Fractionation, stability, and isolate-specificity of QTL for resistance to phytophthora infestans in cultivated tomato (Solanum lycopersicum)

G3: Genes, Genomes, Genetics

Volumn 2, Issue 10, 2012, Pages 1145-1159

  Johnson, Emily B ^a   Erron Haggard, J ^a   St Clair, Dina A ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYSIS OF VARIANCE; ARTICLE; CHROMOSOME MAP; GENETIC LINKAGE; GENETICS; IMMUNOLOGY; PARASITOLOGY; PHYTOPHTHORA INFESTANS; PLANT CHROMOSOME; PLANT DISEASE; QUANTITATIVE TRAIT LOCUS; TOMATO;

ANALYSIS OF VARIANCE; CHROMOSOMES, PLANT; GENETIC LINKAGE; LYCOPERSICON ESCULENTUM; PHYSICAL CHROMOSOME MAPPING; PHYTOPHTHORA INFESTANS; PLANT DISEASES; QUANTITATIVE TRAIT LOCI;

EID: 84883147613     PISSN: None     EISSN: 21601836     Source Type: Journal    
DOI: 10.1534/g3.112.003459     Document Type: Article

References (93)

1. Agrama, H. A., and J. W. Scott, 2006 Quantitative trait loci for Tomato Yellow Leaf Curl Virus and Tomato Mottle Virus resistance in tomato. J. Am. Soc. Hortic. Sci. 131: 267-272.
2. Anbinder, I., M. Reuveni, R. Azari, I. Paran, S. Nahon et al., 2009 Molecular dissection of Tomato leaf curl virus resistance in tomato line TY172 derived from Solanum peruvianum. Theor. Appl. Genet. 119: 519-530.
3. Anderson, J. A., R. W. Stack, S. Liu, B. L. Waldron, A. D. Fjeld et al., 2001 DNA markers for Fusarium head blight resistance QTLs in two wheat populations. Theor. Appl. Genet. 102: 1164-1168.
4. AVRDC, 2008 AVRDC Report 2005. AVRDC-The World Vegetable Center, Shanhua, Taiwan.
5. Bai, Y., C.-C. Huang, R. van der Hulst, F. Meijer-Dekens, G. Bonnema et al., 2003 QTLs for tomato powdery mildew resistance (Oidium lycopersici) in Lycopersicon parviflorum G1.1601 co-localize with two qualitative powdery mildew resistance genes. Mol. Plant Microbe Interact. 16: 169-176.
6. Bernacchi, D., T. Beck-Bunn, Y. Eshed, J. Lopez, V. Petiard et al., 1998 Advanced backcross QTL analysis of tomato. I. Identification of QTL for traits of agronomic importance from Lycopersicon hirsutum. Theor. Appl. Genet. 97: 381-397.
7. Bernardo, R., 2008 Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci. 48: 1649-1664.
8. Black, L. L., T. C. Wang, P. M. Hanson, and J. T. Chen, 1996 Late blight resistance in four wild tomato accessions: effectiveness in diverse locations and inheritance of resistance. Phytopathology 86: S24.
9. Blair, M. W., A. J. Garris, A. S. Iyer, B. Chapman, S. Kresovich et al., 2003 High resoluation genetic mapping and candidate gene identification at the xa5 locus for bacterial blight resistance in rice (Oryza sativa L.). Theor. Appl. Genet. 107: 62-73.
10. Bombarely, A., N. Menda, I. Y. Tecle, R. M. Buels, S. Strickler et al., 2011 The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 39: D1149-D1155.
11. Bradshaw, J. E., B. Pande, G. J. Bryan, C. A. Hackett, K. McLean et al., 2004 Interval mapping of quantitative trait loci for resistance to late blight [Phytophthora infestans (Mont.) de Bary], height and maturity in a tetraploid population of potato (Solanum tuberosum subsp. tuberosum). Genetics 168: 938-995.
