Advertisement

Applications of Linkage Disequilibrium and Association Mapping in Maize

  • Elhan S. Ersoz
  • Jianming YuEmail author
  • Edward S. Buckler
Part of the Biotechnology in Agriculture and Forestry book series (AGRICULTURE, volume 63)

Association mapping, also known as linkage disequilibrium mapping, is a relatively new and promising genetic method for complex trait dissection. Association map ping has the promise of higher mapping resolution through exploitation of historical recombination events at the population level, that may enable gene level mapping on non-model organisms where linkage-based approaches would not be feasible (Risch and Merikangas 1996; Nordborg and Tavare 2002).

Association mapping utilizes ancestral recombinations and natural genetic diver sity within a population to dissect quantitative traits and is built on the basis of the linkage disequilibrium concept (Geiringer 1944; Lewontin and Kojima 1960). One of the working definitions of linkage disequilibrium (which here on will be referred to as LD) is the non-random co-segregation of alleles at two loci.

Keywords

Quantitative Trait Locus Linkage Disequilibrium Association Mapping Transmission Disequilibrium Test Association Population 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abecasis GR, Cookson WO, Cardon LR (2001) The power to detect linkage disequilibrium with quantitative traits in selected samples. Am J Hum Genet 68:1463–1474PubMedCrossRefGoogle Scholar
  2. Ackerman H, Usen S, Mott R, Richardson A, Sisay-Joof F, Katundu P, Taylor T, Ward R, Molyneux M, Pinder M, Kwiatkowski DP (2003) Haplotypic analysis of the TNF locus by association efficiency and entropy. Genome Biol 4:R24PubMedCrossRefGoogle Scholar
  3. Allison DB (1997) Transmission-disequilibrium tests for quantitative traits. Am J Hum Genet 60:676–690PubMedGoogle Scholar
  4. Andersen JR, Schrag T, Melchinger AE, Zein I, Lubberstedt T (2005) Validation of Dwarf8 poly morphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.). Theor Appl Genet 111:206–217PubMedCrossRefGoogle Scholar
  5. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Dean C, Marjoram P, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1:e60PubMedCrossRefGoogle Scholar
  6. Baltunis BS, Huber DA, White TL, Golfard B, Stelzer HE (2005) Genetic effects of rooting loblolly pine stem cuttings from a partial diallel mating design. Can J Forest 35:1098–1108CrossRefGoogle Scholar
  7. Bamshad M, Wooding S, Salisbury BA, Stephens JC (2004) Deconstructing the relationship be tween genetics and race. Nat Rev Genet 5:598–609PubMedCrossRefGoogle Scholar
  8. Barrett JC, Cardon LR (2006) Evaluating coverage of genome-wide association studies. Nat Genet 38:659–662PubMedCrossRefGoogle Scholar
  9. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate — a practical and powerful approach to multiple testing. J R Stat Soc Series B 57:289–300Google Scholar
  10. Blott S, Kim JJ, Moisio S, Schmidt-Kuntzel A, Cornet A, Berzi P, Cambisano N, Ford C, Grisart B, Johnson D, Karim L, Simon P, Snell R, Spelman R, Wong J, Vilkki J, Georges M, Farnir F, Coppieters W (2003) Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone recep tor is associated with a major effect on milk yield and composition. Genetics 163:253– 266PubMedGoogle Scholar
  11. Blouin JD (2003) DNA-based methods for pedigree reconstruction and kinship analysis in natural populations. Trends Ecol Evol 18:503–511CrossRefGoogle Scholar
  12. Breseghello F, Sorrells ME (2006a) Association mapping of kernel size and milling quality in wheat (Triticum aestivum L.) cultivars. Genetics 172:1165–1177CrossRefGoogle Scholar
  13. Breseghello F, Sorrells M (2006b) Association analysis as a strategy for improvement of quantita tive traits in plants. Crop Sci 46:1323–1330CrossRefGoogle Scholar
