Association mapping of quantitative disease resistance in a natural population of loblolly pine (Pinus taeda L.)

Genetics

Volumn 186, Issue 2, 2010, Pages 677-686

  Quesada, Tania ^a,b   Gopal, Vikneswaran ^c   Cumbie, W Patrick ^d   Eckert, Andrew J ^e   Wegrzyn, Jill L ^e   Neale, David B ^e   Goldfarb, Barry ^d   Huber, Dudley A ^b   Casella, George ^b,c   Davis, John M ^a,b  

^a Horticultural Sciences Department   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

^c Department of Statistics ^*  (United States)

^d NORTH CAROLINA STATE UNIVERSITY   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; FUSARIUM; FUSARIUM CIRCINATUM; GENE IDENTIFICATION; GENE MAPPING; GENETIC RESISTANCE; GENOMICS; GENOTYPE; INOCULATION; NONHUMAN; PINE; POPULATION GENETICS; PRIORITY JOURNAL; QUANTITATIVE ANALYSIS; SIGNAL TRANSDUCTION; SINGLE NUCLEOTIDE POLYMORPHISM; STRESS; VALIDATION PROCESS;

CHROMOSOME MAPPING; FUSARIUM; GENES, PLANT; GENETIC ASSOCIATION STUDIES; GENETIC LINKAGE; GENETIC VARIATION; GENOTYPE; HOST-PATHOGEN INTERACTIONS; IMMUNITY, INNATE; INHERITANCE PATTERNS; PHENOTYPE; PINUS TAEDA; PLANT DISEASES; POLYMORPHISM, SINGLE NUCLEOTIDE;

GIBBERELLA CIRCINATA; PINUS TAEDA;

EID: 78951479433     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.110.117549     Document Type: Article

References (71)

