help button home button Genetics Journal Watch
HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrow reprints & permissions
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Kao, C.-H.
Right arrow Articles by Teasdale, R. D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Kao, C.-H.
Right arrow Articles by Teasdale, R. D.
Genetics, Vol. 152, 1203-1216, July 1999, Copyright © 1999

Multiple Interval Mapping for Quantitative Trait Loci

Chen-Hung Kaoa, Zhao-Bang Zengb, and Robert D. Teasdalec
a Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan, Republic of China,
b Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695-8203
c ForBio Research Pty Ltd., Toowong, Queensland 4066, Australia

Corresponding author: Chen-Hung Kao, Institute of Statistical Science, Academia Sinica, Taipei 11529, Taiwan, Republic of China., chkao{at}stat.sinica.edu.tw (E-mail)

Communicating editor: C.-I WU

A new statistical method for mapping quantitative trait loci (QTL), called multiple interval mapping (MIM), is presented. It uses multiple marker intervals simultaneously to fit multiple putative QTL directly in the model for mapping QTL. The MIM model is based on Cockerham's model for interpreting genetic parameters and the method of maximum likelihood for estimating genetic parameters. With the MIM approach, the precision and power of QTL mapping could be improved. Also, epistasis between QTL, genotypic values of individuals, and heritabilities of quantitative traits can be readily estimated and analyzed. Using the MIM model, a stepwise selection procedure with likelihood ratio test statistic as a criterion is proposed to identify QTL. This MIM method was applied to a mapping data set of radiata pine on three traits: brown cone number, tree diameter, and branch quality scores. Based on the MIM result, seven, six, and five QTL were detected for the three traits, respectively. The detected QTL individually contributed from ~1 to 27% of the total genetic variation. Significant epistasis between four pairs of QTL in two traits was detected, and the four pairs of QTL contributed ~10.38 and 14.14% of the total genetic variation. The asymptotic variances of QTL positions and effects were also provided to construct the confidence intervals. The estimated heritabilities were 0.5606, 0.5226, and 0.3630 for the three traits, respectively. With the estimated QTL effects and positions, the best strategy of marker-assisted selection for trait improvement for a specific purpose and requirement can be explored. The MIM FORTRAN program is available on the worldwide web (http://www.stat.sinica.edu.tw/~chkao/).




This article has been cited by other articles:


Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
N. Yi and S. Xu
Bayesian LASSO for Quantitative Trait Loci Mapping
Genetics, June 1, 2008; 179(2): 1045 - 1055.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C.-X. Ma, Q. Yu, A. Berg, D. Drost, E. Novaes, G. Fu, J. S. Yap, A. Tan, M. Kirst, Y. Cui, et al.
A Statistical Model for Testing the Pleiotropic Control of Phenotypic Plasticity for a Count Trait
Genetics, May 1, 2008; 179(1): 627 - 636.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. E. Melchinger, H. F. Utz, and C. C. Schon
Genetic Expectations of Quantitative Trait Loci Main and Interaction Effects Obtained With the Triple Testcross Design and Their Relevance for the Analysis of Heterosis
Genetics, April 1, 2008; 178(4): 2265 - 2274.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Yang, C. Hu, H. Hu, R. Yu, Z. Xia, X. Ye, and J. Zhu
QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations
Bioinformatics, March 1, 2008; 24(5): 721 - 723.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. Yang, W. Wu, and J. Zhu
Mapping Interspecific Genetic Architecture in a Host-Parasite Interaction System
Genetics, March 1, 2008; 178(3): 1737 - 1743.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Kaga, T. Isemura, N. Tomooka, and D. A. Vaughan
The Genetics of Domestication of the Azuki Bean (Vigna angularis)
Genetics, February 1, 2008; 178(2): 1013 - 1036.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Maccaferri, M. C. Sanguineti, S. Corneti, J. L. A. Ortega, M. B. Salem, J. Bort, E. DeAmbrogio, L. F. G. del Moral, A. Demontis, A. El-Ahmed, et al.
Quantitative Trait Loci for Grain Yield and Adaptation of Durum Wheat (Triticum durum Desf.) Across a Wide Range of Water Availability
Genetics, January 1, 2008; 178(1): 489 - 511.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
T.-S. Kim, B. A. Logsdon, S. Park, J. G. Mezey, and K. Lee
Quantitative Trait Loci for the Circadian Clock in Neurospora crassa
Genetics, December 1, 2007; 177(4): 2335 - 2347.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. E. Melchinger, H. F. Utz, H.-P. Piepho, Z.-B. Zeng, and C. C. Schon
The Role of Epistasis in the Manifestation of Heterosis: A Systems-Oriented Approach
Genetics, November 1, 2007; 177(3): 1815 - 1825.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. Yang, H. Gao, X. Wang, J. Zhang, Z.-B. Zeng, and R. Wu
A Semiparametric Approach for Composite Functional Mapping of Dynamic Quantitative Traits
Genetics, November 1, 2007; 177(3): 1859 - 1870.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. Zhong and J.-L. Jannink
Using Quantitative Trait Loci Results to Discriminate Among Crosses on the Basis of Their Progeny Mean and Variance
Genetics, September 1, 2007; 177(1): 567 - 576.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
H. Huang, C. D. Eversley, D. W. Threadgill, and F. Zou
Bayesian Multiple Quantitative Trait Loci Mapping for Complex Traits Using Markers of the Entire Genome
Genetics, August 1, 2007; 176(4): 2529 - 2540.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
D. M. Wills and J. M. Burke
Quantitative Trait Locus Analysis of the Early Domestication of Sunflower
Genetics, August 1, 2007; 176(4): 2589 - 2599.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Yi, D. Shriner, S. Banerjee, T. Mehta, D. Pomp, and B. S. Yandell
An Efficient Bayesian Model Selection Approach for Interacting Quantitative Trait Loci Models With Many Effects
Genetics, July 1, 2007; 176(3): 1865 - 1877.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Zak, A. Baierl, M. Bogdan, and A. Futschik
Locating Multiple Interacting Quantitative Trait Loci Using Rank-Based Model Selection
Genetics, July 1, 2007; 176(3): 1845 - 1854.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Yi, S. Banerjee, D. Pomp, and B. S. Yandell
Bayesian Mapping of Genomewide Interacting Quantitative Trait Loci for Ordinal Traits
Genetics, July 1, 2007; 176(3): 1855 - 1864.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
J. Yang, J. Zhu, and R. W. Williams
Mapping the genetic architecture of complex traits in experimental populations
Bioinformatics, June 15, 2007; 23(12): 1527 - 1536.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. Yang and S. Xu
Bayesian Shrinkage Analysis of Quantitative Trait Loci for Dynamic Traits
Genetics, June 1, 2007; 176(2): 1169 - 1185.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Z. Jia and S. Xu
Mapping Quantitative Trait Loci for Expression Abundance
Genetics, May 1, 2007; 176(1): 611 - 623.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. H. Martin, A. C. Bouck, and M. L. Arnold
The Genetic Architecture of Reproductive Isolation in Louisiana Irises: Flowering Phenology
Genetics, April 1, 2007; 175(4): 1803 - 1812.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
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]

Home page
 GeneticsHome page
H. Li, G. Ye, and J. Wang
A Modified Algorithm for the Improvement of Composite Interval Mapping
Genetics, January 1, 2007; 175(1): 361 - 374.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Y. Cui, D.-Y. Kim, and J. Zhu
On the Generalized Poisson Regression Mixture Model for Mapping Quantitative Trait Loci With Count Data
Genetics, December 1, 2006; 174(4): 2159 - 2172.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C.-H. Kao
Mapping Quantitative Trait Loci Using the Experimental Designs of Recombinant Inbred Populations
Genetics, November 1, 2006; 174(3): 1373 - 1386.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Z. Liu, K. Adamczyk, M. Manzanares-Dauleux, F. Eber, M.-O. Lucas, R. Delourme, A. M. Chevre, and E. Jenczewski
Mapping PrBn and Other Quantitative Trait Loci Responsible for the Control of Homeologous Chromosome Pairing in Oilseed Rape (Brassica napus L.) Haploids
Genetics, November 1, 2006; 174(3): 1583 - 1596.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
P. Hanlon, W. A. Lorenz, Z. Shao, J. M. Harper, A. T. Galecki, R. A. Miller, and D. T. Burke
Three-locus and four-locus QTL interactions influence mouse insulin-like growth factor-I
Physiol Genomics, September 14, 2006; 26(1): 46 - 54.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. Feenstra, I. M. Skovgaard, and K. W. Broman
Mapping Quantitative Trait Loci by an Extension of the Haley-Knott Regression Method Using Estimating Equations
Genetics, August 1, 2006; 173(4): 2269 - 2282.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
R. Yang, Q. Tian, and S. Xu
Mapping Quantitative Trait Loci for Longitudinal Traits in Line Crosses
Genetics, August 1, 2006; 173(4): 2339 - 2356.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. H. Lee and J. H. J. Van der Werf
Simultaneous Fine Mapping of Multiple Closely Linked Quantitative Trait Loci Using Combined Linkage Disequilibrium and Linkage With a General Pedigree
Genetics, August 1, 2006; 173(4): 2329 - 2337.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. Li, S. Wang, and Z.-B. Zeng
Multiple-Interval Mapping for Ordinal Traits
Genetics, July 1, 2006; 173(3): 1649 - 1663.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
A. Baierl, M. Bogdan, F. Frommlet, and A. Futschik
On Locating Multiple Interacting Quantitative Trait Loci in Intercross Designs
Genetics, July 1, 2006; 173(3): 1693 - 1703.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. H. Martin, A. C. Bouck, and M. L. Arnold
Detecting Adaptive Trait Introgression Between Iris fulva and I. brevicaulis in Highly Selective Field Conditions
Genetics, April 1, 2006; 172(4): 2481 - 2489.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
M. Zhao, Z. Zhang, S. Zhang, W. Li, D. P. Jeffers, T. Rong, and G. Pan
Quantitative Trait Loci for Resistance to Banded Leaf and Sheath Blight in Maize
Crop Sci., March 27, 2006; 46(3): 1039 - 1045.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
C. Yagil, M. Sapojnikov, A. Wechsler, A. Korol, and Y. Yagil
Genetic dissection of proteinuria in the Sabra rat
Physiol Genomics, March 13, 2006; 25(1): 121 - 133.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
J. Leips, P. Gilligan, and T. F. C. Mackay
Quantitative Trait Loci With Age-Specific Effects on Fecundity in Drosophila melanogaster
Genetics, March 1, 2006; 172(3): 1595 - 1605.
[Abstract] [Full Text] [PDF]

