M. Aitkin and D. Rubin, Estimation and Hypothesis Testing in Finite Mixture Models, Journal of the Royal Statistical Society, vol.47, pp.67-75, 1985.

H. Akaike, Information theory and an extension of the maximum likelihood principle, 2nd Inter. Symp. on Information Theory, pp.267-281, 1973.

H. Akaike, Theory and an Extension of the Maximum Likelihood Principle, Breakthroughs in Statistics, vol.1, pp.610-624, 1992.

D. B. Allison and M. Heo, Meta-analysis of linkage data under worst-case conditions : a demonstration using the human OB region, Genetics, vol.148, pp.859-865, 1998.

J. R. Andersen, T. Schrag, A. E. Melchinger, I. Zein, and T. Lubberstedt, Validation of Dwarf8 polymorphisms associated with flowering time in elite European inbred lines of maize (Zea mays L.), Theoretical and Applied Genetics, vol.28, issue.Suppl, 2005.
DOI : 10.1007/s00122-005-1996-6

E. Anderson and W. L. Brown, The history of the common maize varieties of the united states corn belt, Agricultural History, vol.26, pp.2-8, 1952.

E. C. Anderson and J. Novembre, Finding Haplotype Block Boundaries by Using the Minimum-Description-Length Principle, The American Journal of Human Genetics, vol.73, issue.2, pp.336-354, 2003.
DOI : 10.1086/377106

C. F. Aquadro, S. F. Desse, M. M. Bland, C. H. Langley, and C. C. Laurie-ahlberg, Molecular population genetics of the alcohol dehydrogenase gene region of Drosophila melanogaster, Genetics, vol.114, pp.1165-1190, 1986.

A. Arcade, A. Labourdette, M. Falque, B. Mangin, and F. Chardon, BioMercator: integrating genetic maps and QTL towards discovery of candidate genes, Bioinformatics, vol.20, issue.14, pp.2324-2326, 2004.
DOI : 10.1093/bioinformatics/bth230

Y. Barriere, G. Aurel, M. Briand, D. Denoue, and A. Gueu, QTL mapping for cell wall constituents and cell wall digestibility in maize recombinant inbred line progeny F838 X F286 harvested at an early forage stage of maturity, 2005.

M. A. Beaumont, Recent developments in genetic data analysis: what can they tell us about human demographic history?, Heredity, vol.92, issue.5, pp.365-379, 2004.
DOI : 10.1038/sj.hdy.6800447

W. Beavis, The power and deceit of QTL experiments : lessons from comparative QTL studies, Proceedings of the Forty-Ninth Annual Corn and Sorghum Industry Research Conference. American Seed Trade Association, pp.250-266, 1994.

Y. Benjamini and Y. Hochberg, Controlling the False Discovery Rate : a pratical and powerful approach to multiple testing, Journal of the Royal Statistical Society, Series B, vol.57, pp.289-300, 1995.

Y. Benjamini and D. Yekutieli, Quantitative Trait Loci Analysis Using the False Discovery Rate, Genetics, vol.171, issue.2, pp.783-790, 2005.
DOI : 10.1534/genetics.104.036699

C. Biernacki and G. Govaert, Choosing models in model-based clustering and discriminant analysis, Journal of Statistical Computation and Simulation, vol.2, issue.1, 1998.
DOI : doi: 10.1214/aos/1176344136
URL : https://hal.archives-ouvertes.fr/inria-00073175

G. Blanc, L. Moreau, B. Mangin, and A. Charcosset, QTL detection in connected populations of maize, 12th Meeting of the EUCARPIA Section of Biometrics in Plant Breeding, 2003.

I. R. Boddeker, H. H. Muller, R. Kress, F. Geller, and A. Ziegler, The use of sequential designs in genome scans for asthma susceptibility loci with affected sib pairs, Genet Epidemiol, vol.21, issue.1, pp.49-54, 2001.

M. Bohn, M. M. Khairallah, D. Gonzalez-de-leon, D. Hoisington, and H. F. Utz, QTL Mapping in Tropical Maize: I. Genomic Regions Affecting Leaf Feeding Resistance to Sugarcane Borer and Other Traits, Crop Science, vol.36, issue.5, pp.1352-1361, 1996.
DOI : 10.2135/cropsci1996.0011183X003600050045x

M. Bohn, B. Schulz, R. Kreps, D. Klein, and A. E. Melchinger, QTL Mapping of resistance agaisnt the European corn borer (Ostrinia nubilalis H.) in early maturing European dent germplasm, Theor. Appl. Genet, vol.1001, pp.907-917, 2000.

A. Bouchez, F. Hospital, M. Causse, A. Gallais, and A. Charcosset, Marker-assisted introgression of favorable alleles at quantitative trait loci between maize elite lines, Genetics, vol.162, pp.1945-1959, 2002.

H. Bozdogan, Model selection and Akaike's Information Criterion (AIC): The general theory and its analytical extensions, Psychometrika, vol.10, issue.2, pp.345-370, 1987.
DOI : 10.1007/BF02294361

H. Bozdogan, On the information-based measure of covariance complexity and its application to the evaluation of multivariate linear models, Communications in Statistics - Theory and Methods, vol.27, issue.3, pp.221-278, 1990.
DOI : 10.1080/03610928308828569

E. S. Buckler and J. M. Thornsberry, Plant molecular diversity and applications to genomics, Current Opinion in Plant Biology, vol.5, issue.2, pp.107-111, 2002.
DOI : 10.1016/S1369-5266(02)00238-8

W. Buntine, Variational Extensions to EM and Multinomial PCA, 2002.
DOI : 10.1007/3-540-36755-1_3
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.18.5167

W. Buntine and A. Jakulin, Applying discrete PCA in data analysis, 2004.

J. B. Buntjer, A. P. Sorensen, and J. D. Peleman, Haplotype diversity: the link between statistical and biological association, Haplotype diversity : the link between statistical and biological association, pp.466-471, 2005.
DOI : 10.1016/j.tplants.2005.08.007

K. P. Burnham and D. R. Anderson, Model Selection and Multimodel Inference : A Pratical Information-Theoretical Approach, 2002.
DOI : 10.1007/b97636

L. Camus-kulandaivelu, J. Veyrieras, D. Madur, V. Combes, and M. Fourmann, Maize Adaptation to Temperate Climate: Relationship Between Population Structure and Polymorphism in the Dwarf8 Gene, Genetics, vol.172, issue.4, pp.2449-2463, 2006.
DOI : 10.1534/genetics.105.048603

