Association Mapping and Haplotype Analysis of a 3.1-Mb Genomic Region Involved in Fusarium Head Blight Resistance on Wheat Chromosome 3BS

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  Hao, Chenyang ^a   Wang, Yuquan ^a   Hou, Jian ^a   Feuillet, Catherine ^b   Balfourier, Francois ^b   Zhang, Xueyong ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b Diversity and Ecophysiology of Cereals   (France)

Author keywords

[No Author keywords available]

Indexed keywords

MOLECULAR MARKER;

ARTICLE; CLUSTER ANALYSIS; CONTIG MAPPING; FHB1 GENE; FLORET; FUSARIUM HEAD BLIGHT; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MAPPING; GENE POOL; GENETIC ASSOCIATION; GENETIC DISTANCE; GENOME SIZE; GENOTYPE; HAPLOTYPE; INFECTION RESISTANCE; MARKER ASSISTED BREEDING; NONHUMAN; PHENOTYPIC VARIATION; PLANT BREEDING; PLANT CHROMOSOME; PLANT CHROMOSOME 3BS; PLANT GENE; POPULATION GENETIC STRUCTURE; SIMPLE SEQUENCE REPEAT; SPIKELET; STATISTICAL MODEL; WHEAT;

CLUSTER ANALYSIS; FUSARIUM; GENETIC MARKERS; GENOME, PLANT; HAPLOTYPES; TRITICUM;

FUSARIUM; TRITICUM AESTIVUM;

EID: 84867145562     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0046444     Document Type: Article

References (64)