  14. Buckner B, Kelson TL, Robertson DS (1990) Cloning of the y1 locus of maize, a gene involved in the biosynthesis of carotenoids. Plant Cell 2:867–876PubMedCrossRefGoogle Scholar
  15. Buckner B, Miguel PS, Janick-Buckner D, Bennetzen JL (1996) The y1 gene of maize codes for phytoene synthase. Genetics 143:479–488PubMedGoogle Scholar
  16. Caldwell KS, Langridge P, Powell W (2004) Comparative sequence analysis of the region harboring the hardness locus in barley and its colinear region in rice. Plant Physiol 136: 3177–3190PubMedCrossRefGoogle Scholar
  17. Caldwell KS, Russell J, Langridge P, Powell W (2006) Extreme population-dependent linkage disequilibrium detected in an inbreeding plant species, Hordeum vulgare. Genetics 172:557–567PubMedCrossRefGoogle Scholar
  18. 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 172:2449–2463PubMedCrossRefGoogle Scholar
  19. Chen L, Storey JD (2006) Relaxed significance criteria for linkage analysis. Genetics 173:2371–2381PubMedCrossRefGoogle Scholar
  20. Ching A, Caldwell KS, Jung M, Dolan M, Smith OS, Tingey S, Morgante M, Rafalski AJ (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet 3:19PubMedCrossRefGoogle Scholar
  21. Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Ge netics 138:963–971Google Scholar
  22. Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype struc ture in the human genome. Nat Genet 29:229–232PubMedCrossRefGoogle Scholar
  23. Devlin B, Roeder K (1999) Genomic control for association studies. Biometrics 55:997–1004PubMedCrossRefGoogle Scholar
  24. Devlin B, Roeder K, Wasserman L (2001) Genomic control, a new approach to genetic-based association studies. Theor Popul Biol 60:155–166PubMedCrossRefGoogle Scholar
  25. Devlin B, Bacanu SA, Roeder K (2004) Genomic control to the extreme. Nat Genet 36:1129–1130; author reply 1131PubMedCrossRefGoogle Scholar
  26. Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative char acter. Genetics 142:285–294PubMedGoogle Scholar
  27. Emik LO, Terrill CE (1949) Systematic procedures for calculating inbreeding coefficients. J Hered 40:51–55PubMedGoogle Scholar
  28. Ersoz ES (2006) Candidate gene-association mapping for dissecting fungal disease resistance in loblolly pine. PhD Dissertation in Genetics, University of California, DavisGoogle Scholar
  29. Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374PubMedCrossRefGoogle Scholar
  30. Flint-Garcia SA, Thuillet AC, Yu J, 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 44:1054–1064PubMedCrossRefGoogle Scholar
  31. Forton J, Kwiatkowski D, Rockett K, Luoni G, Kimber M, Hull J (2005) Accuracy of haplotype reconstruction from haplotype-tagging single-nucleotide polymorphisms. Am J Hum Genet 76:438–448PubMedCrossRefGoogle Scholar
  32. Fulker DW, Cherny SS, Sham PC, Hewitt JK (1999) Combined linkage and association sib-pair analysis for quantitative traits. Am J Hum Genet 64:259–267PubMedCrossRefGoogle Scholar
  33. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225–2229PubMedCrossRefGoogle Scholar
  34. Geiringer H (1944) On the probability theory of linkage in Mendelian heredity. Ann Math Stat 15(1)25–57CrossRefGoogle Scholar
  35. Golding GB (1984) The sampling distribution of linkage disequilibrium. Genetics 108:257–274PubMedGoogle Scholar
  36. Gonzaléz-Martinéz SC, Wheeler N, Ersoz ES, Neale DB (2006) Association genetics in Pinus taeda L.I. Wood property traits. Genetics 175:399–409PubMedCrossRefGoogle Scholar
  37. Halldorsson BV, Bafna V, Lippert R, Schwartz R, De La Vega FM, Clark AG, Istrail S (2004) Optimal haplotype block-free selection of tagging SNPs for genome-wide association studies.Genome Res 14:1633–1640PubMedCrossRefGoogle Scholar