A. J. Cardinal, M. Lee, N. Sharopova, W. L. Woodman-clikeman, and M. J. Long, Genetic Mapping and Analysis of Quantitative Trait Loci for Resistance to Stalk Tunneling by the European Corn Borer in Maize, Crop Science, vol.41, issue.3, pp.835-845, 2001.
DOI : 10.2135/cropsci2001.413835x

C. S. Carlson, M. A. Eberle, L. Kruglyak, and D. A. Nickerson, Mapping complex disease loci in whole-genome association studies, Nature, vol.3, issue.6990, pp.446-452, 2004.
DOI : 10.1161/01.ATV.0000081635.96290.D3

R. B. Cattell, The Scree Test For The Number Of Factors, Multivariate Behavioral Research, vol.1, issue.2, pp.245-276, 1966.
DOI : 10.1207/s15327906mbr0102_10

L. Cavalli-sforza, P. Menozzi, and A. Piazza, The History and Geography of Human Genes, 1994.

G. Celleux and G. Govaert, A classification EM algorithm for clustering and two stochastic versions, Computational Statistics & Data Analysis, vol.14, issue.3, pp.315-332
DOI : 10.1016/0167-9473(92)90042-E

F. Chardon, D. Hourcade, V. Combes, and A. Charcosset, Mapping of a spontaneous mutation for early flowering time in maize highlights contrasting allelic series at two-linked QTL on chromosome 8, Theoretical and Applied Genetics, vol.136, issue.1, pp.1-11, 2005.
DOI : 10.1023/A:1005764209331

F. Chardon, B. Virlon, L. Moreau, M. Falque, and J. Joets, Genetic Architecture of Flowering Time in Maize As Inferred From Quantitative Trait Loci Meta-analysis and Synteny Conservation With the Rice Genome, Genetics, vol.168, issue.4, pp.2169-2185, 2004.
DOI : 10.1534/genetics.104.032375

J. M. Cheverud, A simple correction for multiple comparisons in interval mapping genome scans, Heredity, vol.136, issue.1, pp.52-58, 2001.
DOI : 10.1038/ng1195-241

L. Chikhi, M. W. Bruford, and M. A. Beaumont, Estimation of admixture proportions : a likelihood-based approach using Markov chain Monte Carlo, Genetics, vol.158, pp.1347-1362, 2001.

R. M. Clark, S. Tavare, and J. Doebley, Estimating a Nucleotide Substitution Rate for Maize from Polymorphism at a Major Domestication Locus, Molecular Biology and Evolution, vol.22, issue.11, pp.2304-2312, 2005.
DOI : 10.1093/molbev/msi228

M. Clement, D. Posada, and K. A. Crandall, TCS: a computer program to estimate gene genealogies, Molecular Ecology, vol.11, issue.10, pp.1657-1659, 2000.
DOI : 10.1046/j.1365-294x.2000.01020.x

P. Conneally, J. Edwards, K. Kidd, J. Lalouel, and N. Morton, Report of the committee on methods of linkage analysis and reporting, Cytogenetic and Genome Research, vol.40, issue.1-4, pp.356-359, 1985.
DOI : 10.1159/000132186

S. Crepieux, C. Lebreton, B. Servin, and G. Charmet, Quantitative Trait Loci (QTL) Detection in Multicross Inbred Designs: Recovering QTL Identical-by-Descent Status Information From Marker Data, Genetics, vol.168, issue.3, pp.1737-1749, 2004.
DOI : 10.1534/genetics.104.028993

A. Cutler and M. P. Windham, Information-Based Validity Functionals for Mixture Analysis, Proceedings of the first US-Japan Conference on the Frontiers of Statistical Modeling. Kluwer, pp.149-170, 1993.
DOI : 10.1007/978-94-011-0800-3_5

A. Darvasi and M. Soller, Advanced intercross lines, an experimental population for fine genetic mapping, Genetics, vol.141, pp.1199-1207, 1995.

A. Darvasi and M. Soller, A simple method to calculate resolving power and confidence interval of QTL map location, Behavior Genetics, vol.27, issue.2, pp.125-132, 1997.
DOI : 10.1023/A:1025685324830

A. Darvasi, A. Weinreb, V. Minke, J. Weller, and M. Soller, Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated map, Genetics, vol.134, pp.943-951, 1993.

P. I. De-bakker, R. Yelensky, I. Pe-'er, S. B. Gabriel, and M. J. Daly, Efficiency and power in genetic association studies, Efficiency and power in genetic association studies, pp.1217-1223, 2005.
DOI : 10.1038/ng1488

A. Dempster, N. Laird, and D. Rubin, Maximum Likelihood from incomplete data via the EM algorithm (with discussion), J. Roy Stat. Soc. B, vol.39, pp.1-38, 1977.

J. F. Doebley, M. M. Goodman, and C. W. Stuber, Exceptional Genetic Divergence of Northern Flint Corn, American Journal of Botany, vol.73, issue.1, pp.64-69, 1986.
DOI : 10.2307/2444278

I. S. Duff, Users' Guide for the Harwell-Boeing Sparse Matrix Collection, CERFACS, 1986.

J. Dupuis and D. Siegmund, Statistical methods for mapping quantitative trait loci from a dense set of markers, Genetics, vol.151, pp.373-386, 1999.

C. Durrant, K. T. Zondervan, L. R. Cardon, S. Hunt, and P. Deloukas, Linkage Disequilibrium Mapping via Cladistic Analysis of Single-Nucleotide Polymorphism Haplotypes, The American Journal of Human Genetics, vol.75, issue.1, pp.35-43, 2004.
DOI : 10.1086/422174

N. El-mabrouk and D. Labuda, Haplotypes histories as pathways of recombinations, Bioinformatics, vol.20, issue.12, pp.1836-1841, 2004.
DOI : 10.1093/bioinformatics/bth148

C. Etzel and R. Guerra, Meta-analysis of Genetic-Linkage Analysis of Quantitative-Trait Loci, The American Journal of Human Genetics, vol.71, issue.1, pp.56-65, 2003.
DOI : 10.1086/341126

W. J. Ewens and R. S. Spielman, The Transmission/Disequilibrium Test, Am J Hum Genet, vol.57, pp.455-464, 1995.
DOI : 10.1002/0470022620.bbc33

M. Falque, L. Decousset, D. Dervins, A. Jacob, and J. Joets, Linkage Mapping of 1454 New Maize Candidate Gene Loci, Linkage mapping of 1454 new maize candidate gene Loci, pp.1957-1966, 2005.
DOI : 10.1534/genetics.104.040204

D. Falush, M. Stephens, and J. K. Pritchard, Inference of population structure using multilocus genotype data : linked loci and correlated allele frequencies, Genetics, vol.164, pp.1567-1587, 2003.

