Association mapping of leaf rust response in durum wheat

Molecular Breeding

Volumn 26, Issue 2, 2010, Pages 189-228

  Maccaferri, Marco ^a   Sanguineti, Maria C ^a   Mantovani, Paola ^a   Demontis, Andrea ^b   Massi, Andrea ^b   Ammar, Karim ^c   Kolmer, James A ^d   Czembor, Jerzy H ^e   Ezrati, Smadar ^f   Tuberosa, Roberto ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

^b Società Produttori Sementi Bologna SpA   (Italy)

^c INTERNATIONAL MAIZE AND WHEAT IMPROVEMENT CENTER CIMMYT   (Mexico)

^d USDA Agricultural Research Service Cereal Disease Laboratory   (United States)

^e PLANT BREEDING AND ACCLIMATIZATION INSTITUTE NATIONAL RESEARCH INSTITUTE   (Poland)

^f TEL AVIV UNIVERSITY   (Israel)

Author keywords

Association mapping; Durum wheat; Linkage disequilibrium; Molecular marker; Puccinia triticina Eriks; Quantitative trait locus

Indexed keywords

BIOMARKERS; DNA SEQUENCES; GENES; MAPPING; PLANTS (BOTANY);

ASSOCIATION MAPPING; DISTAL REGIONS; DURUM WHEATS; FIELD TRIAL; LEAF RUST; LINKAGE DISEQUILIBRIUM; MOLECULAR MARKER; PUCCINIA TRITICINA; PUCCINIA TRITICINUM ERIKS; QUANTITATIVE TRAIT LOCUS;

POLYMERASE CHAIN REACTION;

PUCCINIA TRITICINA; TRITICOSECALE; TRITICUM AESTIVUM; TRITICUM TURGIDUM SUBSP. DURUM;

EID: 77955050327     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-009-9353-0     Document Type: Article

References (93)

