Confidence Intervals in QTL Mapping by Bootstrapping

INVESTIGATIONS

Confidence Intervals in QTL Mapping by Bootstrapping

P. M. Visscher, R. Thompson and C. S. Haley
Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, Scotland

The determination of empirical confidence intervals for the location of quantitative trait loci (QTLs) was investigated using simulation. Empirical confidence intervals were calculated using a bootstrap resampling method for a backcross population derived from inbred lines. Sample sizes were either 200 or 500 individuals, and the QTL explained 1, 5, or 10% of the phenotypic variance. The method worked well in that the proportion of empirical confidence intervals that contained the simulated QTL was close to expectation. In general, the confidence intervals were slightly conservatively biased. Correlations between the test statistic and the width of the confidence interval were strongly negative, so that the stronger the evidence for a QTL segregating, the smaller the empirical confidence interval for its location. The size of the average confidence interval depended heavily on the population size and the effect of the QTL. Marker spacing had only a small effect on the average empirical confidence interval. The LOD drop-off method to calculate empirical support intervals gave confidence intervals that generally were too small, in particular if confidence intervals were calculated only for samples above a certain significance threshold. The bootstrap method is easy to implement and is useful in the analysis of experimental data.

This article has been cited by other articles:

X. Liu, H. Zhang, H. Li, N. Li, Y. Zhang, Q. Zhang, S. Wang, Q. Wang, and H. Wang
Fine-Mapping Quantitative Trait Loci for Body Weight and Abdominal Fat Traits: Effects of Marker Density and Sample Size
Poult. Sci., July 1, 2008; 87(7): 1314 - 1319.
[Abstract] [Full Text] [PDF]

K. M. Nichols, A. F. Edo, P. A. Wheeler, and G. H. Thorgaard
The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss
Genetics, July 1, 2008; 179(3): 1559 - 1575.
[Abstract] [Full Text] [PDF]

C. R. Moreno, G. M. Cosseddu, L. Schibler, A. Roig, K. Moazami-Goudarzi, O. Andreoletti, F. Eychenne, D. Lajous, F. Schelcher, E. P. Cribiu, et al.
Identification of New Quantitative Trait Loci (Other Than the PRNP Gene) Modulating the Scrapie Incubation Period in Sheep
Genetics, May 1, 2008; 179(1): 723 - 726.
[Abstract] [Full Text] [PDF]

J. I. Weller, M. Golik, S. Reikhav, R. Domochovsky, E. Seroussi, and M. Ron
Detection and Analysis of Quantitative Trait Loci Affecting Production and Secondary Traits on Chromosome 7 in Israeli Holsteins
J Dairy Sci, February 1, 2008; 91(2): 802 - 813.
[Abstract] [Full Text] [PDF]

D. B. Edwards, C. W. Ernst, R. J. Tempelman, G. J. M. Rosa, N. E. Raney, M. D. Hoge, and R. O. Bates
Quantitative trait loci mapping in an F2 Duroc x Pietrain resource population: I. Growth traits
J Anim Sci, February 1, 2008; 86(2): 241 - 253.
[Abstract] [Full Text] [PDF]

D. B. Edwards, C. W. Ernst, N. E. Raney, M. E. Doumit, M. D. Hoge, and R. O. Bates
Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Carcass and meat quality traits
J Anim Sci, February 1, 2008; 86(2): 254 - 266.
[Abstract] [Full Text] [PDF]

R. D. Houston, C. S. Haley, A. Hamilton, D. R. Guy, A. E. Tinch, J. B. Taggart, B. J. McAndrew, and S. C. Bishop
Major Quantitative Trait Loci Affect Resistance to Infectious Pancreatic Necrosis in Atlantic Salmon (Salmo salar)
Genetics, February 1, 2008; 178(2): 1109 - 1115.
[Abstract] [Full Text] [PDF]

R. D. Ball
Quantifying Evidence for Candidate Gene Polymorphisms: Bayesian Analysis Combining Sequence-Specific and Quantitative Trait Loci Colocation Information
Genetics, December 1, 2007; 177(4): 2399 - 2416.
[Abstract] [Full Text] [PDF]