R. Fan, J. Jung, and L. Jin, High-Resolution Association Mapping of Quantitative Trait Loci: A Population-Based Approach, Genetics, vol.172, issue.1, 2005.
DOI : 10.1534/genetics.105.046417

P. Fearnhead and P. Donnelly, Estimating recombination rates from population genetic data, Genetics, vol.159, pp.1299-1318, 2001.

S. A. Flint-garcia, J. M. Thornsberry, and E. S. Buckler, Structure of Linkage Disequilibrium in Plants, Annual Review of Plant Biology, vol.54, issue.1, pp.357-374, 2003.
DOI : 10.1146/annurev.arplant.54.031902.134907

G. D. Forney, The viterbi algorithm, IEEE, pp.268-278, 1973.
DOI : 10.1109/PROC.1973.9030

S. B. Gabriel, S. F. Schaffner, H. Nguyen, J. M. Moore, and J. Roy, The Structure of Haplotype Blocks in the Human Genome, Science, vol.296, issue.5576, pp.2225-2229, 2002.
DOI : 10.1126/science.1069424

B. S. Gaut and A. D. Long, The Lowdown on Linkage Disequilibrium, THE PLANT CELL ONLINE, vol.15, issue.7, pp.1502-1506, 2003.
DOI : 10.1105/tpc.150730

B. Goffinet and S. Gerber, Quantitative trait loci : a metaanalysis, Genetics, vol.155, pp.463-473, 2000.

R. C. Griffiths and P. Marjoram, Ancestral Inference from Samples of DNA Sequences with Recombination, Journal of Computational Biology, vol.3, issue.4, pp.479-502, 1996.
DOI : 10.1089/cmb.1996.3.479

S. Groh, M. M. Khairallah, D. Gonzales-de-leon, M. Willcox, and C. Jiang, Comparison of QTLs mapped in RILs and their test-cross progenies of tropical maize for insect resistance and agronomic traits, Plant Breeding, vol.136, issue.3, pp.193-202, 1998.
DOI : 10.1007/BF00221905

P. K. Gupta, S. Rustgi, and P. L. , Linkage disequilibrium and association studies in higher plants: Present status and future prospects, Plant Molecular Biology, vol.163, issue.4, pp.461-485, 2005.
DOI : 10.1007/s11103-005-0257-z

J. Hagenblad, C. Tang, J. Molitor, J. Werner, and K. Zhao, Haplotype Structure and Phenotypic Associations in the Chromosomal Regions Surrounding Two Arabidopsis thaliana Flowering Time Loci, Genetics, vol.168, issue.3, pp.1627-1638, 2004.
DOI : 10.1534/genetics.104.029470

E. Halperin, G. Kimmel, and R. Shamir, Tag SNP selection in genotype data for maximizing SNP prediction accuracy, Bioinformatics, vol.21, issue.Suppl 1, pp.195-203, 2005.
DOI : 10.1093/bioinformatics/bti1021

W. Hill, Estimation of effective population size from data on linkage disequilibrium, Genetical Research, vol.30, issue.03, pp.209-216, 1981.
DOI : 10.1038/hdy.1974.89

W. G. Hill, Linkage disequilibrium among multiple neutral alleles produced by mutation in finite population, Theoretical Population Biology, vol.8, issue.2, pp.117-126, 1975.
DOI : 10.1016/0040-5809(75)90028-3

W. G. Hill and A. Robertson, Linkage disequilibrium in finite populations, Linkage disequilibrium in finite populations, pp.226-231, 1968.
DOI : 10.1007/BF01245622

W. G. Hill and B. S. Weir, Maximum-likelihood estimation of gene location by linkage disequilibrium, Am J Hum Genet, vol.54, pp.705-714, 1994.

J. N. Hirschhorn and M. J. Daly, Genome-wide association studies for common diseases and complex traits, Nature Reviews Genetics, vol.158, issue.2, pp.95-108, 2005.
DOI : 10.1086/339258

J. C. Ho, S. Kresovich, and K. R. Lamkey, Extent and Distribution of Genetic Variation in U.S. Maize, Crop Science, vol.45, issue.5, pp.1891-1900, 2005.
DOI : 10.2135/cropsci2003.0494

C. J. Hoggart, E. J. Parra, M. D. Shriver, C. Bonilla, and R. A. Kittles, Control of Confounding of Genetic Associations in Stratified Populations, Control of confounding of genetic associations in stratified populations, pp.1492-1504, 2003.
DOI : 10.1086/375613

C. J. Hoggart, M. D. Shriver, R. A. Kittles, D. G. Clayton, and P. M. Mckeigue, Design and Analysis of Admixture Mapping Studies, The American Journal of Human Genetics, vol.74, issue.5, pp.965-978, 2004.
DOI : 10.1086/420855

J. Hoh and J. Ott, Mathematical multi-locus approaches to localizing complex human trait genes, Nature Reviews Genetics, vol.11, issue.9, pp.701-709, 2003.
DOI : 10.1093/bioinformatics/btf877

J. Hoh, A. Wille, and J. Ott, Trimming, Weighting, and Grouping SNPs in Human Case-Control Association Studies, Genome Research, vol.11, issue.12, pp.2115-2119, 2001.
DOI : 10.1101/gr.204001

J. Hoh, A. Wille, R. Zee, S. Cheng, and R. Reynolds, Selecting SNPs in two-stage analysis of disease association data: a model-free approach, Annals of Human Genetics, vol.64, issue.5, pp.413-417, 2000.
DOI : 10.1046/j.1469-1809.2000.6450413.x

B. D. Horne and N. J. Camp, Principal component analysis for selection of optimal SNP-sets that capture intragenic genetic variation, Genetic Epidemiology, vol.63, issue.1, pp.11-21, 2004.
DOI : 10.1002/gepi.10292

J. P. Hugot, M. Chamaillard, H. Zouali, S. Lesage, and J. P. Cezard, Association of NOD2 leucine-rich repeat variants with susceptibility to Crohn's disease, Nature, vol.411, issue.6837, pp.599-603, 2001.
DOI : 10.1038/35079107