  38. Hamblin MT, Salas Fernandez MG, Casa AM, Mitchell SE, Paterson AH, Kresovich S (2005) Equilibrium processes cannot explain high levels of short- and medium-range linkage disequi librium in the domesticated grass Sorghum bicolor. Genetics 171:1247–1256PubMedCrossRefGoogle Scholar
  39. Harjes CE, Rocheford TR, Bai L,, Brutnell TP, Kandianis CB, Sowinski SG, Stapleton AE, Val-labhaneni R, Williams M, Wurtzel ET, Yan J, Buckler ES (2008 ) Natural genetic variation in lycopene epsilon cyclase tapped for maize biofortification. Science 319(5861):330–333PubMedCrossRefGoogle Scholar
  40. Hedrick PW (1987) Gametic disequilibrium measures — proceed with caution. Genetics 117:331– 341PubMedGoogle Scholar
  41. Henderson CR (1975) Best linear unbiased estimation and prediction under a selection model. Biometrics 31:423–447PubMedCrossRefGoogle Scholar
  42. Henderson CR (1976) Simple method for computing inverse of a numerator relationship matrix used in prediction of breeding values. Biometrics 32:69–83CrossRefGoogle Scholar
  43. Henderson CR (1984) Application of linear models in animal breeding. University of Guelph, GuelphGoogle Scholar
  44. Herbert A, Gerry NP, McQueen MB, Heid IM, Pfeufer A, Illig T, Wichmann HE, Meitinger T, Hunter D, Hu FB, Colditz G, Hinney A, Hebebrand J, Koberwitz K, Zhu X, Cooper R, Ardlie K, Lyon H, Hirschhorn JN, Laird NM, Lenburg ME, Lange C, Christman MF (2006) A common genetic variant is associated with adult and childhood obesity. Science 312:279–283PubMedCrossRefGoogle Scholar
  45. Hill WG, Robertson A (1968) Linkage disequilibrium in finite populations. Theor Appl Genet 38:226–231CrossRefGoogle Scholar
  46. Hirschhorn JN, Daly MJ (2005) Genome-wide association studies for common diseases and com plex traits. Nat Rev Genet 6:95–108PubMedCrossRefGoogle Scholar
  47. Holte S, Quiaoit F, Hsu L, Davidov O, Zhao LP (1997) A population based family study of a common oligogenic disease — part I: association/aggregation analysis. Genet Epidemiol 14:803– 807PubMedCrossRefGoogle Scholar
  48. Horvath S, Xu X, Laird NM (2001) The family based association test method: strategies for study ing general genotype—phenotype associations. Eur J Hum Genet 9:301–306PubMedCrossRefGoogle Scholar
  49. Hudson RR (1985) The sampling distribution of linkage disequilibrium under an infinite allele model without selection. Genetics 109:611–631PubMedGoogle Scholar
  50. Hudson RR (2001) Two-locus sampling distributions and their application. Genetics 159:1805– 1817PubMedGoogle Scholar
  51. Johnson GC, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RC, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SC, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29:233–237PubMedCrossRefGoogle Scholar
  52. Jung M, Ching A, Bhattramakki D, Dolan M, Tingey S, Morgante M, Rafalski A (2004) Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm. Theor Appl Genet 109:681–689PubMedCrossRefGoogle Scholar
  53. Karayiorgou M, Sobin C, Blundell ML, Galke BL, Malinova L, Goldberg P, Ott J, Gogos JA (1999) Family-based association studies support a sexually dimorphic effect of COMT and MAOA on genetic susceptibility to obsessive-compulsive disorder. Biol Psychiatry 45:1178–1189PubMedCrossRefGoogle Scholar
  54. Kayihan GC, Huber DA, Morse AM, White TL, Davis JM (2005) Genetic dissection of fusiform rust and pitch canker disease traits in loblolly pine. Theor Appl Genet 110:948–958PubMedCrossRefGoogle Scholar
  55. Ke X, Cardon LR (2003) Efficient selective screening of haplotype tag SNPs. Bioinformatics 19:287–288PubMedCrossRefGoogle Scholar
  56. Kennedy B, Quinton M, Vanarendonk J (1992) Estimation of effects of single genes on quantitative traits. J Anim Sci 70:2000–2012PubMedGoogle Scholar
  57. Laird NM, Lange C (2006) Family-based designs in the age of large-scale gene-association studies. Nat Rev Genet 7:385–394PubMedCrossRefGoogle Scholar