12. Bradshaw, J. E., C. A. Hackett, R. Lowe, K. McLean, H. E. Stewart et al., 2006 Detection of a quantitative trait locus for both foliage and tuber resistance to late blight [Phytophthora infestans (Mont.) de Bary] on chromosome 4 of a dihaploid potato clone (Solanum tuberosum ssp. tuberosum). Theor. Appl. Genet. 113: 943-951.
13. Brigneti, G., J. Garcia-Mas, and D. C. Baulcombe, 1997 Molecular mapping of the potato virus Y resistance gene Rysto in potato. Theor. Appl. Genet. 94: 198-203.
14. Brouwer, D. J., and D. A. St.Clair, 2004 Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs. Theor. Appl. Genet. 108: 628-638.
15. Brouwer, D. J., E. S. Jones, and D. A. St.Clair, 2004 QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato. Genome 47: 475-492.
16. Brown, C. R., C.-P. Yang, H. Mojtahedi, G. S. Santo, and R. Masuelli, 1996 RFLP analysis of resistance to Columbia root-knot nematode derived from Solanum bulbocastanum in a BC2 population. Theor. Appl. Genet. 92: 572-576.
17. Castro, A. J., X. Chen, A. Corey, T. Filichkina, P. M. Hayes et al., 2003 Pyramiding and validation of quantitative trait loci (QTL) alleles determining resistance to barley stripe rust: effects on adult plant resistance. Crop Sci. 43: 2234-2239.
18. Caten, C. E., and J. L. Jinks, 1968 Spontaneous variability of single isolates of Phytophthora infestans. I. Cultural variation. Can. J. Bot. 46: 329-348.
19. Charcosset, A., M. Causse, L. Moreau, and A. Gallais, 1994 Investigation into the effect of genetic background on QTL expression using three recombinant inbred lines (RIL) populations, pp. 75-84 in Biometrics in Plant Breeding: Applications of Molecular Markers, edited by J. van Ooijen, and J. Jansen. CRPO-DLO, Wageningen, The Netherlands.
20. Chen, H., N. Qian, W. Guo, S. Qingping, B. Li et al., 2010 Using three selected overlapping RILs to fine-map the yield component QTL on Chro. D8 in Upland cotton. Euphytica 176: 321-329.
21. Chen, K.-Y., and S. D. Tanksley, 2004 High-resolution mapping and functional analysis of se2.1: a major stigma exsertion quantitative trait locus associated with the evolution from allogamy to autogamy in the genus Lycopersicon. Genetics 168: 1563-1573.
22. Clements, M. J., J. W. Dudley, and D. G. White, 2000 Quantitative trait loci associated with resistance to gray leaf spot of corn. Phytopathology 90: 1018-1025.
23. Collard, B. C. Y., and D. J. Mackill, 2008 Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 363: 557-572.
24. Collard, B. C. Y., M. Z. Z. Jahufer, J. B. Brouwer, and E. C. K. Pang, 2005 An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142: 169-196.
25. Danan, S., J.-B. Veyrieras, and V. Lefebvre, 2011 Construction of a potato consensus map and QTL mata-analysis offer new insights into the genetic architecture of late blight resistance and plant maturity traits. BMC Plant Biol. 11: 16.
26. Davis, J., D. Yu, W. Evans, T. Gokirmak, R. T. Chetelat et al., 2009 Mapping of loci from Solanum lycopersicoides conferring resistance or susceptibility to Botrytis cinerea in tomato. Theor. Appl. Genet. 119: 305-314.
27. Ender, M., K. Terpstra, and J. D. Kelly, 2008 Marker-assisted selection for white mold resistance in common bean. Mol. Breed. 21: 149-157.
28. Foolad, M. R., L. P. Zhang, A. A. Khan, D. Nino-Liu, and G. Y. Lin, 2002 Identification of QTLs for early blight (Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum · L. hirsutum cross. Theor. Appl. Genet. 104: 945-958.