1. Gilbert J, Tekauz A, (2000) Review: recent developments in research on fusarium head blight of wheat in Canada. Can J Plant Pathol 22: 1-8.
2. Bai GH, Shaner G, (1994) Scab of wheat: prospects for control. Plant Disease 78: 760-766.
3. Dexter JE, Clear RM, Preston KR, (1996) Fusarium head blight: effect on the milling and baking of some Canadian wheats. Cereal Chem 73: 695-701.
4. Dexter JE, Marchylo B, Clear RM, Clarke JM, (1997) Effect of fusarium head blight on semolina milling and pasta-making quality of durum wheat. Cereal Chem 74: 519-525.
5. McMullen M, Jones R, Gallenberg D, (1997) Scab of wheat and barley: a re-emerging disease of devastating impact. Plant Dis 81: 1340-1348.
6. Snijders CHA (1994) Breeding for resistance to fusarium in wheat and maize. In: Miller JD, Trenholm HL (eds) Mycotoxins in grain: compounds other than aflatoxin. St. Paul, MN: Eagan. pp. 37-58.
7. Liu S, Anderson JA, (2003) Marker assisted evaluation of Fusarium head blight resistant wheat germplasm. Crop Sci 43: 760-766.
8. Yu BY, Bai GH, Cai SB, Dong YH, Ban T, (2008) New Fusarium head blight-resistant sources from Asian wheat germplasm. Crop Sci 48: 1090-1097.
9. McCartney CA, Somers DJ, Fedak G, Cao W, (2004) Haplotype diversity at fusarium head blight resistance QTLs in wheat. Theor Appl Genet 109: 261-271.
10. Anderson JA, Stack RW, Liu S, Waldron BL, Fjeld AD, et al. (2001) DNA markers for Fusarium head blight resistance QTLs in two wheat populations. Theor Appl Genet 102: 1164-1168.
11. Somers DJ, Fedak G, Savard M, (2003) Molecular mapping of novel genes controlling Fusarium head blight resistance and deoxynivalenol accumulation in spring wheat. Genome 46: 555-564.
12. Steiner B, Lemmens M, Griesser M, Scholz U, Schondelmaier J, et al. (2004) Molecular mapping of resistance to Fusarium head blight in the spring wheat cultivar Frontana. Theor Appl Genet 109: 215-224.
13. Cuthbert PA, Somers DJ, Thomas J, Cloutier S, Brulé-Babel A, (2006) Fine mapping Fhb1, a major gene controlling fusarium head blight resistance in bread wheat (Triticum aestivum L.). Theor Appl Genet 112: 1465-1472.
14. Ma ZQ, Xue SL, Lin F, Yang SH, Li GQ, et al. (2008) Mapping and validation of scab resistance QTLs in the Nanda2419×Wangshuibai population. Cereal Res Commun (Supplementum B) 36: 245-251.
15. Xue SL, Xu F, Tang MZ, Zhou Y, Li GQ, et al. (2011) Precise mapping Fhb5, a major QTL conditioning resistance to Fusarium infection in bread wheat (Triticum aestivum L.). Theor Appl Genet 123: 1055-1063.
16. Buerstmayr H, Ban T, Anderson JA, (2009) QTL mapping and marker-assisted selection for Fusarium head blight resistance in wheat: a review. Plant Breeding 128: 1-26.
17. Löffler M, Schön CC, Miedaner T, (2009) Revealing the genetic architecture of FHB resistance in hexaploid wheat (Triticum aestivum L.) by QTL meta-analysis. Mol Breed 23: 473-488.
18. Liu S, Zhang X, Pumphrey MO, Stack RW, Gill BS, et al. (2006) Complex microcolinearity among wheat, rice and barley revealed by fine mapping of the genomic region harboring a major QTL for resistance to Fusarium head blight in wheat. Funct Integr Genomics 6: 83-89.
19. Cuthbert PA, Somers DJ, Brulé-Babel A, (2007) Mapping of Fhb2 on chromosome 6BS: a gene controlling Fusarium head blight field resistance in bread wheat (Triticum aestivum L.). Theor Appl Genet 114: 429-437.
20. Xue SL, Li GQ, Jia HY, Xu F, Lin F, et al. (2010) Fine mapping Fhb4 a major QTL conditioning resistance to Fusarium infection in bread wheat (Triticum aestivum L.). Theor Appl Genet 121: 147-156.
21. Waldron BL, Moreno-Sevilla B, Anderson JA, Stack RW, Frohberg RC, (1999) RFLP mapping of QTL for Fusarium head blight resistance in wheat. Crop Sci 39: 805-811.
22. Bai G, Kolb FL, Shaner G, Domier LL, (1999) Amplified fragment length polymorphism markers linked to a major quantitative trait locus controlling scab resistance in wheat. Phytopathology 89: 343-348.
23. Zhou WC, Kolb FL, Bai G, Shaner G, Domier LL, (2002) Genetic analysis of scab resistance QTL in wheat with microsatellite and AFLP markers. Genome 45: 719-727.
24. Yang ZP, Gilbert J, Fedak G, Somers DJ, (2005) Genetic characterization of QTL associated with resistance to Fusarium head blight in a doubled-haploid spring wheat population. Genome 48: 187-196.
25. Pumphrey MO, Bernardo R, Anderson JA, (2007) Validating the Fhb1 QTL for fusarium head blight resistance in near isogenic wheat lines developed from breeding populations. Crop Sci 47: 200-206.
26. Liu S, Pumphrey MO, Gill BS, Trick HN, Zhang JX, et al. (2008) Toward positional cloning of FHB1, a major QTL for fusarium head blight resistance in wheat. Cereal Res Commun (Suppl B) 36: 195-201.
27. Flint-Garcia SA, Thornsberry JM, Buckler ES, (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54: 357-374.
28. Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627-631.
29. Zwart RS, Muylle H, Van Bockstaele E, Roldán-Ruiz I, (2008) Evaluation of genetic diversity of Fusarium head blight resistance in European winter wheat. Theor Appl Genet 117: 813-828.
30. Miedaner T, Würschum T, Maurer HP, Korzun V, Ebmeyer E, et al. (2011) Association mapping for Fusarium head blight resistance in European soft winter wheat. Mol Breed 28: 647-655.