M. Ishiguro, S. Yosiyuki, and K. Genshiro, Bootstrapping Log Likelihood and EIC, an Extension of AIC, Annals of the Institute of Statistical Mathematics, vol.49, issue.3, pp.411-434, 1997.
DOI : 10.1023/A:1003158526504

J. Jannink, M. C. Bink, and R. C. Jansen, Using complex plant pedigrees to map valuable genes, Trends in Plant Science, vol.6, issue.8, pp.337-342, 2001.
DOI : 10.1016/S1360-1385(01)02017-9

J. Jannink and B. Walsh, Association mapping in plant populations., Quantitative Genetics, pp.59-68, 2002.
DOI : 10.1079/9780851996011.0059

R. C. Jansen, Interval mapping of multiple quantitative trait loci, Genetics, vol.135, pp.205-211, 1993.

R. C. Jansen, J. Jannink, and W. D. Beavis, Mapping Quantitative Trait Loci in Plant Breeding Populations, Crop Science, vol.43, issue.3, pp.829-834, 2003.
DOI : 10.2135/cropsci2003.8290

H. Jennings, The numerical results of diverse systems of breeding, with respect to two pairs of characters, linked or independent, with special relation to the effects of linkage, Genetics, vol.2, pp.97-154, 1917.

Y. Ji, D. M. Stelly, M. D. Donato, M. M. Goodman, and C. G. Williams, A candidate recombination modifier gene for Zea mays L, Genetics, vol.151, pp.821-830, 1999.

G. C. Johnson, L. Esposito, B. J. Barratt, A. N. Smith, and . Heward, Haplotype tagging for the identification of common disease genes, Nature Genetics, vol.29, issue.2, pp.233-237, 2001.
DOI : 10.1038/ng1001-233

L. B. Jorde, Linkage disequilibrium as a gene-mapping tool, Am J Hum Genet, vol.56, pp.11-14, 1995.

L. B. Jorde, Linkage Disequilibrium and the Search for Complex Disease Genes, Genome Research, vol.10, issue.10, pp.1435-1444, 2000.
DOI : 10.1101/gr.144500

C. Kao and Z. Zeng, Modeling epistasis of quantitative trait loci using Cockerham's model, Genetics, vol.160, pp.1243-1261, 2002.

M. Kearsey and A. Farquhar, QTL analysis in plants; where are we now?, Heredity, vol.19, issue.2, pp.137-142, 1998.
DOI : 10.1146/annurev.genet.27.1.205

M. Kearsey and H. S. Pooni, The genetical analysis of quantitative traits, 1996.
DOI : 10.1007/978-1-4899-4441-2

P. Keightley and S. Knott, Testing the correspondence between map positions of quantitative trait loci, Genetical Research, vol.74, issue.3, pp.323-328, 1999.
DOI : 10.1017/S0016672399004176

M. Khatkar, P. Thomson, I. Tammen, and H. Raadsma, Quantitative trait loci mapping in dairy cattle: review and meta-analysis, Genetics Selection Evolution, vol.36, issue.2, 2004.
DOI : 10.1186/1297-9686-36-2-163
URL : https://hal.archives-ouvertes.fr/hal-00894480

E. Khavkin and E. H. Coe, Mapped genomic locations for developmental functions and QTLs reflect concerted groups in maize ( Zea mays L.), TAG Theoretical and Applied Genetics, vol.95, issue.3, pp.343-352, 1997.
DOI : 10.1007/s001220050569

E. Khavkin and E. H. Coe, The major quantitative trait loci for plant stature, development and yield are general manifestations of developmental gene clusters, Maize Newslett, vol.72, pp.60-66, 1998.

W. C. Knowler, R. C. Williams, D. J. Pettitt, and A. G. Steinberg, 13,14 and type 2 diabetes mellitus : an association in American Indians with genetic admixture, Gm3 Am J Hum Genet, vol.5, issue.43, pp.520-526, 1988.

M. Koivisto, T. Kivioja, H. Mannila, P. Rastas, and E. Ukkonen, Hidden Markov Modelling Techniques for Haplotype Analysis, ALT 2004, LNAI, pp.37-52, 2004.
DOI : 10.1007/978-3-540-30215-5_4

L. Kruglyak, Prospects for whole-genome linkage disequilibrium mapping of common disease genes, Nature Genetics, vol.22, issue.2, pp.139-144, 1999.
DOI : 10.1038/9642

M. K. Kuhner, J. Yamato, and J. Felsenstein, Maximum likelihood estimation of recombination rates from population data, Genetics, vol.156, pp.1393-1401, 2000.

J. C. Lam, K. Roeder, and B. Devlin, Haplotype Fine Mapping by Evolutionary Trees, The American Journal of Human Genetics, vol.66, issue.2, pp.659-673, 2000.
DOI : 10.1086/302756
URL : http://doi.org/10.1086/302756

E. Lander and L. Kruglyak, Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results, Nature Genetics, vol.265, issue.3, pp.241-247, 1995.
DOI : 10.1038/ng0694supp-246

E. S. Lander and B. D. , Mapping Mendelien factors underlying quantitative traits using RFLP linkage maps, Genetics, vol.121, pp.185-199, 1989.

E. S. Lander, P. Green, J. Abrahamson, A. Barlow, and D. M. , MAPMAKER: An interactive computer package for constructing primary genetic linkage maps of experimental and natural populations, Genomics, vol.1, issue.2, pp.174-181, 1987.
DOI : 10.1016/0888-7543(87)90010-3

R. Lewontin, The interaction of selection and linkage. I. General considerations ; heterotic models, Genetics, vol.49, pp.49-67, 1964.

J. Li and T. Jiang, Haplotype-based linkage disequilibrium mapping via direct data mining, Bioinformatics, vol.21, issue.24, 2005.
DOI : 10.1093/bioinformatics/bti732
URL : http://bioinformatics.oxfordjournals.org/cgi/content/short/21/24/4384

N. Li and M. Stephens, Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data, Genetics, vol.165, pp.2213-2233, 2003.

Y. R. Lin, K. F. Schertz, and A. H. Paterson, Comparative analysis of QTLS affecting plant height and maturity across the poaceae, in reference to an interspecific sorghum population, Genetics, vol.141, pp.391-411, 1995.