M. Chen and C. Kendziorski
A Statistical Framework for Expression Quantitative Trait Loci Mapping
Genetics, October 1, 2007; 177(2): 761 - 771.
[Abstract] [Full Text] [PDF]

L. A. Robertson-Hoyt, C. E. Kleinschmidt, D. G. White, G. A. Payne, C. M. Maragos, and J. B. Holland
Relationships of Resistance to Fusarium Ear Rot and Fumonisin Contamination with Agronomic Performance of Maize
Crop Sci., September 1, 2007; 47(5): 1770 - 1778.
[Abstract] [Full Text] [PDF]

S. Mikawa, T. Morozumi, S.-I. Shimanuki, T. Hayashi, H. Uenishi, M. Domukai, N. Okumura, and T. Awata
Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1)
Genome Res., May 1, 2007; 17(5): 586 - 593.
[Abstract] [Full Text] [PDF]

B. Foley, S. F. Chenoweth, S. V. Nuzhdin, and M. W. Blows
Natural Genetic Variation in Cuticular Hydrocarbon Expression in Male and Female Drosophila melanogaster
Genetics, March 1, 2007; 175(3): 1465 - 1477.
[Abstract] [Full Text] [PDF]

B. Gutierrez-Gil, M. F. El-Zarei, Y. Bayon, L. Alvarez, L. F. de la Fuente, F. S. Primitivo, and J. J. Arranz
Short Communication: Detection of Quantitative Trait Loci Influencing Somatic Cell Score in Spanish Churra Sheep
J Dairy Sci, January 1, 2007; 90(1): 422 - 426.
[Abstract] [Full Text] [PDF]

K. M. Nichols, K. W. Broman, K. Sundin, J. M. Young, P. A. Wheeler, and G. H. Thorgaard
Quantitative Trait Loci x Maternal Cytoplasmic Environment Interaction for Development Rate in Oncorhynchus mykiss
Genetics, January 1, 2007; 175(1): 335 - 347.
[Abstract] [Full Text] [PDF]

E. Karamichou, R. I. Richardson, G. R. Nute, K. P. Gibson, and S. C. Bishop
Genetic analyses and quantitative trait loci detection, using a partial genome scan, for intramuscular fatty acid composition in Scottish Blackface sheep
J Anim Sci, December 1, 2006; 84(12): 3228 - 3238.
[Abstract] [Full Text] [PDF]

M. H. Johansson, M. A. Taylor, M. Jagodic, K. Tus, J. D. Schatzle, E. K. Wakeland, and M. Bennett
Mapping of Quantitative Trait Loci Determining NK Cell-Mediated Resistance to MHC Class I-Deficient Bone Marrow Grafts in Perforin-Deficient Mice
J. Immunol., December 1, 2006; 177(11): 7923 - 7929.
[Abstract] [Full Text] [PDF]

M. Buresova, V. Zidek, A. Musilova, M. Simakova, A. Fucikova, V. Bila, V. Kren, L. Kazdova, R. Di Nicolantonio, and M. Pravenec
Genetic relationship between placental and fetal weights and markers of the metabolic syndrome in rat recombinant inbred strains
Physiol Genomics, September 14, 2006; 26(3): 226 - 231.
[Abstract] [Full Text] [PDF]

A. Manichaikul, J. Dupuis, S. Sen, and K. W. Broman
Poor Performance of Bootstrap Confidence Intervals for the Location of a Quantitative Trait Locus
Genetics, September 1, 2006; 174(1): 481 - 489.
[Abstract] [Full Text] [PDF]

B. S. Schaffer, C. M. Lachel, K. L. Pennington, C. R. Murrin, T. E. Strecker, M. Tochacek, K. A. Gould, J. L. Meza, R. D. McComb, and J. D. Shull
Genetic Bases of Estrogen-Induced Tumorigenesis in the Rat: Mapping of Loci Controlling Susceptibility to Mammary Cancer in a Brown Norway x ACI Intercross.
Cancer Res., August 1, 2006; 66(15): 7793 - 7800.
[Abstract] [Full Text] [PDF]