29. Foolad, M. R., H. L. Merk, and H. Ashrafi, 2008 Genetics, genomics, and breeding of late blight and early blight resistance in tomato. Crit. Rev. Plant Sci. 27: 75-107.
30. Frary, A., E. Graham, J. Jacobs, R. T. Chetelat, and S. D. Tanksley, 1998 Identification of QTL for late blight resistance from L. pimpinellifolium L3708. Report of the Tomato Genetics Cooperative 48: 19-21.
31. Frary, A., T. M. Fulton, D. Zamir, and S. D. Tanksley, 2004 Advanced backcross QTL analysis of a Lycopersicon esculentum · L. pennellii cross and identification of possible orthologs in the Solanaceae. Theor. Appl. Genet. 108: 485-496.
32. Fry, W., 2008 Phytophthora infestans: the plant (and R gene) destroyer. Mol. Plant Pathol. 9: 385-402.
33. Fry, W. E., and S. B. Goodwin, 1997 Resurgence of the Irish Potato Famine fungus. Bioscience 47: 363-371.
34. Fulton, T. M., J. Chunwongse, and S. D. Tanksley, 1995 Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol. Biol. Rep. 13: 207-209.
35. Fulton, T. M., T. Beck-Bunn, D. Emmatty, Y. Eshed, J. Lopez et al., 1997 QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor. Appl. Genet. 95: 881-894.
36. Fulton, T. M., R. van der Hoeven, N. T. Eannetta, and S. D. Tanksley, 2002 Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14: 1457- 1467.
37. Gao, W., J. A. Clancy, F. Han, B. L. Jones, A. Budde et al., 2004 Fine mapping of a malting-quality QTL complex near the chromosome 4H S telomere in barley. Theor. Appl. Genet. 109: 750-760.
38. Gebhardt, C., and J. P. T. Valkonen, 2001 Organization of genes controlling disease resistance in the potato genome. Annu. Rev. Phytopathol. 39: 79-102.
39. Graham, G. I., D. W. Wolff, and C. W. Stuber, 1997 Characterization of a yield quantitative trait locus in maize by fine mapping. Crop Sci. 37: 1601.
40. Grube, R. C., E. R. Radwanski, and M. Jahn, 2000 Comparative genetics of disease resistance within the Solanaceae. Genetics 155: 873-887.
41. Hämäläinen, J. H., K. N. Watanabe, J. P. T. Valkonen, A. Arihara, R. L. Plaisted et al., 1997 Mapping and marker-assisted selection for a gene for extreme resistance to potato virus Y. Theor. Appl. Genet. 94: 192-197.
42. Hamon, C., A. Baranger, C. J. Coyne, R. J. McGee, I. Le Goff et al., 2011 New consistent QTL in pea associated with partial resistance to Aphanomyces euteiches in multiple French and American environments. Theor. Appl. Genet. 123: 261-281. International Potato Center, 2001 Laboratory Manual for P. Infestans Work at CIP-Quito. International Potato Center (CIP), Quito, Peru.
43. Jacobs, J. M. E., H. J. van Eck, K. Horsman, P. F. P. Arens, B. Verkerk-Bakker et al., 1996 Mapping of resistance to the potato cyst nematode Globodera rostochiensis from the wild potato species Solanum vernei. Mol. Breed. 2: 51-60.
44. Judelson, H. S., and F. A. Blanco, 2005 The spores of Phytophthora: weapons of the plant destoyer. Nat. Rev. Microbiol. 3: 47-58.
45. Kirk,W.W., K. J. Felcher, D. S. Douches, B. A. Niemira, and R. Hammerschmidt, 2001 Susceptibility of potato (Solanum tuberosum L.) foliage and tubers to the US8 genotype of Phytophthora infestans. Am. J. Potato Res. 78: 319-322.
46. Lecomte, L., V. Saliba-Colombani, A. Gautier, M. C. Gomez-Jimenez, P. Duffe et al., 2004 Fine mapping of QTLs of chromosome 2 affecting the fruit architecture and composition of tomato. Mol. Breed. 13: 1-14.