K. Liu, M. Goodman, S. Muse, J. S. Smith, and . Buckler, Genetic structure and diversity among maize inbred lines as inferred from DNA microsatellites, Genetics, vol.165, pp.2117-2128, 2003.

S. C. Liu, S. P. Kowalski, T. H. Lan, K. A. Feldmann, and A. H. Paterson, wide high-resolution mapping by recurrent intermating using Arabidopsis thaliana as a model, Genome- Genetics, vol.142, pp.247-258, 1996.

K. E. Lohmueller, C. L. Pearce, M. Pike, E. S. Lander, and J. N. Hirschhorn, Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease, Nature Genetics, vol.33, issue.2, pp.177-182, 2003.
DOI : 10.1038/ng1071

J. C. Long, The genetic structure of admixed populations, Genetics, vol.127, pp.417-428, 1991.

X. Lu, T. Niu, and J. S. Liu, Haplotype Information and Linkage Disequilibrium Mapping for Single Nucleotide Polymorphisms, Genome Research, vol.13, issue.9, pp.2112-2117, 2003.
DOI : 10.1101/gr.586803
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC403705

T. Lubberstedt, A. Melchinger, C. Schon, H. F. Utz, and D. Klein, QTL Mapping in Testcrosses of European Flint Lines of Maize: I. Comparison of Different Testers for Forage Yield Traits, Crop Science, vol.37, issue.3, pp.921-931, 1997.
DOI : 10.2135/cropsci1997.0011183X003700030037x

B. Mangin, B. Goffinet, and A. Reba¨?reba¨?, Constructing confidence intervals for QTL location, Genetics, vol.138, pp.1301-1308, 1994.

J. Marchini, P. Donnelly, and L. R. Cardon, Genome-wide strategies for detecting multiple loci that influence complex diseases, Nature Genetics, vol.14, issue.4, pp.413-417, 2005.
DOI : 10.1038/ng1337

K. Mather, TYPES OF LINKAGE DATA AND THEIR VALUE, Annals of Eugenics, vol.6, issue.3, pp.251-264, 1936.
DOI : 10.1111/j.1469-1809.1936.tb02144.x

E. Mayr, Histoire de la biologie. Diversité, ´ evolution et hérédité, Editions Fayard, 1982.

P. M. Mckeigue, Mapping Genes That Underlie Ethnic Differences in Disease Risk: Methods for Detecting Linkage in Admixed Populations, by Conditioning on Parental Admixture, The American Journal of Human Genetics, vol.63, issue.1, pp.241-251, 1998.
DOI : 10.1086/301908

M. S. Mcpeek and A. Strahs, Assessment of Linkage Disequilibrium by the Decay of Haplotype Sharing, with Application to Fine-Scale Genetic Mapping, The American Journal of Human Genetics, vol.65, issue.3, pp.858-875, 1999.
DOI : 10.1086/302537

V. Mechin, O. Argillier, Y. Hebert, E. Guingo, and L. Moreau, Genetic Analysis and QTL Mapping of Cell Wall Digestibility and Lignification in Silage Maize, Crop Science, vol.41, issue.3, pp.690-697, 2001.
DOI : 10.2135/cropsci2001.413690x

X. Meng and D. B. Rubin, Using EM to Obtain Asymptotic Variance-Covariance Matrices: The SEM Algorithm, Journal of the American Statistical Association, vol.82, issue.416, pp.899-909, 1991.
DOI : 10.1002/9780470316696

Z. Meng, D. V. Zaykin, C. Xu, M. Wagner, and M. G. Ehm, Selection of Genetic Markers for Association Analyses, Using Linkage Disequilibrium and Haplotypes, The American Journal of Human Genetics, vol.73, issue.1, pp.115-130, 2003.
DOI : 10.1086/376561

P. Menozzi, A. Piazza, and L. Cavalli-sforza, Synthetic maps of human gene frequencies in Europeans, Science, vol.201, issue.4358, pp.786-792, 1978.
DOI : 10.1126/science.356262

T. H. Meuwissen and M. E. Goddard, Fine mapping of quantitative trait loci using linkage disequilibria with closely linked marker loci, Genetics, vol.155, pp.421-430, 2000.

R. Mihaljevic, H. F. Utz, and A. E. Melchinger, Congruency of Quantitative Trait Loci Detected for Agronomic Traits in Testcrosses of Five Populations of European Maize, Crop Science, vol.44, issue.1, pp.114-124, 2004.
DOI : 10.2135/cropsci2004.1140

S. A. Mohammadi and B. M. Prasanna, Analysis of Genetic Diversity in Crop Plants???Salient Statistical Tools and Considerations, Crop Science, vol.43, issue.4, pp.1235-1248, 2003.
DOI : 10.2135/cropsci2003.1235

J. Molitor, P. Marjoram, and D. Thomas, Application of Bayesian spatial statistical methods to analysis of haplotypes effects and gene mapping, Genetic Epidemiology, vol.60, issue.2, pp.95-105, 2003.
DOI : 10.1002/gepi.10251

L. Moreau, A. Charcosset, and A. Gallais, Use of trial clustering to study QTL?????environment effects for grain yield and related traits in maize, Theoretical and Applied Genetics, vol.136, issue.1, pp.92-105, 2004.
DOI : 10.1007/s00122-004-1781-y

A. P. Morris, J. C. Whittaker, and D. J. Balding, Bayesian Fine-Scale Mapping of Disease Loci, by Hidden Markov Models, The American Journal of Human Genetics, vol.67, issue.1, pp.155-169, 2000.
DOI : 10.1086/302956

A. P. Morris, J. C. Whittaker, and D. J. Balding, Fine-Scale Mapping of Disease Loci via Shattered Coalescent Modeling of Genealogies, The American Journal of Human Genetics, vol.70, issue.3, pp.686-707, 2002.
DOI : 10.1086/339271

A. P. Morris, J. C. Whittaker, and D. J. Balding, Little Loss of Information Due to Unknown Phase for Fine-Scale Linkage-Disequilibrium Mapping with Single-Nucleotide???Polymorphism Genotype Data, The American Journal of Human Genetics, vol.74, issue.5, pp.945-953, 2004.
DOI : 10.1086/420773

A. P. Morris, J. C. Whittaker, C. Xu, L. K. Hosking, and D. J. Balding, Multipoint linkage-disequilibrium mapping narrows location interval and identifies mutation heterogeneity, Proceedings of the National Academy of Sciences, vol.29, issue.2, pp.13442-13446, 2003.
DOI : 10.1038/ng1001-217
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC263833

N. E. Morton, Sequential tests for the detection of linkage, Am J Hum Genet, vol.7, pp.277-318, 1955.

N. E. Morton, The detection and estimation of linkage between the genes for elliptocytosis and the Rh blood type, Am J Hum Genet, vol.8, pp.80-96, 1956.