  58. Laird NM, Horvath S, Xu X (2000) Implementing a unified approach to family-based tests of association. Genet Epidemiol 19:S36–S42PubMedCrossRefGoogle Scholar
  59. Lake SL, Blacker D, Laird NM (2000) Family-based tests of association in the presence of linkage. Am J Hum Genet 67:1515–1525PubMedCrossRefGoogle Scholar
  60. Lange C, Lyon H, DeMeo D, Raby B, Silverman EK, Weiss ST (2003) A new powerful non-parametric two-stage approach for testing multiple phenotypes in family-based association stud ies. Hum Hered 56:10–17PubMedCrossRefGoogle Scholar
  61. Lewis CM (2002) Genetic association studies: design, analysis and interpretation. Brief Bioinform 3:146–153PubMedCrossRefGoogle Scholar
  62. Lewontin RC (1988) On measures of gametic disequilibrium. Genetics 120:849–852PubMedGoogle Scholar
  63. Lewontin RC, Kojima K (1960) The evolutionary dynamics of complex polymorphisms. Evolution 14:458–472CrossRefGoogle Scholar
  64. Long AD, Langley CH (1999) The power of association studies to detect the contribution of can didate genetic loci to variation in complex traits. Genome Res 9:720–731PubMedGoogle Scholar
  65. Lukens L, Doebley J (2001) Molecular evolution of the teosinte branched gene among maize and related grasses. Mol Biol Evol 18:627–638PubMedGoogle Scholar
  66. Lynch M, Ritland K (1999) Estimation of pairwise relatedness with molecular markers. Genetics 152:1753–1766PubMedGoogle Scholar
  67. Maccaferri M, Sanguineti MC, Noli E, Tuberosa R (2005) Population structure and long-range disequilibrium in a durum wheat elite collection. Mol Breed 15:271–290CrossRefGoogle Scholar
  68. Meuwissen TH, Goddard ME (1997) Estimation of effects of quantitative trait loci in large complex pedigrees. Genetics 146:409–416PubMedGoogle Scholar
  69. Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic re gions by using segregating populations. Proc Natl Acad Sci USA 88:9828–9832PubMedCrossRefGoogle Scholar
  70. Monks SA, Kaplan NL, Weir BS (1998) A comparative study of sibship tests of linkage and/or association. Am J Hum Genet 63:1507–1516PubMedCrossRefGoogle Scholar
  71. Mueller J (2004) Linkage disequilibrium for different scales and applications. Brief Bioinfo 5:355– 364CrossRefGoogle Scholar
  72. Niebur W, Rafalski JA, Smith OS, Cooper M (2004) New directions for a diverse planet. Proceed ings of the 4th International Crop Science Congress, BrisbaneGoogle Scholar
  73. Nordborg M (2000) Linkage disequilibrium, gene trees, selfing: an ancestral recombination graph with partial self-fertilization. Genetics 154:923–929PubMedGoogle Scholar
  74. Nordborg M, Tavare S (2002) Linkage disequilibrium: what history has to tell us. Trends Genet 18:83–90PubMedCrossRefGoogle Scholar
  75. Nordborg M, Borevitz JO, Bergelson J, Berry CC, Chory J, Hagenblad J, Kreitman M, Maloof JN, Noyes T, Oefner PJ, Stahl EA, Weigel D (2002) The extent of linkage disequilibrium inArabidopsis thaliana. Nat Genet 30:190–193PubMedCrossRefGoogle Scholar
  76. Nordborg M, Hu TT, Ishino Y, Jhaveri J, Toomajian C, Zheng H, Bakker E, Calabrese P, Gladstone J, Goyal R, Jakobsson M, Kim S, Morozov Y, Padhukasahasram B, Plagnol V, Rosenberg NA, Shah C, Wall JD, Wang J, Zhao K, Kalbfleisch T, Schulz V, Kreitman M, Bergelson J (2005) The pattern of polymorphism inArabidopsis thaliana. PLoS Biol 3:e196PubMedCrossRefGoogle Scholar
  77. Oliehoek PA, Windig JJ, van Arendonk JA, Bijma P (2006) Estimating relatedness between in dividuals in general populations with a focus on their use in conservation programs. Genetics 173:483–496PubMedCrossRefGoogle Scholar
  78. Olsen KM, Halldorsdottir SS, Stinchcombe JR, Weinig C, Schmitt J, Purugganan MD (2004) Link age disequilibrium mapping of Arabidopsis CRY2 flowering time alleles. Genetics 167:1361– 1369PubMedCrossRefGoogle Scholar