47. Livingstone, K. D., V. K. Lackney, J. R. Blauth, R. van Wijk, and M. K. Jahn, 1999 Genome mapping in the Capsicum and the evolution of genome structure in the Solanaceae. Genetics 152: 1183-1202.
48. Lobo, M., and R. Navarro, 1987 Late blight horizontal resistance in L. esculentum · L. hirsutum hybrids. Rep. Tomato Genet. Coop. 37: 53.
49. Mackay, T. F. C., E. A. Stone, and J. F. Ayroles, 2009 The genetics of quantitative traits: challenges and prospects. Nature 10: 565-577.
50. Marcel, T. C., R. K. Varshney, M. Barbieri, H. Jafary, M. J. D. de Kock et al., 2007 A high-density consensus map of barley to compare the distribution of QTLs for partial resistance to Puccinia hordei and of defense gene homologs. Theor. Appl. Genet. 114: 487-500.
51. Mayton, H., H. Griffiths, I. Simko, S. Cheng, J. Lorenzen et al., 2010 Foliar and tuber late blight resistance in a Solanum tuberosum breeding population. Plant Breed. 129: 197-201.
52. Mazourek, M., E. T. Cirulli, S. M. Collier, L. G. Landry, B.-C. Kang et al., 2009 The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of disease resistance in the Solanaceae. Genetics 182: 1351-1364.
53. Miklas, P. N., 2007 Marker-assisted backcrossing QTL for partial resistance to Sclerotinia white mold in dry bean. Crop Sci. 47: 935-942.
54. Miklas, P. N., J. D. Kelly, S. E. Beebe, and M. W. Blair, 2006 Common bean breeding for resistance against biotic and abiotic stresses: from classical to MAS breeding. Euphytica 147: 105-131.
55. Momotaz, A., J. W. Scott, and D. J. Schuster, 2010 Identification of quantitative trait loci conferring resistance to Bemisia tabaci in an F2 population of Solanum lycopersicum · Solanum habrochaites accession LA1777. J. Am. Soc. Hortic. Sci. 135: 134-142.
56. Mutlu, N., P. Miklas, J. Reiser, and D. Coyne, 2005 Backcross breeding for improved resistance to common bacterial blight in pinto bean (Phaseolus vulgaris L.). Plant Breed. 124: 282-287.
57. National Agriculture Statistics Service, 2011 Vegetables 2010 Summary. US Department of Agriculture, National Agriculture Statistics Service. Available at: http://usda01.library.cornell.edu/usda/nass/VegeSumm// 2010s/2011/VegeSumm-01-27-2011_new_format.pdf.
58. Oberhagemann, P., C. Chatot-Balandras, R. Schafer-Pregl, D. Wegener, C. Palomino et al., 1999 A genetic analysis of quantitative resistance to late blight in potato: towards marker-assisted selection. Mol. Breed. 5: 399-415.
59. Park, T.-H., V. G. A. A. Vleeshouwers, J.-B. Kim, R. C. B. Hutten, and R. G. F. Visser, 2005 Dissection of foliage and tuber late blight resistance in mapping populations of potato. Euphytica 143: 75-83.
60. Pilet, M. L., G. Duplan, M. Archipiano, P. Barret, C. Baron et al., 2001 Stability of QTL for field resistance to blackleg across two genetic backgrounds in oilseed rape. Crop Sci. 41: 197-205.
61. Qi, X., F. Fufa, D. Sijtsma, R. E. Niks, P. Lindhout et al., 2000 The evidence for abundance of QTLs for partial resistance to Puccinia hordei on the barley genome. Mol. Breed. 6: 1-9.
62. Quirin, E. A., E. A. Ogundiwin, J. P. Prince, M. Mazourek, M. O. Briggs et al., 2005 Development of sequence characterized amplified region (SCAR) primers for the detection of Phyto.5.2, a major QTL for resistance to Phytophthora capsici Leon. in pepper. Theor. Appl. Genet. 110: 605-612.