M. R. Munafo and J. Flint, Meta-analysis of genetic association studies, Trends in Genetics, vol.20, issue.9, pp.439-444, 2004.
DOI : 10.1016/j.tig.2004.06.014

M. Nei and W. H. Li, Non-random association between electromorphs and inversion chromosomes in finite populations, Genetical Research, vol.68, issue.01, pp.65-83, 1980.
DOI : 10.1007/BF00486100

D. M. Nielsen, M. G. Ehm, D. V. Zaykin, and B. S. Weir, Effect of Two- and Three-Locus Linkage Disequilibrium on the Power to Detect Marker/Phenotype Associations, Genetics, vol.168, issue.2, pp.1029-1040, 2004.
DOI : 10.1534/genetics.103.022335

T. Niu, Algorithms for inferring haplotypes, Genetic Epidemiology, vol.164, issue.4, pp.334-347, 2004.
DOI : 10.1002/gepi.20024

M. Nordborg, Linkage disequilibrium, gene trees and selfing : an ancestral recombination graph with partial self-fertilization, Genetics, vol.154, pp.923-929, 2000.

M. Nordborg and S. Tavare, Linkage disequilibrium: what history has to tell us, Trends in Genetics, vol.18, issue.2, pp.83-90, 2002.
DOI : 10.1016/S0168-9525(02)02557-X

P. Onkamo, V. Ollikainen, P. Sevon, H. T. Toivonen, and H. Mannila, Association analysis for quantitative traits by data mining: QHPM, Annals of Human Genetics, vol.66, issue.6, pp.419-429, 2002.
DOI : 10.1046/j.1469-1809.2002.00131.x

I. Paran and D. Zamir, Quantitative traits in plants: beyond the QTL, Trends in Genetics, vol.19, issue.6, pp.303-306, 2003.
DOI : 10.1016/S0168-9525(03)00117-3

A. H. Paterson, E. S. Lander, J. D. Hewitt, S. Peterson, and S. E. Lincoln, Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms, Nature, vol.335, issue.6192, pp.521-529, 1988.
DOI : 10.1038/335721a0

A. H. Paterson, Y. R. Lin, K. F. Schertz, J. F. Doebley, and S. R. Pinson, Convergent Domestication of Cereal Crops by Independent Mutations at Corresponding Genetic Loci, Science, vol.269, issue.5231, pp.1714-1718, 1995.
DOI : 10.1126/science.269.5231.1714

N. Patil, A. J. Berno, D. A. Hinds, W. A. Barrett, and J. M. Doshi, Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21, Science, vol.294, issue.5547, pp.1719-1723, 2001.
DOI : 10.1126/science.1065573

C. L. Pfaff, E. J. Parra, C. Bonilla, K. Hiester, and P. M. Mckeigue, Population Structure in Admixed Populations: Effect of Admixture Dynamics on the Pattern of Linkage Disequilibrium, The American Journal of Human Genetics, vol.68, issue.1, pp.198-207, 2001.
DOI : 10.1086/316935

A. Pichot, Histoire de la notion de g` ene, 1999.

D. Posada, T. J. Maxwell, and A. R. Templeton, TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees, Bioinformatics, vol.21, issue.9, pp.2130-2132, 2005.
DOI : 10.1093/bioinformatics/bti293

W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, Numerical Recipe in C : The Art of Scientific Computing, 1992.

J. K. Pritchard and M. Przeworski, Linkage Disequilibrium in Humans: Models and Data, The American Journal of Human Genetics, vol.69, issue.1, pp.1-14, 2001.
DOI : 10.1086/321275

J. K. Pritchard, M. Stephens, and P. Donnelly, Inference of population structure using multilocus genotype data, Genetics, vol.155, pp.945-959, 2000.

J. K. Pritchard, M. Stephens, N. A. Rosenberg, and P. Donnelly, Association Mapping in Structured Populations, The American Journal of Human Genetics, vol.67, issue.1, pp.170-181, 2000.
DOI : 10.1086/302959

M. Przeworski, Estimating the time since the fixation of a beneficial allele, Genetics, vol.164, pp.1667-1676, 2003.

L. R. Rabiner, A tutorial on hidden Markov models and selected applications in speech recognition, Proceedings of the IEEE, vol.77, issue.2, pp.257-286, 1989.
DOI : 10.1109/5.18626

A. Rafalski and M. Morgante, Corn and humans: recombination and linkage disequilibrium in two genomes of similar size, Trends in Genetics, vol.20, issue.2, pp.103-111, 2004.
DOI : 10.1016/j.tig.2003.12.002

B. Rannala and J. P. Reeve, High-Resolution Multipoint Linkage-Disequilibrium Mapping in the Context of a Human Genome Sequence, The American Journal of Human Genetics, vol.69, issue.1, pp.159-178, 2001.
DOI : 10.1086/321279

A. Rebai, P. Blanchard, D. Perret, and P. Vincourt, Mapping quantitative trait loci controlling silking date in a diallel cross among four lines of maize, TAG Theoretical and Applied Genetics, vol.95, issue.3, pp.451-459, 1997.
DOI : 10.1007/s001220050582

C. Rebourg, M. Chastanet, B. Gouesnard, C. Welcker, and P. Dubreuil, Maize introduction into Europe: the history reviewed in the light of molecular data, Theoretical and Applied Genetics, vol.106, issue.5, pp.895-903, 2003.
DOI : 10.1007/s00122-002-1140-9

D. L. Remington, J. M. Thornsberry, Y. Matsuoka, L. M. Wilson, and S. R. Whitt, Structure of linkage disequilibrium and phenotypic associations in the maize genome, Proceedings of the National Academy of Sciences, vol.67, issue.1, pp.11479-11484, 2001.
DOI : 10.1086/302959

J. Ribaut, D. Hoisington, J. A. Deutsch, C. Jiang, D. Gonzalez-de et al., Identification of quantitative trait loci under drought conditions in tropical maize. 1. Flowering parameters and the anthesis-silking interval, Theoretical and Applied Genetics, vol.92, issue.7, pp.905-914, 1996.
DOI : 10.1007/BF00221905

C. Sabatti, S. Service, and N. Freimer, False discovery rate in linkage and association genome screens for complex disorders, Genetics, vol.164, pp.829-833, 2003.

