Effect of population structure corrections on the results of association mapping tests in complex maize diversity panels

Theoretical and Applied Genetics

Volumn 122, Issue 6, 2011, Pages 1149-1160

  Mezmouk, Sofiane ^a,b   Dubreuil, Pierre ^a   Bosio, Mickaël ^a   Décousset, Laurent ^a   Charcosset, Alain ^c   Praud, Sébastien ^a   Mangin, Brigitte ^b  

^a UNIVERSITÉ DE HAUTE ALSACE   (France)

^b CEMAGREF   (France)

^c INRA Institut National de la Recherche Agronomique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION MAPPING; BAYESIAN; DATA SETS; DIMENSIONAL REDUCTION; GENETIC STRUCTURE; INBRED LINE; META-ANALYSIS; PANEL STRUCTURES; PLANT DIVERSITY; POPULATION STRUCTURES; ROBUST ASSOCIATION; STRUCTURE MODELS;

MAPPING;

ARTICLE; BAYES THEOREM; CHROMOSOME MAP; COMPUTER PROGRAM; GENETIC LINKAGE; GENETIC POLYMORPHISM; GENETICS; GENOTYPE; HISTOLOGY; HUMAN; MAIZE; METHODOLOGY; PHENOTYPE; PRINCIPAL COMPONENT ANALYSIS;

BAYES THEOREM; CHROMOSOME MAPPING; GENETIC LINKAGE; GENOTYPE; HUMANS; PHENOTYPE; POLYMORPHISM, GENETIC; PRINCIPAL COMPONENT ANALYSIS; SOFTWARE; ZEA MAYS;

ZEA MAYS;

EID: 79953686775     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-010-1519-y     Document Type: Article

References (56)