D. M. Menge, D. Zhong, T. Guda, L. Gouagna, J. Githure, J. Beier, and G. Yan
Quantitative Trait Loci Controlling Refractoriness to Plasmodium falciparum in Natural Anopheles gambiae Mosquitoes From a Malaria-Endemic Region in Western Kenya
Genetics, May 1, 2006; 173(1): 235 - 241.
[Abstract] [Full Text] [PDF]

B. Guo, D. A. Sleper, P. Lu, J. G. Shannon, H. T. Nguyen, and P. R. Arelli
QTLs Associated with Resistance to Soybean Cyst Nematode in Soybean: Meta-Analysis of QTL Locations
Crop Sci., February 1, 2006; 46(2): 595 - 602.
[Abstract] [Full Text] [PDF]

P. L. Johnson, J. C. McEwan, K. G. Dodds, R. W. Purchas, and H. T. Blair
Meat quality traits were unaffected by a quantitative trait locus affecting leg composition traits in Texel sheep
J Anim Sci, December 1, 2005; 83(12): 2729 - 2735.
[Abstract] [Full Text] [PDF]

P. L. Johnson, J. C. McEwan, K. G. Dodds, R. W. Purchas, and H. T. Blair
A directed search in the region of GDF8 for quantitative trait loci affecting carcass traits in Texel sheep
J Anim Sci, September 1, 2005; 83(9): 1988 - 2000.
[Abstract] [Full Text] [PDF]

M. F. Allan, E. J. Eisen, and D. Pomp
Genomic Mapping of Direct and Correlated Responses to Long-Term Selection for Rapid Growth Rate in Mice
Genetics, August 1, 2005; 170(4): 1863 - 1877.
[Abstract] [Full Text] [PDF]

J.-J. Kim, M. F. Rothschild, J. Beever, S. Rodriguez-Zas, and J. C. M. Dekkers
Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci
J Anim Sci, June 1, 2005; 83(6): 1229 - 1240.
[Abstract] [Full Text] [PDF]

N. Bing and I. Hoeschele
Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference
Genetics, June 1, 2005; 170(2): 533 - 542.
[Abstract] [Full Text] [PDF]

R. D. Schnabel, J.-J. Kim, M. S. Ashwell, T. S. Sonstegard, C. P. Van Tassell, E. E. Connor, and J. F. Taylor
Fine-mapping milk production quantitative trait loci on BTA6: Analysis of the bovine osteopontin gene
PNAS, May 10, 2005; 102(19): 6896 - 6901.
[Abstract] [Full Text] [PDF]

T. E. Strecker, T. J. Spady, B. S. Schaffer, K. A. Gould, A. E. Kaufman, F. Shen, M. T. McLaughlin, K. L. Pennington, J. L. Meza, and J. D. Shull
Genetic Bases of Estrogen-Induced Pituitary Tumorigenesis: Identification of Genetic Loci Determining Estrogen-Induced Pituitary Growth in Reciprocal Crosses Between the ACI and Copenhagen Rat Strains
Genetics, April 1, 2005; 169(4): 2189 - 2197.
[Abstract] [Full Text] [PDF]

D. Zhong, A. Pai, and G. Yan
Costly Resistance to Parasitism: Evidence From Simultaneous Quantitative Trait Loci Mapping for Resistance and Fitness in Tribolium castaneum
Genetics, April 1, 2005; 169(4): 2127 - 2135.
[Abstract] [Full Text] [PDF]

K. A. Gould, M. Tochacek, B. S. Schaffer, T. M. Reindl, C. R. Murrin, C. M. Lachel, E. A. VanderWoude, K. L. Pennington, L. A. Flood, K. K. Bynote, et al.
Genetic Determination of Susceptibility to Estrogen-Induced Mammary Cancer in the ACI Rat: Mapping of Emca1 and Emca2 to Chromosomes 5 and 18
Genetics, December 1, 2004; 168(4): 2113 - 2125.
[Abstract] [Full Text] [PDF]

S. N. Forbes, R. K. Valenzuela, P. Keim, and P. M. Service
Quantitative Trait Loci Affecting Life Span in Replicated Populations of Drosophila melanogaster. I. Composite Interval Mapping
Genetics, September 1, 2004; 168(1): 301 - 311.
[Abstract] [Full Text] [PDF]