Home page
 Crop Sci.Home page
T. D. Brooks, M. C. Willcox, W. P. Williams, and P. M. Buckley
Quantitative Trait Loci Conferring Resistance to Fall Armyworm and Southwestern Corn Borer Leaf Feeding Damage
Crop Sci., October 27, 2005; 45(6): 2430 - 2434.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. J. Coffman, R. W. Doerge, K. L. Simonsen, K. M. Nichols, C. K. Duarte, R. D. Wolfinger, and L. M. McIntyre
Model Selection in Binary Trait Locus Mapping
Genetics, July 1, 2005; 170(3): 1281 - 1297.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Yi, B. S. Yandell, G. A. Churchill, D. B. Allison, E. J. Eisen, and D. Pomp
Bayesian Model Selection for Genome-Wide Epistatic Quantitative Trait Loci Analysis
Genetics, July 1, 2005; 170(3): 1333 - 1344.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
H. Wang, Y.-M. Zhang, X. Li, G. L. Masinde, S. Mohan, D. J. Baylink, and S. Xu
Bayesian Shrinkage Estimation of Quantitative Trait Loci Parameters
Genetics, May 1, 2005; 170(1): 465 - 480.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Zhang, K. L. Montooth, M. T. Wells, A. G. Clark, and D. Zhang
Mapping Multiple Quantitative Trait Loci by Bayesian Classification
Genetics, April 1, 2005; 169(4): 2305 - 2318.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C. Lexer, D. M. Rosenthal, O. Raymond, L. A. Donovan, and L. H. Rieseberg
Genetics of Species Differences in the Wild Annual Sunflowers, Helianthus annuus and H. petiolaris
Genetics, April 1, 2005; 169(4): 2225 - 2239.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Kirst, C. J. Basten, A. A. Myburg, Z.-B. Zeng, and R. R. Sederoff
Genetic Architecture of Transcript-Level Variation in Differentiating Xylem of a Eucalyptus Hybrid
Genetics, April 1, 2005; 169(4): 2295 - 2303.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Y.-M. Zhang, Y. Mao, C. Xie, H. Smith, L. Luo, and S. Xu
Mapping Quantitative Trait Loci Using Naturally Occurring Genetic Variance Among Commercial Inbred Lines of Maize (Zea mays L.)
Genetics, April 1, 2005; 169(4): 2267 - 2275.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Z.-B. Zeng, T. Wang, and W. Zou
Modeling Quantitative Trait Loci and Interpretation of Models
Genetics, March 1, 2005; 169(3): 1711 - 1725.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
F. Zou, J. P. Fine, J. Hu, and D. Y. Lin
An Efficient Resampling Method for Assessing Genome-Wide Statistical Significance in Mapping Quantitative Trait Loci
Genetics, December 1, 2004; 168(4): 2307 - 2316.
[Abstract] [Full Text] [PDF]

Home page
 J. Lipid Res.Home page
N. Yi, S. Chiu, D. B. Allison, J. S. Fisler, and C. H. Warden
Epistatic interaction between two nonstructural loci on chromosomes 7 and 3 influences hepatic lipase activity in BSB mice
J. Lipid Res., November 1, 2004; 45(11): 2063 - 2070.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
G. Diao, D. Y. Lin, and F. Zou
Mapping Quantitative Trait Loci With Censored Observations
Genetics, November 1, 2004; 168(3): 1689 - 1698.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
C.-H. Kao
Multiple-Interval Mapping for Quantitative Trait Loci Controlling Endosperm Traits
Genetics, August 1, 2004; 167(4): 1987 - 2002.
[Abstract] [Full Text] [PDF]