31. Garner C, Slatkin M, (2003) On selecting markers for association studies: patterns of linkage disequilibrium between two and three diallelic loci. Genet Epidemiol 24: 57-67.
32. Andersen J, Lübberstedt T, (2003) Functional markers in plants. Trends Plant Sci 8: 554-560.
33. Hao CY, Perretant MR, Choulet F, Wang LF, Paux E, et al. (2010) Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations. Theor Appl Genet 121: 1209-1225.
34. Yu J, Buckler E, (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotech 17: 155-160.
35. Yan JB, Shah T, Warburton ML, Buckler ES, McMullen MD, et al. (2009) Genetic characterization and linkage disequilibrium estimation of a global maize collection using SNP markers. Plos One 4 (12):: e8451 doi:10.1371/journal.pone.0008451.
36. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203-208.
37. Zhang ZW, Ersoz E, Lai CQ, Fodhunter RJ, Tiwari HK, et al. (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42: 355-360.
38. Buerstmayr H, Lemmens M, Hartl L, Doldi L, Steiner B, et al. (2002) Molecular mapping of QTL for Fusarium head blight resistance in spring wheat. I. Resistance to fungal spread (type II resistance). Theor Appl Genet 104: 84-91.
39. Bourdoncle W, Ohm HW, (2003) Quantitative trait loci for resistance to Fusarium head blight in recombinant inbred wheat lines from the cross Huapei 57-2/Patterson. Euphytica 131: 131-136.
40. Shen X, Zhou M, Lu W, Ohm H, (2003) Detection of Fusarium head blight resistance QTL in a wheat population using bulked segregant analysis. Theor Appl Genet 106: 1041-1047.
41. Zhang X, Zhou MP, Ren LJ, Bai GH, Ma HX, et al. (2004) Molecular characterization of Fusarium head blight resistance from wheat variety Wangshuibai. Euphytica 139: 59-64.
42. Lin F, Kong ZX, Zhu HL, Xue SL, Wu JZ, et al. (2004) Mapping QTL associated with resistance to Fusarium head blight in the Nanda2419×Wangshuibai population. I. Type II resistance. Theor Appl Genet 109: 1504-1511.
43. Lemmens M, Scholz U, Berthiller F, Dall'Asta C, Koutnik A, et al. (2005) The ability to detoxify the mycotoxin deoxynivalenol colocalizes with a major quantitative trait locus for fusarium head blight resistance in wheat. Mol Plant Microbe Interact 18: 1318-1324.
44. Zhang XY, Tong YP, You GX, Hao CY, Ge HM, et al. (2007) Hitchhiking effect mapping: A new approach for discovering agronomically important genes. Agri Sci China 6: 255-264.
45. Nordborg M, Weigel D, (2008) Next-generation genetics in plants. Nature 456: 720-723.
46. Yan JB, Warburton M, Crouch J, (2011) Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Sci 51: 433-449.
47. Gupta P, Rustgi S, Kulwal P, (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57: 461-485.
48. Barrero RA, Bellgard M, Zhang X, (2011) Diverse approaches to achieving grain yield in wheat. Funct Integr Genomics 11: 37-48.
49. Malysheva-Otto LV, Röder MS, (2006) Haplotype diversity in the endosperm specific β-amylase gene Bmy1 of cultivated barley (Hordeum vulgare L.). Mol Breeding 18: 143-156.
50. Stracke S, Presterl T, Stein N, Perovic D, Ordon F, et al. (2007) Effects of introgression and recombination on haplotype structure and linkage disequilibrium surrounding a locus encoding Bymovirus resistance in barley. Genetics 175: 805-817.
51. Gore MA, Chia JM, Elshire RJ, Sun Q, Ersoz ES, et al. (2009) A first-generation haplotype map of maize. Science 326: 1115-1117.
52. Breseghello F, Sorrells ME, (2006) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172: 1165-1177.
53. Zhang JN, Hao CY, Ren Q, Chang XP, Liu GR, et al. (2011) Association mapping of dynamic developmental plant height in common wheat. Planta 234: 891-902.
54. Koebner RMD, Summers RW, (2003) 21st century wheat breeding: plot selection or plate detection. Trends in Biotechnology 21: 59-63.
55. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J, et al. (2010) Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22: 1686-1701.
56. Paux E, Faure S, Choulet F, Roger D, Gauthier V, et al. (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8: 196-210.
57. Pritchard JK, Stephens M, Donnelly P, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
58. Evanno G, Regnaut S, Goudet J, (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14: 2611-2620.
59. Hao CY, Wang LF, Ge HM, Dong YC, Zhang XY, (2011) Genetic diversity and linkage disequilibrium in Chinese bread wheat (Triticum aestivum L.) revealed by SSR markers. Plos One 6 (2):: e17279 doi: 10.1371/journal.pone.0017279.
60. Perrier X, Flori A, Bonnot F (2003) Data analysis methods. In: Hamon P, Seguin M, Perrier X, Glaszmann JC (eds) Genetic diversity of cultivated tropical plants. Enfield, Science Publishers, Montpellier, pp 43-76.
61. Rohlf FJ (2000) NTSYS-pc: numerical taxonomy and multivariate analysis system, version 2.1. Exeter Software, Setauket, NY.
62. Hardy OJ, Vekemans X, (2002) SPAGeDi: a versatile computer program to analyze spatial genetic structure at the individual or population levels. Mol Ecol Notes 2: 618-620.
63. Loiselle BA, Sork VL, Nason J, Graham C, (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82: 1420-1425.
64. Bradbury PJ, Zhang ZW, Kroon DE, Casstevens TM, Ramdoss Y, et al. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.