G. A. Walling, P. M. Visscher, A. D. Wilson, B. L. McTeir, G. Simm, and S. C. Bishop
Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations
J Anim Sci, August 1, 2004; 82(8): 2234 - 2245.
[Abstract] [Full Text] [PDF]

C. Zhang, D.-J. de Koning, J. Hernandez-Sanchez, C. S. Haley, J. L. Williams, and P. Wiener
Mapping of Multiple Quantitative Trait Loci Affecting Bovine Spongiform Encephalopathy
Genetics, August 1, 2004; 167(4): 1863 - 1872.
[Abstract] [Full Text] [PDF]

P. M. Service
How Good Are Quantitative Complementation Tests?
Sci. Aging Knowl. Environ., March 24, 2004; 2004(12): pe13 - pe13.
[Abstract] [Full Text]

M. Ron, E. Feldmesser, M. Golik, I. Tager-Cohen, D. Kliger, V. Reiss, R. Domochovsky, O. Alus, E. Seroussi, E. Ezra, et al.
A Complete Genome Scan of the Israeli Holstein Population for Quantitative Trait Loci by a Daughter Design
J Dairy Sci, February 1, 2004; 87(2): 476 - 490.
[Abstract] [Full Text] [PDF]

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 Sci., January 1, 2004; 44(1): 114 - 124.
[Abstract] [Full Text] [PDF]

M. D. Krakowsky, M. Lee, W. L. Woodman-Clikeman, M. J. Long, and N. Sharopova
QTL Mapping of Resistance to Stalk Tunneling by the European Corn Borer in RILs of Maize Population B73 x De811
Crop Sci., January 1, 2004; 44(1): 274 - 282.
[Abstract] [Full Text] [PDF]

O. Hanotte, Y. Ronin, M. Agaba, P. Nilsson, A. Gelhaus, R. Horstmann, Y. Sugimoto, S. Kemp, J. Gibson, A. Korol, et al.
Mapping of quantitative trait loci controlling trypanotolerance in a cross of tolerant West African N'Dama and susceptible East African Boran cattle
PNAS, June 24, 2003; 100(13): 7443 - 7448.
[Abstract] [Full Text] [PDF]

D. J. de Koning, D. Windsor, P. M. Hocking, D. W. Burt, A. Law, C. S. Haley, A. Morris, J. Vincent, and H. Griffin
Quantitative trait locus detection in commercial broiler lines using candidate regions
J Anim Sci, May 1, 2003; 81(5): 1158 - 1165.
[Abstract] [Full Text] [PDF]

D. Steinberger, D. S. Reynolds, P. Ferris, R. Lincoln, S. Datta, J. Stanley, A. Paterson, G. R. Dawson, and J. Flint
Genetic Mapping of Variation in Spatial Learning in the Mouse
J. Neurosci., March 15, 2003; 23(6): 2426 - 2433.
[Abstract] [Full Text] [PDF]

O. Loudet, S. Chaillou, A. Krapp, and F. Daniel-Vedele
Quantitative Trait Loci Analysis of Water and Anion Contents in Interaction With Nitrogen Availability in Arabidopsis thaliana
Genetics, February 1, 2003; 163(2): 711 - 722.
[Abstract] [Full Text] [PDF]

M. Reymond, B. Muller, A. Leonardi, A. Charcosset, and F. Tardieu
Combining Quantitative Trait Loci Analysis and an Ecophysiological Model to Analyze the Genetic Variability of the Responses of Maize Leaf Growth to Temperature and Water Deficit
Plant Physiology, February 1, 2003; 131(2): 664 - 675.
[Abstract] [Full Text] [PDF]

S. Blott, J.-J. Kim, S. Moisio, A. Schmidt-Kuntzel, A. Cornet, P. Berzi, N. Cambisano, C. Ford, B. Grisart, D. Johnson, et al.
Molecular Dissection of a Quantitative Trait Locus: A Phenylalanine-to-Tyrosine Substitution in the Transmembrane Domain of the Bovine Growth Hormone Receptor Is Associated With a Major Effect on Milk Yield and Composition
Genetics, January 1, 2003; 163(1): 253 - 266.
[Abstract] [Full Text] [PDF]