1. Aguilar-Rincon VH, Singh RP, Castillo-Gonzalez F, Huerta-Espino J (2001) Genes of leaf rust resistance in a synthetic hexaploid wheat. Rev Fitotec Mex 24: 161-169.
2. Akhunov E, Nicolet C, Dvorak J (2009) Single nucleotide polymorphism genotyping in polyploidy wheat with the Illumina GoldenGate assay. Theor Appl Genet 119: 507-517.
3. Amaro LAM, Mir SGL, Huerta-Espino J, Mir EV (2007) Genetics of leaf rust resistence (Puccinia triticina E.) in elite durum wheat lines. Rev Fitotec Mex 30: 33-38.
4. Bansal UK, Hayden MJ, Venkata BP, Khanna R, Saini RG, Bariana HS (2008) Genetic mapping of adult plant leaf rust resistance genes Lr48 and Lr49 in common wheat. Theor Appl Genet 117: 307-312.
5. Belaid A (2000) Durum wheat in WANA (West Asia and North Africa): production, trade, and gains from technological change. In: Royo C, Nachit MM, Di Fonzo N, Araus JL (eds) Durum wheat improvement in the Mediterranean region: new challenges, vol 40. Options Méditerranéennes. CIHEAM-IAMZ, Zaragoza, pp 35-39.
6. Beló A, Zheng PZ, Luck S, Shen B, Meyer DJ, Li BL, Tingey S, Rafalski A (2008) Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics 279: 1-10.
7. Bolton MD, Kolmer JA, Garvin DF (2008) Wheat leaf rust caused by Puccinia triticina. Mol Plant Pathol 9: 563-575.
8. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
9. Breseghello F, Sorrells ME (2006a) Association analysis as a strategy for improvement of quantitative traits in plants. Crop Sci 46: 1323-1330.
10. Breseghello F, Sorrells ME (2006b) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
11. Calus MPL, Meuwissen THE, Windig JJ, Knol EF, Schrooten C, Vereijken ALJ, Veerkamp RF (2009) Effects of the number of markers per haplotype and clustering of haplotypes on the accuracy of QTL mapping and prediction of genomic breeding values. Genet Sel Evol 41: 11.
12. Chao SM, Zhang WJ, Dubcovsky J, Sorrells M (2007) Evaluation of genetic diversity and genome-wide linkage disequilibrium among US wheat (Triticum aestivum L.) germplasm representing different market classes. Crop Sci 47: 1018-1030.
13. Cockram J, White J, Leigh FJ, Lea VJ, Chiapparino E, Laurie DA, Mackay IJ, Powell W, O'Sullivan DM (2008) Association mapping of partitioning loci in barley. BMC Genet 9: 16.
14. Crossa J, Burgueno J, Dreisigacker S, Vargas M, Herrera-Foessel SA, Lillemo M, Singh RP, Trethowan R, Warburton M, Franco J, Reynolds M, Crouch JH, Ortiz R (2007) Association analysis of historical bread wheat germplasm using additive genetic covariance of relatives and population structure. Genetics 177: 1889-1913.
15. Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
16. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
17. Flint-Garcia SA, Thuillet AC, Yu JM, Pressoir G, Romero SM, Mitchell SE, Doebley J, Kresovich S, Goodman MM, Buckler ES (2005) Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J 44: 1054-1064.
18. Ganal MW, Röder MS (2007) Microsatellite and SNP markers in wheat breeding. In: Varshney R, Tuberosa R (eds) Genomic assisted crop improvement: vol 2: genomics applications in crops. Springer, Dordrecht, pp 1-24.
19. Gennaro A, Koebner RMD, Ceoloni C (2009) A candidate for Lr19, an exotic gene conditioning leaf rust resistance in wheat. Funct Integr Genomic 9: 325-334.
20. Giunta F, Motzo R, Pruneddu G (2007) Trends since 1900 in the yield potential of Italian-bred durum wheat cultivars. Eur J Agron 27: 12-24.
21. Grapes L, Firat MZ, Dekkers JC, Rothschild MF, Fernando RL (2006) Optimal haplotype structure for linkage disequilibrium-based fine mapping of quantitative trait loci using identity by descent. Genetics 172: 1955-1965.
22. Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
23. Habash DZ, Kehel Z, Nachit M (2009) Genomic approaches for designing durum wheat ready for climate change with a focus on drought. J Exp Bot 60: 2805-2815.
24. Herrera-Foessel SA, Singh RP, Huerta-Espino J, Yuen J, Djurle A (2005) New genes for leaf rust resistance in CIMMYT durum wheats. Plant Dis 89: 809-814.
25. Herrera-Foessel SA, Singh RP, Huerta-Espino J, Crossa J, Yuen J, Djurle A (2006) Effect of leaf rust on grain yield and yield traits of durum wheats with race-specific and slow-rusting resistance to leaf rust. Plant Dis 90: 1065-1072.