N. Saitou and M. Nei, The neighbor-joining method : a new method for reconstructing phylogenetic trees, Mol Biol Evol, vol.4, pp.406-425, 1987.

S. Salvi and R. Tuberosa, To clone or not to clone plant QTLs: present and future challenges, Trends in Plant Science, vol.10, issue.6, pp.297-304, 2005.
DOI : 10.1016/j.tplants.2005.04.008

S. Salvi, R. Tuberosa, E. Chiapparino, M. Maccaferri, and S. Veillet, Toward positional cloning of Vgt1, a QTL controlling the transition from the vegetative to the reproductive phase in maize, Plant Molecular Biology, vol.48, issue.5/6, pp.601-614, 2002.
DOI : 10.1023/A:1014838024509

T. Sasaki, T. Matsumoto, K. Yamamoto, K. Sakata, and T. Baba, The genome sequence and structure of rice chromosome 1, Nature, vol.14, issue.6913, pp.312-316, 2002.
DOI : 10.1006/jmbi.1997.0951

G. A. Satten, W. D. Flanders, and Q. Yang, Accounting for Unmeasured Population Substructure in Case-Control Studies of Genetic Association Using a Novel Latent-Class Model, The American Journal of Human Genetics, vol.68, issue.2, pp.466-477, 2001.
DOI : 10.1086/318195

D. J. Schaid, C. M. Rowland, D. E. Tines, R. M. Jacobson, and G. A. Poland, Score Tests for Association between Traits and Haplotypes when Linkage Phase Is Ambiguous, The American Journal of Human Genetics, vol.70, issue.2, pp.425-434, 2002.
DOI : 10.1086/338688

. Schiex, Carthagene : constructing and joining maximum likelihood maps, pp.258-267, 1997.

R. Schwartz, Algorithms for association study design using a generalized model of haplotype conservation, Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004., 2004.
DOI : 10.1109/CSB.2004.1332421

R. Schwartz, A. G. Clark, and S. Istrail, Methods for Inferring Block-Wise Ancestral History from Haploid Sequences. The Haplotype Coloring Problem, WABI 2002, pp.44-59, 2002.

. Schwarz, Estimating the Dimension of a Model, The Annals of Statistics, vol.6, issue.2, pp.461-464, 1978.
DOI : 10.1214/aos/1176344136

T. F. Sharbel, B. Haubold, and T. Mitchell-olds, Genetic isolation by distance in Arabidopsis thaliana: biogeography and postglacial colonization of Europe, Molecular Ecology, vol.23, issue.3, pp.2109-2118, 2000.
DOI : 10.1016/0160-9327(96)10019-3

M. J. Sillanpaa and K. Auranen, Replication in genetic studies of complex traits, Annals of Human Genetics, vol.154, issue.Suppl. 1, pp.646-657, 2004.
DOI : 10.1046/j.1529-8817.2004.00122.x

M. W. Smith and S. J. O-'brien, Mapping by admixture linkage disequilibrium: advances, limitations and guidelines, Nature Reviews Genetics, vol.5, issue.8, pp.623-632, 2005.
DOI : 10.1007/s00223-001-1068-0

L. J. Stadler, The Variability of Crossing Over in Maize, Genetics, vol.11, pp.1-37, 1925.

P. Stam, Construction of integrated genetic linkage maps by means of a new computer package: Join Map, The Plant Journal, vol.5, issue.5, pp.739-744, 1993.
DOI : 10.1111/j.1365-313X.1993.00739.x

J. C. Stephens, D. Briscoe, and S. J. O-'brien, Mapping by admixture linkage disequilibrium in human populations : limits and guidelines, Am J Hum Genet, vol.55, pp.809-824, 1994.

M. P. Stumpf and D. B. Goldstein, Demography, Recombination Hotspot Intensity, and the Block Structure of Linkage Disequilibrium, Current Biology, vol.13, issue.1, pp.1-8, 2003.
DOI : 10.1016/S0960-9822(02)01404-5

N. Sugiura, Further Analysis of the Data by Akaike's Information Criterion and the Finite Corrections, Communications in Statistics Theory and Methods, vol.A, pp.13-26, 1978.

K. Takeuchi, Distribution of informational statistics and a criterion model fitting, Math. Sci, vol.153, pp.12-18, 1976.

A. R. Templeton, A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping or DNA sequencing. V. Analysis of case/control sampling designs : Alzheimer's disease and the apoprotein E locus, Genetics, vol.140, pp.403-409, 1995.

A. R. Templeton, E. Boerwinkle, and C. F. , Sing, 1987 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila, Genetics, vol.117, pp.343-351

A. R. Templeton, K. A. Crandall, and C. F. , Sing, 1992 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation, Genetics, vol.132, pp.619-633

A. R. Templeton, T. Maxwell, D. Posada, J. H. Stengard, and E. Boerwinkle, Tree Scanning: A Method for Using Haplotype Trees in Phenotype/Genotype Association Studies, Genetics, vol.169, issue.1, pp.441-453, 2005.
DOI : 10.1534/genetics.104.030080

A. R. Templeton and C. F. , Sing, 1993 A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination, Genetics, vol.134, pp.659-669

A. R. Templeton, C. F. Sing, A. Kessling, and S. Humphries, A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations, Genetics, vol.120, pp.1145-1154, 1988.