O. Loudet, S. Chaillou, P. Merigout, J. Talbotec, and F. Daniel-Vedele
Quantitative Trait Loci Analysis of Nitrogen Use Efficiency in Arabidopsis
Plant Physiology, January 1, 2003; 131(1): 345 - 358.
[Abstract] [Full Text] [PDF]

J. Slate, P. M. Visscher, S. MacGregor, D. Stevens, M. L. Tate, and J. M. Pemberton
A Genome Scan for Quantitative Trait Loci in a Wild Population of Red Deer (Cervus elaphus)
Genetics, December 1, 2002; 162(4): 1863 - 1873.
[Abstract] [Full Text] [PDF]

H. G. Olsen, L. Gomez-Raya, D. I. Vage, I. Olsaker, H. Klungland, M. Svendsen, T. Adnoy, A. Sabry, G. Klemetsdal, N. Schulman, et al.
A Genome Scan for Quantitative Trait Loci Affecting Milk Production in Norwegian Dairy Cattle
J Dairy Sci, November 1, 2002; 85(11): 3124 - 3130.
[Abstract] [Full Text] [PDF]

J. I. Weller, H. Weller, D. Kliger, and M. Ron
Estimation of Quantitative Trait Locus Allele Frequency via a Modified Granddaughter Design
Genetics, October 1, 2002; 162(2): 841 - 849.
[Abstract] [Full Text] [PDF]

M. D. Krakowsky, M. J. Brinkman, W. L. Woodman-Clikeman, and M. Lee
Genetic Components of Resistance to Stalk Tunneling by the European Corn Borer in Maize
Crop Sci., July 1, 2002; 42(4): 1309 - 1315.
[Abstract] [Full Text] [PDF]

J. Bennewitz, N. Reinsch, and E. Kalm
Improved Confidence Intervals in Quantitative Trait Loci Mapping by Permutation Bootstrapping
Genetics, April 1, 2002; 160(4): 1673 - 1686.
[Abstract] [Full Text] [PDF]

R. D. Ball
Bayesian Methods for Quantitative Trait Loci Mapping Based on Model Selection: Approximate Analysis Using the Bayesian Information Criterion
Genetics, November 1, 2001; 159(3): 1351 - 1364.
[Abstract] [Full Text] [PDF]

M. Ron, D. Kliger, E. Feldmesser, E. Seroussi, E. Ezra, and J. I. Weller
Multiple Quantitative Trait Locus Analysis of Bovine Chromosome 6 in the Israeli Holstein Population by a Daughter Design
Genetics, October 1, 2001; 159(2): 727 - 735.
[Abstract] [Full Text] [PDF]

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 Sci., May 1, 2001; 41(3): 835 - 845.
[Abstract] [Full Text] [PDF]

S. P. Otto and C. D. Jones
Detecting the Undetected: Estimating the Total Number of Loci Underlying a Quantitative Trait
Genetics, December 1, 2000; 156(4): 2093 - 2107.
[Abstract] [Full Text]

Z. W. Luo, S. H. Tao, and Z-B. Zeng
Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations
Genetics, September 1, 2000; 156(1): 457 - 467.
[Abstract] [Full Text]

G. A. Walling, P. M. Visscher, L. Andersson, M. F. Rothschild, L. Wang, G. Moser, M. A. M. Groenen, J.-P. Bidanel, S. Cepica, A. L. Archibald, et al.
Combined Analyses of Data From Quantitative Trait Loci Mapping Studies: Chromosome 4 Effects on Porcine Growth and Fatness
Genetics, July 1, 2000; 155(3): 1369 - 1378.
[Abstract] [Full Text]

N. Yi and S. Xu
Bayesian Mapping of Quantitative Trait Loci for Complex Binary Traits
Genetics, July 1, 2000; 155(3): 1391 - 1403.
[Abstract] [Full Text]

M. Pérez-Enciso and L. Varona
Quantitative Trait Loci Mapping in F2 Crosses Between Outbred Lines
Genetics, May 1, 2000; 155(1): 391 - 405.
[Abstract] [Full Text]