  79. Palaisa KA, Morgante M, Williams M, Rafalski A (2003) Contrasting effects of selection on se quence diversity and linkage disequilibrium at two phytoene synthase loci. Plant Cell 15:1795– 1806PubMedCrossRefGoogle Scholar
  80. Palaisa K, Morgante M, Tingey S, Rafalski A (2004) Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. Proc Natl Acad Sci USA 101:9885–9890PubMedCrossRefGoogle Scholar
  81. Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742PubMedGoogle Scholar
  82. Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjorib-anks C, McDonough DP, Nguyen BT, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SP, Cox DR (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719–1723PubMedCrossRefGoogle Scholar
  83. Pe'er I, Chretien YR, de Bakker PI, Barrett JC, Daly MJ, Altshuler DM (2006) Biases and rec onciliation in estimates of linkage disequilibrium in the human genome. Am J Hum Genet 78:588–603PubMedCrossRefGoogle Scholar
  84. Podlich D, Winkler C, Cooper M (2004) Mapping as you go. Crop Sci 44:1560–1571Google Scholar
  85. Price AH (2006) Believe it or not, QTLs are accurate! Trends Plant Sci 11:213–216PubMedCrossRefGoogle Scholar
  86. Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal compo nents analysis corrects for stratification in genome-wide association studies. Nat Genet 38:904– 909PubMedCrossRefGoogle Scholar
  87. Pritchard JK (2001) Deconstructing maize population structure. Nat Genet 28:203–204PubMedCrossRefGoogle Scholar
  88. Pritchard JK, Przeworski M (2001) Linkage disequilibrium in humans: models and data. Am J Hum Genet 69:1–14PubMedCrossRefGoogle Scholar
  89. Pritchard JK, Stephens M, Donnelly P (2000a) Inference of population structure using multilocus genotype data. Genetics 155:945–959Google Scholar
  90. Pritchard JK, Stephens M, Rosenberg NA, Donnelly P (2000b) Association mapping in structured populations. Am J Hum Genet 67:170–181CrossRefGoogle Scholar
  91. Rabinowitz D (1997) A transmission disequilibrium test for quantitative trait loci. Hum Hered 47:342–350PubMedCrossRefGoogle Scholar
  92. Remington DL, Ungerer MC, Purugganan MD (2001a) Map-based cloning of quantitative trait loci: progress and prospects. Genet Res 78:213–218CrossRefGoogle Scholar
  93. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001b) Structure of linkage disequilibrium and phenotypic associ ations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484CrossRefGoogle Scholar
  94. Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517PubMedCrossRefGoogle Scholar
  95. Sebastiani P, Lazarus R, Weiss ST, Kunkel LM, Kohane IS, Ramoni MF (2003) Minimal haplotype tagging. Proc Natl Acad Sci USA 100:9900–9905PubMedCrossRefGoogle Scholar
  96. Shaw SH, Carrasquillo MM, Kashuk C, Puffenberger EG, Chakravarti A (1998) Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Res 8:111–123PubMedGoogle Scholar
  97. Spielman RS, McGinnis RE, Ewens WJ (1993) Transmission test for linkage disequilibrium: the insulin gene region and insulin-dependent diabetes mellitus (IDDM). Am J Hum Genet 52:506– 516PubMedGoogle Scholar
  98. Spielman RS, McGinnis RE, Ewens WJ (1994) The transmission/disequilibrium test detects coseg-regation and linkage. Am J Hum Genet 54:559–560; author reply 560–553PubMedGoogle Scholar
  99. Stich B, Melchinger AE, Piepho H-P, Heckenberger M, Maurer HP, Reif JC (2006) New test for family-based association mapping with inbred lines from plant breeding programs. Theor Appl Genet 113(6):1121–1130PubMedCrossRefGoogle Scholar
  100. Storey JD (2002) A direct approach to false discovery rates. J R Stat Soc Series B 64(3):479–498CrossRefGoogle Scholar
  101. Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. P Natl Acad Sci USA 100:9440–9445CrossRefGoogle Scholar