Home page
 Plant Physiol.Home page
M. Kirst, A. A. Myburg, J. P.G. De Leon, M. E. Kirst, J. Scott, and R. Sederoff
Coordinated Genetic Regulation of Growth and Lignin Revealed by Quantitative Trait Locus Analysis of cDNA Microarray Data in an Interspecific Backcross of Eucalyptus
Plant Physiology, August 1, 2004; 135(4): 2368 - 2378.
[Abstract] [Full Text] [PDF]

Home page
 FASEB J.Home page
M. S. ROGERS, R. M. ROHAN, A. E. BIRSNER, and R. J. D'AMATO
Genetic loci that control the angiogenic response to basic fibroblast growth factor
FASEB J, July 1, 2004; 18(10): 1050 - 1059.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
B. Feenstra and I. M. Skovgaard
A Quantitative Trait Locus Mixture Model That Avoids Spurious LOD Score Peaks
Genetics, June 1, 2004; 167(2): 959 - 965.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Bogdan, J. K. Ghosh, and R. W. Doerge
Modifying the Schwarz Bayesian Information Criterion to Locate Multiple Interacting Quantitative Trait Loci
Genetics, June 1, 2004; 167(2): 989 - 999.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
M. Slotman, A. della Torre, and J. R. Powell
The Genetics of Inviability and Male Sterility in Hybrids Between Anopheles gambiae and An. arabiensis
Genetics, May 1, 2004; 167(1): 275 - 287.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Y.-M. Zhang and S. Xu
Mapping Quantitative Trait Loci in F2 Incorporating Phenotypes of F3 Progeny
Genetics, April 1, 2004; 166(4): 1981 - 1993.
[Abstract] [Full Text] [PDF]

Home page
 DiabetesHome page
H. Lan, M. E. Rabaglia, K. L. Schueler, C. Mata, B. S. Yandell, and A. D. Attie
Distinguishing Covariation From Causation in Diabetes: A Lesson From the Protein Disulfide Isomerase mRNA Abundance Trait
Diabetes, January 1, 2004; 53(1): 240 - 244.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
A. Lionikas, D. A. Blizard, D. J. Vandenbergh, M. G. Glover, J. T. Stout, G. P. Vogler, G. E. McClearn, and L. Larsson
Genetic architecture of fast- and slow-twitch skeletal muscle weight in 200-day-old mice of the C57BL/6J and DBA/2J lineage
Physiol Genomics, December 16, 2003; 16(1): 141 - 152.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
F. Zou, B. S. Yandell, and J. P. Fine
Rank-Based Statistical Methodologies for Quantitative Trait Locus Mapping
Genetics, November 1, 2003; 165(3): 1599 - 1605.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Yi, S. Xu, and D. B. Allison
Bayesian Model Choice and Search Strategies for Mapping Interacting Quantitative Trait Loci
Genetics, October 1, 2003; 165(2): 867 - 883.
[Abstract] [Full Text] [PDF]

Home page
 Physiol. GenomicsHome page
M. A. Lyons, H. Wittenburg, R. Li, K. A. Walsh, M. R. Leonard, G. A. Churchill, M. C. Carey, and B. Paigen
New quantitative trait loci that contribute to cholesterol gallstone formation detected in an intercross of CAST/Ei and 129S1/SvImJ inbred mice
Physiol Genomics, August 15, 2003; 14(3): 225 - 239.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
Y. Tao, Z.-B. Zeng, J. Li, D. L. Hartl, and C. C. Laurie
Genetic Dissection of Hybrid Incompatibilities Between Drosophila simulans and D. mauritiana. II. Mapping Hybrid Male Sterility Loci on the Third Chromosome
Genetics, August 1, 2003; 164(4): 1399 - 1418.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
H. Lan, J. P. Stoehr, S. T. Nadler, K. L. Schueler, B. S. Yandell, and A. D. Attie
Dimension Reduction for Mapping mRNA Abundance as Quantitative Traits
Genetics, August 1, 2003; 164(4): 1607 - 1614.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
T. C. Lystig
Adjusted P Values for Genome-Wide Scans
Genetics, August 1, 2003; 164(4): 1683 - 1687.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
N. Yi, V. George, and D. B. Allison
Stochastic Search Variable Selection for Identifying Multiple Quantitative Trait Loci
Genetics, July 1, 2003; 164(3): 1129 - 1138.