H. F. Utz, A. E. Melchinger, and C. C. Schön
Bias and Sampling Error of the Estimated Proportion of Genotypic Variance Explained by Quantitative Trait Loci Determined From Experimental Data in Maize Using Cross Validation and Validation With Independent Samples
Genetics, April 1, 2000; 154(4): 1839 - 1849.
[Abstract] [Full Text]

S. J. Macdonald and D. B. Goldstein
A Quantitative Genetic Analysis of Male Sexual Traits Distinguishing the Sibling Species Drosophila simulans and D. sechellia
Genetics, December 1, 1999; 153(4): 1683 - 1699.
[Abstract] [Full Text]

J. Dupuis and D. Siegmund
Statistical Methods for Mapping Quantitative Trait Loci From a Dense Set of Markers
Genetics, January 1, 1999; 151(1): 373 - 386.
[Abstract] [Full Text]

C. M. Lebreton, P. M. Visscher, C. S. Haley, A. Semikhodskii, and S. A. Quarrie
A Nonparametric Bootstrap Method for Testing Close Linkage vs. Pleiotropy of Coincident Quantitative Trait Loci
Genetics, October 1, 1998; 150(2): 931 - 943.
[Abstract] [Full Text]

Q. Zhang, D. Boichard, I. Hoeschele, C. Ernst, A. Eggen, B. Murkve, M. Pfister-Genskow, L. A. Witte, F. E. Grignola, P. Uimari, et al.
Mapping Quantitative Trait Loci for Milk Production and Health of Dairy Cattle in a Large Outbred Pedigree
Genetics, August 1, 1998; 149(4): 1959 - 1973.
[Abstract] [Full Text] [PDF]

				K. M. Nichols, A. F. Edo, P. A. Wheeler, and G. H. Thorgaard The Genetic Basis of Smoltification-Related Traits in Oncorhynchus mykiss Genetics, July 1, 2008; 179(3): 1559 - 1575. [Abstract] [Full Text] [PDF]

				C. R. Moreno, G. M. Cosseddu, L. Schibler, A. Roig, K. Moazami-Goudarzi, O. Andreoletti, F. Eychenne, D. Lajous, F. Schelcher, E. P. Cribiu, et al. Identification of New Quantitative Trait Loci (Other Than the PRNP Gene) Modulating the Scrapie Incubation Period in Sheep Genetics, May 1, 2008; 179(1): 723 - 726. [Abstract] [Full Text] [PDF]

				J. I. Weller, M. Golik, S. Reikhav, R. Domochovsky, E. Seroussi, and M. Ron Detection and Analysis of Quantitative Trait Loci Affecting Production and Secondary Traits on Chromosome 7 in Israeli Holsteins J Dairy Sci, February 1, 2008; 91(2): 802 - 813. [Abstract] [Full Text] [PDF]

				D. B. Edwards, C. W. Ernst, R. J. Tempelman, G. J. M. Rosa, N. E. Raney, M. D. Hoge, and R. O. Bates Quantitative trait loci mapping in an F2 Duroc x Pietrain resource population: I. Growth traits J Anim Sci, February 1, 2008; 86(2): 241 - 253. [Abstract] [Full Text] [PDF]

				D. B. Edwards, C. W. Ernst, N. E. Raney, M. E. Doumit, M. D. Hoge, and R. O. Bates Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Carcass and meat quality traits J Anim Sci, February 1, 2008; 86(2): 254 - 266. [Abstract] [Full Text] [PDF]

				R. D. Houston, C. S. Haley, A. Hamilton, D. R. Guy, A. E. Tinch, J. B. Taggart, B. J. McAndrew, and S. C. Bishop Major Quantitative Trait Loci Affect Resistance to Infectious Pancreatic Necrosis in Atlantic Salmon (Salmo salar) Genetics, February 1, 2008; 178(2): 1109 - 1115. [Abstract] [Full Text] [PDF]

				R. D. Ball Quantifying Evidence for Candidate Gene Polymorphisms: Bayesian Analysis Combining Sequence-Specific and Quantitative Trait Loci Colocation Information Genetics, December 1, 2007; 177(4): 2399 - 2416. [Abstract] [Full Text] [PDF]