M. I. Tenaillon, M. C. Sawkins, A. D. Long, R. L. Gaut, and J. F. Doebley, Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.), Proceedings of the National Academy of Sciences, vol.22, issue.3, pp.9161-9166, 2001.
DOI : 10.1038/10290

M. I. Tenaillon, J. U-'ren, O. Tenaillon, and B. S. Gaut, Selection Versus Demography: A Multilocus Investigation of the Domestication Process in Maize, Molecular Biology and Evolution, vol.21, issue.7, pp.1214-1225, 2004.
DOI : 10.1093/molbev/msh102

J. D. Terwilliger and K. M. Weiss, Linkage disequilibrium mapping of complex disease: fantasy or reality?, Current Opinion in Biotechnology, vol.9, issue.6, pp.578-594, 1998.
DOI : 10.1016/S0958-1669(98)80135-3

D. Titterington, A. Smith, and U. Markov, Statistical Analysis of Finite Mixture Distributions, 1985.

H. Toivonen, P. Onkamo, P. Hintsanen, E. Terzi, and P. Sevon, Data mining for gene mapping, 2004.

H. T. Toivonen, P. Onkamo, K. Vasko, V. Ollikainen, and P. Sevon, Data Mining Applied to Linkage Disequilibrium Mapping, The American Journal of Human Genetics, vol.67, issue.1, pp.133-145, 2000.
DOI : 10.1086/302954
URL : http://doi.org/10.1086/302954

E. Ukkonen, Finding Founder Sequences from a Set of Recombinants, WABI 2002, pp.277-286, 2002.
DOI : 10.1007/3-540-45784-4_21

P. Van-zandt and S. Mopper, A Meta-Analysis of Adaptive Deme Formation in Phytophagous Insect Populations, The American Naturalist, vol.152, issue.4, pp.595-604, 1998.
DOI : 10.2307/2463359

P. M. Visscher and M. E. Goddard, Prediction of the Confidence Interval of Quantitative Trait Loci Location, Behavior Genetics, vol.34, issue.4, pp.477-482, 2004.
DOI : 10.1023/B:BEGE.0000023652.93162.e8

R. Vitalis and D. Couvet, Estimation of effective population size and migration rate from one-and two-locus identity measures, Genetics, vol.157, pp.911-925, 2001.
URL : https://hal.archives-ouvertes.fr/hal-00535518

A. J. Viterbi, Error bounds for convolutional codes and an asymptotically optimum decoding algorithm, IEEE Transactions on Information Theory, vol.13, issue.2, pp.260-269, 1967.
DOI : 10.1109/TIT.1967.1054010

C. Vladutu, J. Mclaughlin, and R. L. Phillips, Fine mapping and characterization of linked quantitative trait loci involved in the transition of the maize apical meristem from vegetative to generative structures, Genetics, vol.153, pp.993-1007, 1999.

L. A. Vollestad, K. Hindar, and A. P. Moller, A meta-analysis of fluctuating asymmetry in relation to heterozygosity, Heredity, vol.67, issue.2, pp.206-218, 1999.
DOI : 10.1016/0044-8486(95)01117-X

J. D. Wall and J. K. Pritchard, Assessing the Performance of the Haplotype Block Model of Linkage Disequilibrium, The American Journal of Human Genetics, vol.73, issue.3, pp.502-515, 2003.
DOI : 10.1086/378099

J. Wang, Estimation of effective population sizes from data on genetic markers, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.92, issue.4, pp.1395-1409, 2005.
DOI : 10.1017/S001667239700270X

R. L. Wang, A. Stec, J. Hey, L. Lukens, and J. Doebley, The limits of selection during maize domestication, Nature, vol.398, pp.236-239, 1999.

X. Wang, I. L. Roy, E. Nicodeme, R. Li, and R. Wagner, Using Advanced Intercross Lines for High-Resolution Mapping of HDL Cholesterol Quantitative Trait Loci, Genome Research, vol.13, issue.7, pp.1654-1664, 2003.
DOI : 10.1101/gr.1185803

J. H. Ward, Hierarchical Grouping to Optimize an Objective Function, Journal of the American Statistical Association, vol.58, issue.301, pp.236-244, 1963.
DOI : 10.1007/BF02289263

J. I. Weller, J. Z. Song, D. W. Heyen, H. A. Lewin, and M. Ron, A new approach to the problem of multiple comparisons in the genetic dissection of complex traits, Genetics, vol.150, pp.1699-1706, 1998.

T. Wiberg, Computation of principal components when data are missing, Proc. Second Symp, pp.229-236, 1976.

C. G. Williams, M. M. Goodman, and C. W. Stuber, Comparative recombination distances among Zea mays L. inbreds, wide crosses and interspecific hybrids, Genetics, vol.141, pp.1573-1581, 1995.

M. Windham and A. Cutler, Information Ratios for Validating Mixture Analyses, Journal of the American Statistical Association, vol.4, issue.420, pp.1188-1192, 1992.
DOI : 10.1207/s15327906mbr0503_6

C. R. Winkler, N. M. Jensen, M. Cooper, D. W. Podlich, and O. S. Smith, On the determination of recombination rates in intermated recombinant inbred populations, Genetics, vol.164, pp.741-745, 2003.

J. Wolfe, A Monte Carlo study of sampling distribution of the likelihood ration for mixtures of multinormal distributions, 1971.

S. Xu, Theoretical basis of the Beavis effect, Genetics, vol.165, pp.2259-68, 2003.

I. Yap, D. Schneider, J. Kleinberg, D. Matthews, and S. Cartinhour, A graph-theoretic approach to comparing and integrating genetic, physical and sequence-based maps, Genetics, vol.165, pp.2235-2247, 2003.

G. Yule, On the Association of Attributes in Statistics: With Illustrations from the Material of the Childhood Society, &c, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol.194, issue.252-261, pp.257-319, 1900.
DOI : 10.1098/rsta.1900.0019

Z. B. Zeng, Precision mapping of quantitative trait loci, Genetics, vol.136, pp.1457-1468, 1994.

Z. Zeng, T. Wang, and W. Zou, Modeling Quantitative Trait Loci and Interpretation of Models, Genetics, vol.169, issue.3, pp.1711-1725, 2005.
DOI : 10.1534/genetics.104.035857

K. Zhang, P. Calabrese, M. Nordborg, and F. Sun, Haplotype Block Structure and Its Applications to Association Studies: Power and Study Designs, The American Journal of Human Genetics, vol.71, issue.6, pp.1386-1394, 2002.
DOI : 10.1086/344780

K. Zhang, Z. S. Qin, J. S. Liu, T. Chen, and M. S. Waterman, Haplotype Block Partitioning and Tag SNP Selection Using Genotype Data and Their Applications to Association Studies, Genome Research, vol.14, issue.5, pp.908-916, 2004.
DOI : 10.1101/gr.1837404
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479119

W. Zhang, A. Collins, and N. E. Morton, Does haplotype diversity predict power for association mapping of disease susceptibility?, Human Genetics, vol.115, issue.2, pp.157-164, 2004.
DOI : 10.1007/s00439-004-1122-x

S. Zollner and J. K. Pritchard, Coalescent-Based Association Mapping and Fine Mapping of Complex Trait Loci, Genetics, vol.169, issue.2, pp.1071-1092, 2005.
DOI : 10.1534/genetics.104.031799