26. Herrera-Foessel SA, Singh RP, Huerta-Espino J, Crossa J, Djurle A, Yuen J (2007a) Evaluation of slow rusting resistance components to leaf rust in CIMMYT durum wheats. Euphytica 155: 361-369.
27. Herrera-Foessel SA, Singh RP, Huerta-Espino J, William HM, Rosewarne G, Djurle A, Yuen J (2007b) Identification and mapping of Lr3 and a linked leaf rust resistance gene in durum wheat. Crop Sci 47: 1459-1466.
28. Herrera-Foessel SA, Djurle A, Yuen J, Singh RP, William HM, Garcia V, Huerta-Espino J (2008a) Identification and molecular characterization of leaf rust resistance gene Lr14a in durum wheat. Plant Dis 92: 469-473.
29. Herrera-Foessel SA, Singh RP, Huerta-Espino J, William HM, Djurle A, Yuen J (2008b) Molecular mapping of a leaf rust resistance gene on the short arm of chromosome 6B of durum wheat. Plant Dis 92: 1650-1654.
30. Herrera-Foessel SA, Singh RP, Huerta-Espino J, William HM, Djurle A, Yuen J (2008c) Genetic analysis of slow-rusting resistance to leaf rust in durum wheat. Crop Sci 48: 2132-2140.
31. Holland J (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10: 156-161.
32. Hospital F, Charcosset A (1997) Marker-assisted introgression of quantitative trait loci. Genetics 147: 1469-1485.
33. Kaur N, Street K, Mackay M, Yahiaoui N, Keller B (2008) Molecular approaches for characterization and use of natural disease resistance in wheat. Eur J Plant Pathol 121: 387-397.
34. Keller B, Feuillet C, Yahiaoui N (2005) Map-based isolation of disease resistance genes from bread wheat: cloning in a supersize genome. Genet Res 85: 93-100.
35. Keller B, Bieri S, Bossolini E, Yahiaoui N (2007) Cloning genes and QTLs for disease resistance in cereals. In: Varshney R, Tuberosa R (eds) Genomic assisted crop improvement: vol 2: genomics applications in crops. Springer, Dordrecht, pp 103-127.
36. Kim Y, Duggal P, Gillanders EM, Kim H, Bailey-Wilson JE (2008) Examining the effect of linkage disequilibrium between markers on the Type I error rate and power of nonparametric multipoint linkage analysis of two-generation and multigenerational pedigrees in the presence of missing genotype data. Genet Epidemiol 32: 41-51.
37. Knott DR, Bai DP, Zale J (2005) The transfer of leaf and stem rust resistance from wild emmer wheats to durum and common wheat. Can J Plant Sci 85: 49-57.
38. Kolmer JA (1996) Genetics of resistance to wheat leaf rust. Annu Rev Phytopathol 34: 435-455.
39. Krattinger SG, Lagudah ES, Spielmeyer W, Singh RP, Huerta-Espino J, McFadden H, Bossolini E, Selter LL, Keller B (2009) A putative ABC transporter confers durable resistance to multiple fungal pathogens in wheat. Science 323: 1360-1363.
40. Long DL, Kolmer JA (1989) A North American system of nomenclature for Puccinia recondita f. sp. tritici. Phytopathology 79: 525-529.
41. Maccaferri M, Sanguineti MC, Donini P, Tuberosa R (2003) Microsatellite analysis reveals a progressive widening of the genetic basis in the elite durum wheat germplasm. Theor Appl Genet 107: 783-797.
42. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range linkage disequilibrium in a durum wheat elite collection. Mol Breed 15: 271-289.
43. Maccaferri M, Sanguineti MC, Natoli V, Ortega JLA, Ben Salem M, Bort J, Chenenaoui C, De Ambrogio E, del Moral LG, De Montis A, El-Ahmed A, Maalouf F, Machlab H, Moragues M, Motawaj J, Nachit M, Nserallah N, Ouabbou H, Royo C, Tuberosa R (2006) A panel of elite accessions of durum wheat (Triticum durum Desf.) suitable for association mapping studies. Plant Gen Res 4: 79-85.
44. Maccaferri M, Sanguineti MC, Xie C, Smith JS, Tuberosa R (2007) Relationships among durum wheat accessions. II. A comparison of molecular and pedigree information. Genome 50: 385-399.
45. Maccaferri M, Mantovani P, Tuberosa R, DeAmbrogio E, Giuliani S, Demontis A, Massi A, Sanguineti MC (2008a) A major QTL for durable leaf rust resistance widely exploited in durum wheat breeding programs maps on the distal region of chromosome arm 7BL. Theor Appl Genet 117: 1225-1240.