1. AL-RABAB'AH, M. A., and C. G. WILLIAMS, 2002 Population dynamics of Pinus taeda L. based on nuclear microsatellites. For. Ecol. Manage. 163: 263-271.
2. BALINT-KURTI, P. J., J. C. ZWONITZER, M. E. PE, G. PEA, M. LEE et al., 2008 Identification of quantitative trait loci for resistance to southern leaf blight and days to anthesis in two maize recombinant inbred line populations. Phytopathology 98: 315-320.
3. BEAVIS, W. D., 1998 QTL analysis: power, precision, and accuracy, pp. 145-162 in Molecular Dissection of Complex Traits, edited by A. H. PATERSON. CRC Press, Boca Raton, FL.
4. BRITZ, H., T. A. COUTINHO, B. D. WINGFIELD, W. F. O.MARASAS and M. J. WINGFIELD, 2005 Diversity and differentiation in two populations of Gibberella circinata in South Africa. Plant Pathol. 54: 46-52.
5. BROWN, G. R., G. P. GILL, R. J. KUNTZ, C. H. LANGLEY and D. B. NEALE, 2004 Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. USA 101: 15255-15260.
6. BUCKLER, E. S., J. B. HOLLAND, P. J. BRADBURY, C. B. ACHARYA, P. J. BROWN et al., 2009 The genetic architecture of maize flowering time. Science 325: 714-718.
7. CAREY, W. A., S. W. OAK and S. A. ENEBAK, 2005 Pitch canker ratings of longleaf pine clones correlate with Fusarium circinatum infestation of seeds and seedling mortality in containers. For. Pathol. 35: 205-212.
8. CHARLIER, C.,W. COPPIETERS, F. ROLLIN, D. DESMECHT, J. S.AGERHOLM et al., 2008 Highly effective SNP-based association mapping and management of recessive defects in livestock. Nat. Genet. 40: 449-454.
9. COURDAVAULT, V., V. BURLAT, B. ST-PIERRE and N. GIGLIOLI-GUIVARC'H, 2009 Proteins prenylated by type I protein geranyl-geranyltransferase act positively on the jasmonate signalling pathway triggering the biosynthesis of monoterpene indole alkaloids in Catharanthus roseus. Plant Cell Rep. 28: 83-93.
10. COVERT, S. F., A. BRILEY, M. M. WALLACE, V.T. MCKINNEY 1999 Partial MAT-2 gene structure and the influence of temperature on mating success in Gibberella circinata. Fungal Genet. Biol. 28: 43-54.
11. D'ALFONSO, S., M. MELLAI, M. GIORDANO, A. PASTORE, G. MALFERRARI et al., 2002 Identification of single nucleotide variations in the coding and regulatory regions of the myelin-associated glycoprotein gene and study of their association with multiple sclerosis. J. Neuroimmunol. 126: 196-204.
12. DANGL, J. L., and J. D. G. JONES, 2001 Plant pathogens and integrated defence responses to infection. Nature 411: 826-833.
13. DWINELL, L. D., J. B. BARROWSBROADDUS and E. G. KUHLMAN, 1985 Pitch canker: a disease complex of southern pines. Plant Dis. 69: 270-276.
14. EASTON, D. F., K. A. POOLEY, A. M. DUNNING, P. D. PHAROAH, D. THOMPSON et al., 2007 Genome-wide association study identifies novel breast cancer susceptibility loci. Nature 447: 1087-1093.
15. ECKERT, A. J., A. D. BOWER, J. L. WEGRZYN, B. PANDE, K.D. JERMSTAD et al., 2009a Association genetics of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii, Pinaceae) I. Cold-hardiness related traits. Genetics 182: 1289-1302.
16. ECKERT, A. J., E. S. ERSOZ, B. PANDE, M.H. WRIGHT, V. K. RASHBROOK et al., 2009b High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.). Tree Genet. Genome 5: 225-234.
17. ECKERT, A. J., J. VAN HEERWAARDEN, J. L. WEGRZYN, C. D. NELSON, J. ROSS-IBARRA et al., 2010 Patterns of population structure and environmental associations to aridity across the 4 ranges of loblolly pine (Pinus taeda L., Pinaceae). Genetics 185: 969-982.
18. ENEBAK, S. A., and G. R. STANOSZ, 2003 Responses of conifer species of the Great Lakes region of North America to inoculation with the pitch canker pathogen Fusarium circinatum. For. Pathol. 33: 333-338.
19. FLINT, J., and T. F. MACKAY, 2009 Genetic architecture of quantitative traits in mice, flies, and humans. Genome Res. 19: 723-733.
20. FLINT-GARCIA, S. A., J. M. THORNSBERRY and E. S. BUCKLER, 2003 Structure of linkage disequilibrium in plants. Annu. Rev. Plant Biol. 54: 357-374.
21. FLINT-GARCIA, S. A., A. C. THUILLET, J. M. YU, G. PRESSOIR, S. M. ROMERO et al., 2005 Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J. 44: 1054-1064.
22. GILMOUR, A. R., B. J. GOGEL, B. R. CULLIS and R. THOMPSON, 2006 ASReml User Guide Release 2.0. VSN International Ltd, Hemel Hempstead, UK.
23. GODDARD, M. E., and B. J. HAYES, 2009 Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10: 381-391.