63. Rauscher, G., I. Simko, H. Mayton, M. Bonierbale, C. D. Smart et al., 2010 Quantitative resistance to late blight from Solanum berthaultii cosegregates with RPi-ber: insights in stability through isolates and environment. Theor. Appl. Genet. 121: 1553-1567.
64. Rensink, W. A., Y. Lee, J. Liu, S. Iobst, S. Ouyang et al., 2005 Comparative analyses of six solanaceous transcriptomes reveal a high degree of sequence conservation and species-specific transcripts. BMC Genomics 6: 124.
65. Richardson, K. L., M. I. Vales, J. G. Kling, C. C. Mundt, and P. M. Hayes, 2006 Pyramiding and dissecting disease resistance QTL to barley stripe rust. Theor. Appl. Genet. 113: 485-495.
66. Robbins, M. D., M. A. T. Masud, D. R. Panthee, R. G. Gardner, D. M. Francis et al., 2010 Marker-assisted selection for coupling phase resistance to Tomato spotted wilt virus and Phytophthora infestans (late blight) in tomato. HortScience 45: 1424-1428.
67. Saxton, A. M., 1998 A macro for converting mean separation output to letter groupings in PROC MIXED, pp. 1243-1246 in Proceedings of the Twenty-Third SAS Users Group International. SAS Institute, Cary, NC.
68. Shaner, G., and R. E. Finney, 1977 The effect of nitrogen fertilizer on the expression of slow-mildewing resistance in Knox wheat. Phytopathology 67: 1051-1056.
69. Simko, I., S. Costanzo, V. Ramanjulu, B. J. Christ, and K. G. Haynes, 2006 Mapping polygenes for tuber resistance to late blight in a diploid Solanum phureja · S. stenotomum hybrid population. Plant Breed. 125: 385-389.
70. Sliwka, J., H. Jakuczun, R. Lebecka, W. Marczewski, C. Gebhardt et al., 2007 Tagging QTLs for late blight resistance and plant maturity from diploid wild relatives in a cultivated potato (Solanum tuberosum) background. Theor. Appl. Genet. 115: 101-112.
71. Smart, C. D., S. D. Tanksley, H. Mayton, and W. E. Fry, 2007 Resistance to Phytophthora infestans in Lycopersicon pennellii. Plant Dis. 91: 1045- 1049.
72. St.Clair, D. A., 2010 Quantitative disease resistance and quantitative resistance loci in breeding. Annu. Rev. Phytopathol. 48: 247-268.
73. Stevens, R., M. Buret, P. Duffe, C. Garchery, P. Baldet et al., 2007 Candidate genes and quantitative trait loci affecting ascorbic acid content in three tomato populations. Plant Physiol. 143: 1943-1953.
74. Studer, A. J., and J. F. Doebley, 2011 Do large effect QTL fractionate? A case study at the maize domestication QTL teosinte branched1. Genetics 188: 673-681.
75. Tan, M. Y. A., T.-H. Park, R. Alles, R. C. B. Hutten, R. G. F. Visser et al., 2009 GpaXIltar originating from Solanum tarijense is a major resistance locus to Globodera pallida and is localised on chromosome 11 of potato. Theor. Appl. Genet. 119: 1477-1487.
76. Thabius, A., A. Palloix, S. Pflieger, A.-M. Daubeze, C. Caranta et al., 2003 Comparative mapping of Phytophthora resistance loci in pepper germplasm: evidence for conserved resistance loci across Solanaceae and for a large genetic diversity. Theor. Appl. Genet. 106: 1473-1485.
77. Thabius, A., A. Palloix, B. Servin, A. M. Daubeze, P. Signoret et al., 2004 Marker-assisted introgression of 4 Phytophthora capsici resistance QTL alleles into a bell pepper line: validation of additive and epistatic effects. Mol. Breed. 14: 9-20.