  102. Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic fac tors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132:823–839PubMedGoogle Scholar
  103. Szalma SJ, Buckler ES, Snook ME, McMullen MD (2005) Association analysis of candidate genes for maysin and chlorogenic acid accumulation in maize silks. Theor Appl Genet 110:1324–1333PubMedCrossRefGoogle Scholar
  104. 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. maysL.). Proc Natl Acad Sci USA 98:9161–9166PubMedCrossRefGoogle Scholar
  105. Tenaillon MI, Sawkins MC, Anderson LK, Stack SM, Doebley J, Gaut BS (2002) Patterns of diversity and recombination along chromosome 1 of maize (Zea mays ssp. maysL.). Genetics 162:1401–1413PubMedGoogle Scholar
  106. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Nielsen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  107. Thumma BR, Nolan MF, Evans R, Moran GF (2005) Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle inEucalyptusspp. Genetics 171:1257–1265PubMedCrossRefGoogle Scholar
  108. Tracy WF, Whitt SR, Buckler ES (2006) Recurrent mutation and genome evolution: example ofSugary1and the origin of sweet maize. Crop Sci 46:1–7CrossRefGoogle Scholar
  109. Thornsberry JM, Goodman MM, Doebley J, Kresovich S, Niel sen D, Buckler ES (2001) Dwarf8 polymorphisms associate with variation in flowering time. Nat Genet 28:286–289PubMedCrossRefGoogle Scholar
  110. Thumma BR, Nolan MF, Evans R, Moran GF (2005) Polymorphisms in cinnamoyl CoA reductase (CCR) are associated with variation in microfibril angle in Eucalyptus spp. Genetics 171:1257–1265PubMedCrossRefGoogle Scholar
  111. Tracy WF, Whitt SR, Buckler ES (2006) Recurrent mutation and genome evolution: example of Sugary1 and the origin of sweet maize. Crop Sci 46:1–7CrossRefGoogle Scholar
  112. Wall JD, Pritchard JK (2003) Haplotype blocks and linkage disequilibrium in the human genome. Nat Rev Genet 4:587–597PubMedCrossRefGoogle Scholar
  113. Wang H, Nussbaum-Wagler T, Li B, Zhao Q, Vigouroux Y, Faller M, Bomblies K, Lukens L, Doebley JF (2005) The origin of the naked grains of maize. Nature 436:714–719PubMedCrossRefGoogle Scholar
  114. Wang J (2002) An estimator for pairwise relatedness using molecular markers. Genetics 160:1203–1215PubMedGoogle Scholar
  115. Wang Y, Rannala B (2005) In silico analysis of disease-association mapping strategies using the coalescent process and incorporating ascertainment and selection. Am J Hum Genet 76:1066–1073PubMedCrossRefGoogle Scholar
  116. Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733PubMedCrossRefGoogle Scholar
  117. Wright SI, Gaut BS (2005) Molecular population genetics and the search for adaptive evolution in plants. Mol Biol Evol 22:506–519PubMedCrossRefGoogle Scholar
  118. Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, Gaut BS (2005) The effects of artificial selection on the maize genome. Science 308:1310–1314PubMedCrossRefGoogle Scholar
  119. Yu J, Holland JB, McMullen MD, Buckler ES (2006a) Genetic design and statistical power of nested association mapping in maize genetics. Nat Genetics 178:539–551Google Scholar
  120. Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006b) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208CrossRefGoogle Scholar
  121. Zhang K, Jin L (2003) HaploBlockFinder: haplotype block analyses. Bioinformatics 19:1300–1301PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, B.V 2009

Authors and Affiliations

  • Elhan S. Ersoz
    • 1
  • Jianming Yu
    • 2
    Email author
  • Edward S. Buckler
    • 3
    • 4
  1. 1.Institute for Genomic DiversityCornell UniversityIthacaUSA
  2. 2.Department of AgronomyKansas State UniversityManhattenUSA
  3. 3.USDA-ARS, US PlantSoil and Nutrition LaboratoryIthacaUSA
  4. 4.Institute for Genomic Diversity159 Biotechnology, Cornell UniversityIthacaUSA

Personalised recommendations