitative traits. Sinauer, Sunderland, pp 448–450
45. Negeri AT, Coles ND, Holland JB, Balint-Kurti PJ (2011) Mapping QTL controlling southern leaf blight resistance by joint analysis of three related recombinant inbred line populations. Crop Sci 51:1571–1579
46. Palloix A, Ayme V, Moury B (2009) Durability of plant major resistance genes to pathogens depends on the genetic background, experimental evidence and consequences for breeding strategies. New Phytol 183:190–199
47. Paulo MJ, Boer M, Huang XQ, Koornneef M, van Eeuwijk F (2008) A mixed model QTL analysis for a complex cross population consisting of a half diallel of two-way hybrids in Arabidopsis thaliana: analysis of simulated data. Euphytica 161:107–114
48. Pauly L, Flajoulot S, Garon J, Julier B, Béguier V, Barre P (2012) Detection of favorable alleles for plant height and crown rust tolerance in three connected populations of perennial ryegrass (Lolium perenne L.). Theor Appl Genet 124:1139–1153
49. Pierre JB, Huguet T, Barre P, Huyghe C, Julier B (2008) Detection of QTLs for flowering date in three mapping populations of the model legume species Medicago truncatula. Theor Appl Genet 117:609–620
50. 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
51. Pilet ML, Duplan G, Archipiano M, Barret P, Baron C, Horvais R, Tanguy X, Lucas M, 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
52. Piquemal J, Cinquin E, Couton F, Rondeau C, Seignoret E, Doucet I, Perret D, Villeger MJ, Vincourt P, Blanchard P (2005) Construction of an oilseed rape (Brassica napus L.) genetic map with SSR markers. Theor Appl Genet 111:1514–1523
53. Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14:21–29
54. Quenouille J, Montarry J, Palloix A, Moury B (2013) Farther, slower, stronger: how the plant genetic background protects a major resistance gene from breakdown. Mol Plant Pathol 14:109–118
55. Radoev M, Becker HC, Ecke W (2008) Genetic analysis of heterosis for yield and yield components in rapeseed (Brassica napus L.) by quantitative trait locus mapping. Genetics 179:1547–1558
56. 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 (2012) 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
57. Rebai A, Goffinet B (1993) Power of tests for QTL detection using replicated progenies derived from a diallel cross. Theor Appl Genet 86:1014–1022
58. Rimmer SR (2006) Resistance genes to Leptosphaeria maculans in Brassica napus. Can J Plant Pathol-Revue Canadienne de Phytopathologie 28:S288–S297
59. Rouxel T, Penaud A, Pinochet X, Brun H, Gout L, Delourme R, Schmit J, Balesdent MH (2003) A 10-year survey of populations of Leptosphaeria maculans in France indicates a rapid adaptation towards the Rlm1 resistance gene of oilseed rape. Eur J Plant Pathol 109:871–881
60. Rowe HC, Hansen BG, Halkier BA, Kliebenstein DJ (2008) Biochemical networks and epistasis shape the Arabidopsis thaliana metabolome. Am Soc Plant Biol 20:1199–1216
61. Roy NN, Fisher HM, Tarr A (1983) Wesbrook—a new prime variety of rapeseed. In: Proceedings fourth Australian rapeseed agronomists and breeders workshop, Lyndoch, 4 pp
62. SAS II (1989) SAS/STAT users guide, version 6.0, 4th edn. SAS institute Inc, Cary
63. Schwegler DD, Liu W, Gowda M, Würschum T, Schulz B, Reif JC (2013) Multiple-line cross quantitative trait locus mapping in sugar beet (Beta vulgaris L.). Theor Appl Genet 31:279–287
64. Steinhoff J, Liu W, Maurer HP, Würschum T, Longin H, Friedrich C, Ranc N, Reif JC (2011) Multiple-line cross quantitative trait locus mapping in European Elite maize. Crop Sci 51:2505–2516
65. Stuber CW, Edwards MD, Wendel JF (1987) Molecular marker-facilitated investigations of quantitative trait loci in maize. 2. Factors influencing yield and its components traits. Crop Sci 27:639–648
66. Sun Z, Wang Z, Tu J, Zhang J, Yu F, McVetty P, Li G (2007) An ultradense genetic recombination map for Brassica napus, consisting of 13551 SRAP markers. Theor Appl Genet 114:1305–1317
67. Suwabe K, Iketani H, Nunome T, Kage T, Hirai M (2002) Isolation and characterization of microsatellites in Brassica rapa L. Theor Appl Genet 104:1092–1098
68. Suwabe K, Morgan C, Bancroft I (2008) Integration of Brassica a genome genetic linkage map between Brassica napus and B. rapa. Genome 51:169–176
69. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066
70. Vanooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811
71. Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Heredity 93:77–78
72. 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
73. Wang JW, Lydiat DJ, Parkin IAP, Falentin C, Delourme R, Carion PWC, King GJ (2011) Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. BMC Genom 12:101
74. West JS, Kharbanda PD, Barbetti MJ, Fitt BDL (2001) Epidemiology and management of Leptosphaeria maculans (phoma stem canker) on oilseed rape in Australia, Canada and Europe. Plant Pathol 50:10–27