1. Abdurakhmonov IY, Saha S, Jenkins JN, Buriev ZT, Shermatov SE, Scheffler BE, Pepper AE, Yu JZ, Kohel RJ, Abdukarimov A (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136: 401-417.
2. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc 57: 289-300.
3. Buckler ES, Stevens NM (2005) Maize origins, domestication, and selection. In: Motley TJ, Zerega N, Cross H (eds) Darwin's harvest. Columbia University Press, New York, pp 67-90.
4. Cacharrón J, Saedler H, Theißen G (1999) Expression of MADS box genes ZMM8 and ZMM14 during inflorescence development of Zea mays discriminates between the upper and the lower floret of each spikelet. Dev Genes Evol 209: 411-420.
5. Camus-Kulandaivelu L, Veyrieras JB, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A (2006) Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene. Genetics 172: 2449-2463.
6. Camus-Kulandaivelu L, Veyrieras JB, Gouesnard B, Charcosset A, Manicacci D (2007) Evaluating the reliability of structure outputs in case of relatedness between individuals. Crop Sci 47: 887-890.
7. Cavanagh C, Morell M, Mackay I, Powell W (2008) From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. Curr Opin Plant Biol 11: 215-221.
8. Chessel D, Dufour AB, Thioulouse J (2004) The ade4 package-I-one-table methods. R News 4: 5-10.
9. Corander J, Waldmann P, Sillanpää MJ (2003) Bayesian analysis of genetic differentiation between populations. Genetics 163: 367-374.
10. Danilevskaya ON, Meng X, Selinger DA, Deschamps S, Hermon P, Vansant G, Gupta R, Ananiev EV, Muszynski MG (2008) Involvement of the MADS-Box Gene ZMM4 in floral induction and inflorescence development in maize. Plant Physiol 147: 2054-2069.
11. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55: 997-1004.
12. Ducrocq S, Madur D, Veyrieras JB, Camus-Kulandaivelu L, Kloiber-Maitz M, Presterl T, Ouzunova M, Domenica M, Charcosset A (2008) Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information. Genetics 178: 2433-2437.
13. Ersoz ES, Yu J, Buckler ES (2007) Applications of linkage disequilibrium and association mapping in crop plants. Genomics-assisted crop improvement. Springer, The Netherlands.
14. 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.
15. Falque M, Décousset L, Dervins D, Jacob AM, Joets J, Martinant JP, Raffoux X, Ribière N, Ridel C, Samson D, Charcosset A, Murigneux A (2005) Linkage mapping of 1454 new maize candidate gene loci. Genetics 170: 1957-1966.
16. 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.
17. Flint-Garcia SA, Thuillet AC, Yu J, Pressoir G, Romero SM, Sharon EM, 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. Hamblin MT, Warburton ML, Buckler ES (2007) Empirical comparison of simple sequence repeats and single nucleotide polymorphisms in assessment of maize diversity and relatedness. PLoS One 2(12): e1367.
19. Hannah LC (2007) Starch formation in the cereal endosperm. Endosperm: developmental and molecular biology, vol 8. Springer, Berlin/Heidelberg, pp 179-193.
20. Hedge VL, Olkin I (1985) Statistical methods for meta-analysis. Academic Press, London.
21. Heuer S, Lörz H, Dresselhaus T (2000) The MADS box gene ZmMADS 2 is specifically expressed in maize pollen and during maize pollen tube growth. Sex Plant Reprod 13: 21-27.
22. Heuertz M, Hausman JF, Hardy OJ, Vendramin GG, Frascaria-Lacoste N, Vekemans X (2004) Nuclear microsatellites reveal contrasting patterns of genetic structure between Western and Southeastern European populations of the common ash (Fraxinus excelsior L.). Evolution 58(5): 976-988.
23. Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic association studies. Genet Med 4(2): 45-61.
24. Khoury MJ, Bertram L, Boffetta P, Butterworth AS, Chanock SJ, Dolan SM, Fortier I, Garcia-Closas M, Gwinn M, Higgins JPT, Janssens ACJW, Ostell J, Owen RP, Pagon RA, Rebbeck TR, Rothman N, Bernstein JL, Burton PR, Campbell H, Chockalingam A, Furberg H, Little J, O'Brien TR, Seminara D, Vineis P, Winn DM, Yu W, Ioannidis JPA (2009) Genome-wide association studies, field synopses, and the development of the knowledge base on genetic variation and human diseases. Am J Epidemiol 170(3): 269-279.
25. Lia VV, Poggio L, Confalonieri VA (2009) Microsatellite variation in maize landraces from Northwestern Argentina: genetic diversity, population structure and racial affiliations. Theor Appl Genet 119: 1053-1067.
26. Lin CH, Yeakley JM, McDaniel TK, Shen R (2008) Medium- to high-throughput SNP genotyping using VeraCode Microbeads in DNA and RNA profiling in human blood. Methods Protoc 496: 129-142.
27. Loiselle BA, Sork VL, Nason J, Graham G (1995) Spatial genetic structure of a tropical understory shrub, Psychotria officinalis (Rubiaceae). Am J Bot 82: 1420-1425.
28. Lu Y, Yan J, Guimarães CT, Taba S, Hao Z, Gao S, Chen S, Li J, Zhang S, Vivek BS, Magorokosho C, Mugo S, Makumbi D, Parentoni SN, Shah T, Rong T, Crouch JH, Xu Y (2009) Molecular characterization of global maize breeding germplasm based on genome-wide single nucleotide polymorphisms. Theor Appl Genet 120: 93-115.
29. Maenhout S, De Baets B, Haesaert G (2009) Marker-based estimation of the coefficient of coancestry in hybrid breeding programmes. Theor Appl Genet 118: 1181-1192.
30. Manicacci D, Camus-Kulandaivelu L, Fourmann M, Arar C, Barrault S, Rousselet A, Feminias N, Consoli L, Francès L, Méchin V, Murigneux A, Prioul J, Charcosset A, Damerval C (2009) Epistatic interactions between Opaque2 transcriptional activator and its target gene CyPPDK1 control kernel trait variation in maize. Plant Physiol 150: 506-520.
31. Matsuoka Y, Vigouroux Y, Goodman MM, Sanchez JG, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. PNAS 99(9): 6080-6084.
32. McVean G (2009) A genealogical interpretation of principal components analysis. PLoS Genet 5(10): e1000686.
33. Nelson OE, Rines HW (1962) The enzymatic deficiency in the waxy mutant of maize. Biochem Biophys Res Commun 9: 297-300.
34. Patterson N, Price AL, Reich D (2006) Population structure and eigenanalysis. PloS Genet 2(12): e190.
35. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8): 904-909.
36. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
37. Pritchard JK, Wen X, Falush D (2007) Documentation for structure software: version 2. 2. http://pritch. bsd. uchicago. edu/software.
38. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. PNAS 98(20): 11479-11484.
39. Ritland K (1996) Estimators for pairwise relatedness and inbreeding coefficients. Genet Res 67: 175-186.
40. Schwarz G (1978) Estimating dimension of a model. Ann Stat 6: 461-464.
41. Shendure J, Ji H (2008) Next-generation DNA sequencing. Nat Biotechnol 26: 1135-1145.
42. Steemers FJ, Gunderson KL (2007) Whole genome genotyping technologies on the BeadArrayTM platform. Biotechnol J 2: 41-49.
43. Stich B, Melchinger AE (2009) Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis. BMC Genomics 10: 94.
44. Stich B, Möhring J, Piepho HP, Heckenberger M, Buckler ES, Melchinger AE (2008) Comparison of mixed-model approaches for association mapping. Genetics 178: 1745-1754.
45. Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc Ser B 64: 479-498.
46. Tenaillon MI, Sawkins MC, Long AD, Gaut RL, Doebley JF, Gaut BS (2001) Patterns of DNA sequence polymorphism along chromosome 1 of Maize (Zea mays ssp. mays L.). PNAS 98(16): 9161-9166.
47. Tenenhaus M, Young F (1985) An analysis and synthesis of multiple correspondence analysis, optimal scaling, dual scaling, homogeneity analysis and other methods for quantifying categorical multivariate data. Psychometrika 50: 91-119.
48. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28: 286-289.
49. Tracy CA, Widom H (1994) Level spacing distributions and the airy kernel. Commun Math Phys 159: 151-174.
50. Wang R, Yu Y, Zhao J, Shi Y, Song Y, Wang T, Li Y (2008) Population structure and linkage disequilibrium of a mini core set of maize inbred lines in China. Theor Appl Genet 117: 1141-1153.
51. Wang J, Lin M, Crenshaw A, Hutchinson A, Hicks B, Yeager M, Berndt S, Huang WY, Hayes RB, Chanock SJ, Jones RC, Ramakrishnan R (2009) High-throughput single nucleotide polymorphism genotyping using nanofluidic dynamic arrays. BMC Genomics 10: 561.
52. Yu J, 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.
53. Yu J, Holland JB, McMullen MD, Buckler ES (2008) Genetic design and statistical power of nested association mapping in maize. Genetics 178: 539-551.
54. Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, Tang C, Toomajian C, Zheng H, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3(1): e4.
55. Zhu C, Yu J (2009) Nonmetric multidimensional scaling corrects for population structure in association mapping with different sample types. Genetics 182: 875-888.
56. Zhu C, Gore M, Buckler ES, Yu J (2008) Status and prospects of association mapping in plants. Plant Genome 1: 5-20.