46. Maccaferri M, Sanguineti MC, Corneti S, Ortega JLA, Ben Salem M, Bort J, DeAmbrogio E, del Moral LFG, Demontis A, El-Ahmed A, Maalouf F, Machlab H, Martos V, Moragues M, Motawaj J, Nachit M, Nserallah N, Ouabbou H, Royo C, Slama A, Tuberosa R (2008b) Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genetics 178: 489-511.
47. Maccaferri M, Sanguineti MC, del Moral LFG, Demontis A, El-Ahmed A, Maalouf F, Machlab H, Martos V, Moragues M, Motawaj J, Nachit M, Nserallah N, Ouabbou H, Royo C, Slama A, Tuberosa R (2009) Association mapping in durum wheat grown across a broad range of water regimes and yield potential. Genetics (submitted).
48. Malosetti M, van der Linden CG, Vosman B, van Eeuwijk FA (2007) A mixed-model approach to association mapping using pedigree information with an illustration of resistance to Phytophthora infestans in potato. Genetics 175: 879-889.
49. Mantovani P (2009) Identificazione di un QTL principale per resistenza a ruggine bruna sul cromosoma 7B di frumento duro. Ph. D. thesis, University of Bologna.
50. Mantovani P, Maccaferri M, Sanguineti MC, Tuberosa R, Catizone I, Wenzl P, Thomson B, Carling J, Eric H, DeAmbrogio E, Kilian A (2008) An integrated DArT-SSR linkage map of durum wheat. Mol Breed 22: 629-648.
51. Mantovani P, Maccaferri M, Tuberosa R, Kolmer J (2009) Virulence phenotypes and molecular genotypes of Puccinia triticina isolates from Italy. Plant Dis (accepted).
52. Marone D, Del Olmo AI, Laido G, Sillero JC, Emeran AA, Russo MA, Ferragonio P, Giovanniello V, Mazzucotelli E, De Leonardis AM, De Vita P, Blanco A, Cattivelli L, Rubiales D, Mastrangelo AM (2009) Genetic analysis of durable resistance against leaf rust in durum wheat. Mol Breed 24: 25-39.
53. Martinez F, Sillero JC, Rubiales D (2005) Pathogenic specialization of Puccinia triticina in Andalusia from 1998 to 2000. J Phytopathol 153: 344-349.
54. Martinez F, Sillero JC, Rubiales D (2007) Resistance to leaf rust in cultivars of bread wheat and durum wheat grown in Spain. Plant Breed 126: 13-18.
55. McIntosh RA (2009) History and status of the wheat rusts. In: Proceedings of the 2009 Technical Workshop Borlaug Global Rust Initiative, Cd. Obregon, Sonora, Mexico, March 17-20, pp 1-16.
56. McIntosh RA, Dyck PL (1975) Cytogenetical studies in wheat. VII. Gene Lr23 for reaction to Puccinia recondita in Gabo and related cultivars. Austr J Biol Sci 28: 201-211.
57. McIntosh RA, Park RF, Wellings CR (1995) Wheat rusts: an atlas of resistance genes. CSIRO Press, East Melbourne, Australia.
58. McIntosh RA, Devos KM, Dubcovsky J, Rogers WJ, Morris CF, Appels R, Somers DJ, Anderson OA (2008) Catalogue of gene symbols for wheat: 2008 supplement. Available at http://wheat. pw. usda. gov/ggpages/wgc/2008upd. pdf.
59. Meuwissen THE, Goddard ME (2000) Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci. Genetics 155: 421-430.
60. Morancho J (1995) World durum wheat trade. In: Di Fonzo N, Kaan F, Nachit M (eds) Durum wheat quality in the Mediterranean region, vol 22. Options Méditerranéennes. CIHEAM-IAMZ, Zaragoza, pp 213-219.
61. Nachit MM (2000) ICARDA germplasm program. Annual report for 2000. Durum wheat germplasm improvement for increased productivity, yield stability and grain quality in West Asia and North Africa (Project 1. 2). pp 125-152.
62. Nelson JC, Singh RP, Autrique JE, Sorrells ME (1997) Mapping genes conferring and suppressing leaf rust resistance in wheat. Crop Sci 37: 1928-1935.
63. Nsarellah N, Lhaloui S, Nachit M (2000) Breeding durum wheat for biotic stresses in the Mediterranean region. In: Royo C, Nachit MM, Di Fonzo N, Araus JL (eds) Durum wheat improvement in the Mediterranean region: new challenges, vol 40. Options Méditerranéennes. CIHEAM-IAMZ, Zaragoza, pp 341-347.
64. Ordoñez ME, Kolmer JA (2007) Virulence phenotypes of a world-wide collection of Puccinia triicina from durum wheat. Phytopathology 97: 344-351.
65. Pasquini M, Casulli F (1993) Resistenza "durevole" a Puccinia recondita f. sp. tritici ed Erysiphe graminis f. sp. tritici in frumenti duri italiani. Phytopathol Mediterr 32: 135-142.
66. Peleman JD, van der Voort JR (2003) Breeding by design. Trends Plant Sci 8: 330-334.