24. GONZALEZ-MARTINEZ, S. C., N. C. WHEELER, E. ERSOZ, C. D. NELSON and D. B. NEALE, 2007 Association genetics in Pinus taeda L. I. Wood property traits. Genetics 175: 399-409.
25. GONZALEZ-MARTINEZ, S. C., D. HUBER, E. ERSOZ, J. M. DAVIS and D. B. NEALE, 2008 Association genetics in Pinus taeda L. II. Carbon isotope discrimination. Heredity 101: 19-26.
26. GOPAL, V., Z. LI and G. CASELLA, 2009 BAMD: Bayesian Association Model for genomic data with missing covariates. R package version 3.1. http://CRAN.R-project.org/package=BAMD.
27. GORING, H. H. H., J. D. TERWILLIGER and J. BLANGERO, 2001 Large upward bias in estimation of locus-specific effects from genomewide scans. Am. J. Hum. Genet. 69: 1357-1369.
28. GORITSCHNIG, S., T. WEIHMANN, Y. L. ZHANG, P. FOBERT, P. MCCOURT et al., 2008 A novel role for protein farnesylation in plant innate immunity. Plant Physiol. 148: 348-357. (Pubitemid 352847611)
29. HERBERS, K., G. MONKE, R. BADUR and U. SONNEWALD, 1995 A simplified procedure for the subtractive cDNA cloning of photoassimilate-responding genes: isolation of cDNAs encoding a new class of pathogenesis-related proteins. Plant Mol. Biol. 29: 1027-1038.
30. HERBERS, K., P. MEUWLY, W. B. FROMMER, J. P. METRAUX and U. SONNEWALD, 1996 Systemic acquired resistance mediated by the ectopic expression of invertase: possible hexose sensing in the secretory pathway. Plant Cell 8: 793-803.
31. HODGE, G. R., and W. S. DVORAK, 2000 Differential responses of Central American and Mexican pine species and Pinus radiata to infection by the pitch canker fungus. New Forests 19: 241-258.
32. HODGE, G. R., and W. S. DVORAK, 2007 Variation in pitch canker resistance among provenances of Pinus patula and Pinus tecunumanii from Mexico and Central America. New Forests 33: 193-206.
33. INGVARSSON, P. K., M. V. GARCIA, V. LUQUEZ, D. HALL and S. JANSSON, 2008 Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226.
34. INOSTROZA, L., A. DEL POZO, I. MATUS, D. CASTILLO, P. HAYES et al., 2009 Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp spontaneum as a source of donor alleles in a Hordeum vulgare subsp vulgare background. Mol. Breed. 23: 365-376.
35. JIANG, N., E. EMBERLY, O. CUVIER and C. M. HART, 2009 Genomewide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription. Mol. Cell. Biol. 29: 3556-3568.
36. JOHAL, G. S., and S. P. BRIGGS, 1992 Reductase-activity encoded by the Hm1 disease resistance gene in maize. Science 258: 985-987.
37. JONES, J. D. G., and J. L. DANGL, 2006 The plant immune system. Nature 444: 323-329.
38. KANZAKI, H., H. SAITOH, Y. TAKAHASHI, T. BERBERICH, A. ITO et al., 2008 NbLRK1, a lectin-like receptor kinase protein of Nicotiana benthamiana, interacts with Phytophthora infestans INF1 elicitin and mediates INF1-induced cell death. Planta 228: 977-987.
39. KAYIHAN, G. C., D. A. HUBER, A. M. MORSE, T. L. WHITE and J. M. DAVIS, 2005 Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theor. Appl. Genet. 110: 948-958.
40. KENNINGTON, W. J., A. A. HOFFMANN and L. PARTRIDGE, 2007 Mapping regions within cosmopolitan inversion In(3R) Payne associated with natural variation in body size in Drosophila melanogaster. Genetics 177: 549-556.
41. LEBUDE, A. V., B. GOLDFARB, F. A. BLAZICH, F. C. WISE and J. FRAMPTON, 2004 Mist, substrate water potential and cutting water potential influence rooting of stem cuttings of loblolly pine. Tree Physiol. 24: 823-831.
42. LEE, J. H., R. CHENG, N. SCHUPF, J. MANLY, R. LANTIGUA et al., 2007 The association between genetic variants in SORL1 and Alzheimer disease in an urban, multiethnic, community-based cohort. Arc. Neurol. 64: 501-506.
43. LI, Z., 2008 Bayesian methodologies for genomic data with missing covariates. Ph.D. Dissertation, University of Florida, Gainesville, FL.
44. LLORENTE, F., P. MUSKETT, A. SANCHEZ-VALLET, G. LOPEZ, B. RAMOS et al., 2008 Repression of the auxin response pathway increases Arabidopsis susceptibility to necrotrophic fungi. Mol. Plant 1: 496-509.
45. LOOPSTRA, C. A., and R. R. SEDEROFF, 1995 Xylem-specific gene-expression in loblolly-pine. Plant Mol. Biol. 27: 277-291.
46. MA, L-J., H. C. VAN DER DOES, K. A. BORKOVICH, J. J. COLEMAN, M-J. DABOUSSI et al., 2010 Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium. Nature 464: 367-373.
47. MALOSETTI, M., C. G. VAN DER LINDEN, B. VOSMAN and F. A. VAN EEUWIJK, 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.