				M. Chen and C. Kendziorski A Statistical Framework for Expression Quantitative Trait Loci Mapping Genetics, October 1, 2007; 177(2): 761 - 771. [Abstract] [Full Text] [PDF]

				L. A. Robertson-Hoyt, C. E. Kleinschmidt, D. G. White, G. A. Payne, C. M. Maragos, and J. B. Holland Relationships of Resistance to Fusarium Ear Rot and Fumonisin Contamination with Agronomic Performance of Maize Crop Sci., September 1, 2007; 47(5): 1770 - 1778. [Abstract] [Full Text] [PDF]

				S. Mikawa, T. Morozumi, S.-I. Shimanuki, T. Hayashi, H. Uenishi, M. Domukai, N. Okumura, and T. Awata Fine mapping of a swine quantitative trait locus for number of vertebrae and analysis of an orphan nuclear receptor, germ cell nuclear factor (NR6A1) Genome Res., May 1, 2007; 17(5): 586 - 593. [Abstract] [Full Text] [PDF]

				B. Foley, S. F. Chenoweth, S. V. Nuzhdin, and M. W. Blows Natural Genetic Variation in Cuticular Hydrocarbon Expression in Male and Female Drosophila melanogaster Genetics, March 1, 2007; 175(3): 1465 - 1477. [Abstract] [Full Text] [PDF]

				B. Gutierrez-Gil, M. F. El-Zarei, Y. Bayon, L. Alvarez, L. F. de la Fuente, F. S. Primitivo, and J. J. Arranz Short Communication: Detection of Quantitative Trait Loci Influencing Somatic Cell Score in Spanish Churra Sheep J Dairy Sci, January 1, 2007; 90(1): 422 - 426. [Abstract] [Full Text] [PDF]

				K. M. Nichols, K. W. Broman, K. Sundin, J. M. Young, P. A. Wheeler, and G. H. Thorgaard Quantitative Trait Loci x Maternal Cytoplasmic Environment Interaction for Development Rate in Oncorhynchus mykiss Genetics, January 1, 2007; 175(1): 335 - 347. [Abstract] [Full Text] [PDF]

				E. Karamichou, R. I. Richardson, G. R. Nute, K. P. Gibson, and S. C. Bishop Genetic analyses and quantitative trait loci detection, using a partial genome scan, for intramuscular fatty acid composition in Scottish Blackface sheep J Anim Sci, December 1, 2006; 84(12): 3228 - 3238. [Abstract] [Full Text] [PDF]

				M. H. Johansson, M. A. Taylor, M. Jagodic, K. Tus, J. D. Schatzle, E. K. Wakeland, and M. Bennett Mapping of Quantitative Trait Loci Determining NK Cell-Mediated Resistance to MHC Class I-Deficient Bone Marrow Grafts in Perforin-Deficient Mice J. Immunol., December 1, 2006; 177(11): 7923 - 7929. [Abstract] [Full Text] [PDF]

				M. Buresova, V. Zidek, A. Musilova, M. Simakova, A. Fucikova, V. Bila, V. Kren, L. Kazdova, R. Di Nicolantonio, and M. Pravenec Genetic relationship between placental and fetal weights and markers of the metabolic syndrome in rat recombinant inbred strains Physiol Genomics, September 14, 2006; 26(3): 226 - 231. [Abstract] [Full Text] [PDF]

				A. Manichaikul, J. Dupuis, S. Sen, and K. W. Broman Poor Performance of Bootstrap Confidence Intervals for the Location of a Quantitative Trait Locus Genetics, September 1, 2006; 174(1): 481 - 489. [Abstract] [Full Text] [PDF]

				B. S. Schaffer, C. M. Lachel, K. L. Pennington, C. R. Murrin, T. E. Strecker, M. Tochacek, K. A. Gould, J. L. Meza, R. D. McComb, and J. D. Shull Genetic Bases of Estrogen-Induced Tumorigenesis in the Rat: Mapping of Loci Controlling Susceptibility to Mammary Cancer in a Brown Norway x ACI Intercross. Cancer Res., August 1, 2006; 66(15): 7793 - 7800. [Abstract] [Full Text] [PDF]