67. Peterson RF, Campbell AB, Hannah AE (1948) A diagrammatic scale for estimating rust intensity of leaves and stem of cereals. Can J Res Sect C 26: 496-500.
68. Pritchard JK, Rosenberg NA (1999) Use of unlinked genetic markers to detect population stratification in association studies. Am J Hum Genet 65: 220-228.
69. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
70. Qiu D, Mao J, Yang X, Zeng H (2009) Expression of an elicitor-encoding gene from Magnaporthe grisea enhances resistance against blast disease in transgenic rice. Plant Cell Rep 28: 925-933.
71. Rafalski A (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr Opin Plant Biol 5: 94-100.
72. Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier MH, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149: 2007-2023.
73. Rostoks N, Ramsay L, MacKenzie K, Cardle L, Bhat PR, Roose ML, Svensson JT, Stein N, Varshney RK, Marshall DF, Graner A, Close TJ, Waugh R (2006) Recent history of artificial outcrossing facilitates whole-genome association mapping in elite inbred crop varieties. Proc Natl Acad Sci USA 103: 18656-18661.
74. Saghai Maroof MA, Solima KM, Jorgenson RA, Allard RW (1984) Ribosomal DNA spacer-length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 8: 8014-8018.
75. Salvi S, Tuberosa R (2005) To clone or not to clone plant QTLs: present and future challenges. Trends Plant Sci 10: 297-304.
76. Schrag TA, Möhring J, Maurer HP, Dhillon BS, Melchinger AE, Piepho HP, Sørensen AP, Frisch M (2009) Molecular marker-based prediction of hybrid performance in maize using unbalanced data from multiple experiments with factorial crosses. Theor Appl Genet 118: 741-751.
77. Seyfarth R, Feuillet C, Schachermayr G, Messmer M, Winzeler M, Keller B (2000) Molecular mapping of the adult-plant leaf rust resistance gene Lr13 in wheat (Triticum aestivum L.). J Genet Breed 54: 193-198.
78. Shaner G, Finney RE (1977) The effect of nitrogen fertilization on the expression of slow-mildewing resistance in Knox wheat. Phytopathology 67: 1051-1056.
79. Singh H, Dhaliwal HS, Gill KS (1992) Diversity for leaf rust resistance in Triticumdurum germplasm. Cereal Rusts Powdery Mildews Bull 20: 62-67.
80. Singh RP, Huerta-Espino J, Pfeiffer W, Figueroa-Lopez P (2004) Occurrence and impact of a new leaf rust race on durum wheat in northwestern Mexico from 2001 to 2003. Plant Dis 88: 703-708.
81. Singh RP, Huerta-Espino J, Fuentes G, Duveiller E, Gilchrist L, Henry M, Nicol MJ (2005) Resistance to diseases. In: Royo C, Nachit MM, Di Fonzo N, Araus JL, Pfeiffer WH, Slafer GA (eds) Durum wheat breeding: current approaches and future strategies. Food Product Press, Binghamton, pp 291-315.
82. Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109: 1105-1114.
83. Somers DJ, Banks T, DePauw R, Fox S, Clarke J, Pozniak C, McCartney C (2007) Genome-wide linkage disequilibrium analysis in bread wheat and durum wheat. Genome 50: 557-567.
84. Stam P (1993) Construction of integrated genetic linkage maps by means of a new computer package: JOINMAP. Plant J 3: 739-744.
85. van Ooijen JW, Voorrips RE (2006) JoinMap version 4. 0: software for the calculation of genetic linkage maps. Plant Research International, Wageningen.
86. Varshney RK, Tuberosa R (2007) Genomics-assisted crop improvement, vol 1: genomics approaches and platforms. Springer, Dordrecht.
87. Varshney RK, Langridge P, Graner A (2007) Application of genomics to molecular breeding of wheat and barley. Adv Genet 58: 121-155.
88. Villumsen TM, Janss L, Lund MS (2009) The importance of haplotype length and heritability using genomic selection in dairy cattle. J Anim Breed Genet 126: 3-13.
89. Waugh R, Jannink JL, Muehlbauer GJ, Ramsay L (2009) The emergence of whole genome association scans in barley. Curr Opin Plant Biol 12: 218-222.
90. Wilhelm EP, Turner AS, Laurie DA (2009) Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theor Appl Genet 118: 285-294.
91. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
92. Zhang H, Knott DR (1990) Inheritance of leaf rust resistance in durum wheat. Crop Sci 30: 1218-1222.
93. Zhang H, Knott DR (1993) Inheritance of adult plant resistance to leaf rust in six durum wheat cultivars. Crop Sci 33: 694-697.