48. MARTINEZ, M. L., M. A. MACHADO, C. S. NASCIMENTO, M. V. SILVA, R. L. TEODORO et al., 2006 Association of BoLA-DRB3.2 alleles with tick (Boophilus microplus) resistance in cattle. Genet. Mol. Res. 5: 513-524.
49. MCGUFFIN, P., K. TANDON and A. CORSICO, 2003 Linkage and association studies of schizophrenia. Curr. Psychiatr. Rep. 5: 121-127.
50. MORSE, A. M., C. D. NELSON, S. F. COVERT, A. G. HOLLIDAY, K. E. SMITH et al., 2004 Pine genes regulated by the necrotrophic pathogen Fusarium circinatum. Theor. Appl. Genet. 109: 922-932.
51. MURRAY, S. C., W. L. ROONEY, M. T. HAMBLIN, S. E. MITCHELL and S. KRESOVICH, 2009 Sweet sorghum genetic diversity and association mapping for brix and height. Plant Genome 2: 48-62.
52. NAVARRO, L., R. BARI, P. ACHARD, P. LISON, A. NEMRI et al., 2008a DELLAs control plant immune responses by modulating the balance and salicylic acid signaling. Curr. Biol. 18: 650-655.
53. NAVARRO, L., R. BARI, A. SEILANIANTZ, A. NEMRI and J. D. G. JONES, 2008b Roles of Plant Hormones in Plant Resistance and Susceptibility to Pathogens. Springer-Verlag, New York.
54. NEALE, D. B., and O. SAVOLAINEN, 2004 Association genetics of complex traits in conifers. Trends Plant. Sci. 9: 325-330.
55. NERSISSIAN, A. M., C. IMMOOS, M. G. HILL, P. J. HART, G. WILLIAMS et al., 1998 Uclacyanins, stellacyanins, and plantacyanins are distinct subfamilies of phytocyanins: plant-specific mononuclear blue copper proteins. Prot. Sci. 7: 1915-1929.
56. NORRY, F. M., F. H. GOMEZ and V. LOESCHCKE, 2007 Knockdown resistance to heat stress and slow recovery from chill coma are genetically associated in a quantitative trait locus region of chromosome 2 in Drosophila melanogaster. Mol. Ecol. 16: 3274-3284.
57. POLAND, J. A., P. J. BALINT-KURTI, R. J.WISSER, R. C. PRATT and R. J. NELSON, 2009 Shades of gray: the world of quantitative disease resistance. Trends Plant Sci. 14: 21-29.
58. PRITCHARD, J. K., M. STEPHENS and P. DONNELLY, 2000 Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
59. R DEVELOPMENT CORE TEAM, 2005 R: A language and environment for statistical computing, reference index version 3.3.1. R Foundation for Statistical. Computing, Vienna, Austria, http://www.R-project.org
60. SAKAMOTO, J. M., and T. R. GORDON, 2006 Factors influencing infection of mechanical wounds by Fusarium circinatum on Monterey pines (Pinus radiata). Plant Pathol. 55: 130-136.
61. SCHMIDTLING, R. C., E. CARROLL and T. LAFARGE, 1999 Allozyme diversity of selected and natural loblolly pine populations. Silvae Genetica 48: 35-45.
62. STICH, B., H. P. PIEPHO, B. SCHULZ and A. E. MELCHINGER, 2008 Multi-trait association mapping in sugar beet (Beta vulgaris L.). Theor. Appl. Genet. 117: 947-954.
63. STRACKE, S., G. HASENEYER, J.-B. VEYRIERAS, H. H. GEIGER, S. SAUER et al., 2009 Association mapping reveals gene action and interactions in the determination of flowering time in barley. Theor. Appl. Genet. 118: 259-273.
64. THUMMA, B. R., M. F. NOLAN, R. EVANS and G. F. MORAN, 2005 Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171: 1257-1265.
65. WANG, J., P. E. MCCLEAN, R. LEE, R. J. GOOS and T. HELMS, 2008 Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor. Appl. Genet. 116: 777-787.
66. WEI, X. M., P. A. JACKSON, C. L. MCINTYRE, K. S. AITKEN and B. CROFT, 2006 Associations between DNA markers and resistance to diseases in sugarcane and effects of population substructure. Theor. Appl. Genet. 114: 155-164.
67. YAHIAOUI, S., A. M. CASAS, M. A. MORALEJO, B. MEDINA, M. P. GRACIA et al., 2008 Genome-wide association mapping in barley. Options Mediterraneennes. Series A, Seminaires Mediterraneens: 123-126.
68. YOSHIDA, S., M. ITO, I. NISHIDA and A. WATANABE, 2002 Identification of a novel gene HYS1/CPR5 that has a repressive role in the induction of leaf senescence and pathogen-defence responses in Arabidopsis thaliana. Plant J. 29: 427-437.
69. YOUNG, C. H., B. S. MINTON and J. J. BRONSON, 2006 Resistance Screening Center Procedures Manual: A Guide Used in the Operational Screening of Pines for Resistance to Pitch Canker Disease. United States Department of Agriculture, Southern Region, Forest Health Protection.
70. YU, J. M., and E. S. BUCKLER, 2006 Genetic association mapping and genome organization of maize. Curr.Opin. Biotechnol. 17: 155-160.
71. ZHAO, J., M. J. PAULO, D. JAMAR, P. LOU, F. VAN EEUWIJK et al., 2007 Association mapping of leaf traits, flowering time, and phytate content in Brassica rapa. Genome 50: 963-973.