78. Toojinda, T., E. Baird, A. Booth, L. Broers, P. Hayes et al., 1998 Introgression of quantitative trait loci (QTLs) determining stripe rust resistance in barley: an example of marker-assisted line development. Theor. Appl. Genet. 96: 123-131.
79. Truco, M. J., L. B. Randall, A. J. Bloom, and D. A. St.Clair, 2000 Detection of QTLs associated with shoot wilting and root ammonium uptake under chilling temperatures in an interspecific backcross population from Lycopersicon esculentum · L. hirsutum. Theor. Appl. Genet. 101: 1082- 1092.
80. van Ooijen, J. W., and R. E. Voorrips, 2001 JoinMap 3.0, Software for the Calculation of Genetic Linkage Maps. Plant Research International, Wageningen, The Netherlands.
81. Villamon, F. G., D. M. Spooner, M. Orrillo, E. Mihovilovich, W. Perez et al., 2005 Late blight resistance linkages in a novel cross of the wild potato species Solanum paucissectum (series Piurana). Theor. Appl. Genet. 111: 1201-1214.
82. Voorrips, R. E., 2002 MapChart: software for the graphical presentation of linkage maps and QTLs. J. Hered. 93: 77-78.
83. Wang, S., C. J. Basten, and Z.-B. Zeng, 2011 Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC. Available at: http://statgen.ncsu.edu/qtlcart/WQTLCart.htm.
84. Wang, Y., A. Diehl, F. Wu, J. Vrebalov, J. Giovannoni et al., 2008 Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics 180: 391-408.
85. Wastie, R. L., 1991 Breeding for resistance, pp. 193-224 in Advances in Plant Pathology: Phytophthora infestans, the Cause of Late Blight in Potato, edited by D. Ingram, and P. Williams. Academic Press, London.
86. Wilde, F., C. C. Schon, V. Korzun, E. Ebmeyer, M. Schmolke et al., 2008 Marker-based introduction of three quantitative-trait loci conferring resistance to Fusarium head blight into an independent elite winter wheat breeding population. Theor. Appl. Genet. 117: 29-35.
87. Xu, Y., and J. H. Crouch, 2008 Marker-assisted selection in plant breeding: from publications to practice. Crop Sci. 48: 391-407.
88. Yang, W., E. J. Sacks, M. L. Lewis Ivey, S. A. Miller, and D. M. Francis, 2005 Resistance in Lycopersicon esculentum intraspecific crosses to race T1 strains of Xanthomonas campestris pv. vesicatoria causing bacterial spot of tomato. Phytopathology 95: 519-527.
89. Yang, Z. P., J. Gilbert, D. J. Somers, G. Fedak, J. D. Procunier et al., 2003 Marker assisted selection of Fusarium head blight resistance genes in two doubled haploid populations of wheat. Mol. Breed. 12: 309-317.
90. Yu, Z. H., J. F. Wang, R. E. Stall, and C. E. Vallejos, 1995 Genomic localization of tomato genes that control a hypersensitive reaction to Xanthamonas campestris pv. vesicatoria (Doidge) Dye. Genetics 141: 675-682.
91. Zhang, L. P., G. Y. Lin, D. Niño-Liu, and M. R. Foolad, 2003 Mapping QTLs conferring early blight (Alternaria solani) resistance in a Lycopersicon esculentum · L. hirsutum cross and selective genotyping. Mol. Breed. 12: 3-19.
92. Zhou, W.-C., F. L. Kolb, G.-H. Bai, L. L. Domier, L. K. Boze et al., 2003 Validation of a major QTL for scab resistance with SSR markers and use of marker-assisted selection in wheat. Plant Breed. 122: 40-46.
93. Zimnoch-Guzowska, E., W. Marczewski, R. Lebecka, B. Flis, R. Schäfer-Pregl et al., 2000 QTL analysis of new sources of resistance to Erwinia carotovora ssp. atroseptica in potato done by AFLP, RFLP, and resistancegene- like markers. Crop Sci. 40: 1156-1167.