				D. M. Menge, D. Zhong, T. Guda, L. Gouagna, J. Githure, J. Beier, and G. Yan Quantitative Trait Loci Controlling Refractoriness to Plasmodium falciparum in Natural Anopheles gambiae Mosquitoes From a Malaria-Endemic Region in Western Kenya Genetics, May 1, 2006; 173(1): 235 - 241. [Abstract] [Full Text] [PDF]

				B. Guo, D. A. Sleper, P. Lu, J. G. Shannon, H. T. Nguyen, and P. R. Arelli QTLs Associated with Resistance to Soybean Cyst Nematode in Soybean: Meta-Analysis of QTL Locations Crop Sci., February 1, 2006; 46(2): 595 - 602. [Abstract] [Full Text] [PDF]

				P. L. Johnson, J. C. McEwan, K. G. Dodds, R. W. Purchas, and H. T. Blair Meat quality traits were unaffected by a quantitative trait locus affecting leg composition traits in Texel sheep J Anim Sci, December 1, 2005; 83(12): 2729 - 2735. [Abstract] [Full Text] [PDF]

				M. F. Allan, E. J. Eisen, and D. Pomp Genomic Mapping of Direct and Correlated Responses to Long-Term Selection for Rapid Growth Rate in Mice Genetics, August 1, 2005; 170(4): 1863 - 1877. [Abstract] [Full Text] [PDF]

				J.-J. Kim, M. F. Rothschild, J. Beever, S. Rodriguez-Zas, and J. C. M. Dekkers Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci J Anim Sci, June 1, 2005; 83(6): 1229 - 1240. [Abstract] [Full Text] [PDF]

				N. Bing and I. Hoeschele Genetical Genomics Analysis of a Yeast Segregant Population for Transcription Network Inference Genetics, June 1, 2005; 170(2): 533 - 542. [Abstract] [Full Text] [PDF]

				R. D. Schnabel, J.-J. Kim, M. S. Ashwell, T. S. Sonstegard, C. P. Van Tassell, E. E. Connor, and J. F. Taylor Fine-mapping milk production quantitative trait loci on BTA6: Analysis of the bovine osteopontin gene PNAS, May 10, 2005; 102(19): 6896 - 6901. [Abstract] [Full Text] [PDF]

				T. E. Strecker, T. J. Spady, B. S. Schaffer, K. A. Gould, A. E. Kaufman, F. Shen, M. T. McLaughlin, K. L. Pennington, J. L. Meza, and J. D. Shull Genetic Bases of Estrogen-Induced Pituitary Tumorigenesis: Identification of Genetic Loci Determining Estrogen-Induced Pituitary Growth in Reciprocal Crosses Between the ACI and Copenhagen Rat Strains Genetics, April 1, 2005; 169(4): 2189 - 2197. [Abstract] [Full Text] [PDF]

				D. Zhong, A. Pai, and G. Yan Costly Resistance to Parasitism: Evidence From Simultaneous Quantitative Trait Loci Mapping for Resistance and Fitness in Tribolium castaneum Genetics, April 1, 2005; 169(4): 2127 - 2135. [Abstract] [Full Text] [PDF]

				K. A. Gould, M. Tochacek, B. S. Schaffer, T. M. Reindl, C. R. Murrin, C. M. Lachel, E. A. VanderWoude, K. L. Pennington, L. A. Flood, K. K. Bynote, et al. Genetic Determination of Susceptibility to Estrogen-Induced Mammary Cancer in the ACI Rat: Mapping of Emca1 and Emca2 to Chromosomes 5 and 18 Genetics, December 1, 2004; 168(4): 2113 - 2125. [Abstract] [Full Text] [PDF]

				S. N. Forbes, R. K. Valenzuela, P. Keim, and P. M. Service Quantitative Trait Loci Affecting Life Span in Replicated Populations of Drosophila melanogaster. I. Composite Interval Mapping Genetics, September 1, 2004; 168(1): 301 - 311. [Abstract] [Full Text] [PDF]

				G. A. Walling, P. M. Visscher, A. D. Wilson, B. L. McTeir, G. Simm, and S. C. Bishop Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations J Anim Sci, August 1, 2004; 82(8): 2234 - 2245. [Abstract] [Full Text] [PDF]