High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

INVESTIGATIONS

High Resolution of Quantitative Traits Into Multiple Loci via Interval Mapping

R. C. Jansen and P. Stam
Centre for Plant Breeding and Reproduction Research (CPRO-DLO), Department of Population Biology, P.O. Box 16, 6700 AA Wageningen, The Netherlands

A very general method is described for multiple linear regression of a quantitative phenotype on genotype [putative quantitative trait loci (QTLs) and markers] in segregating generations obtained from line crosses. The method exploits two features, (a) the use of additional parental and F(1) data, which fixes the joint QTL effects and the environmental error, and (b) the use of markers as cofactors, which reduces the genetic background noise. As a result, a significant increase of QTL detection power is achieved in comparison with conventional QTL mapping. The core of the method is the completion of any missing genotypic (QTL and marker) observations, which is embedded in a general and simple expectation maximization (EM) algorithm to obtain maximum likelihood estimates of the model parameters. The method is described in detail for the analysis of an F(2) generation. Because of the generality of the approach, it is easily applicable to other generations, such as backcross progenies and recombinant inbred lines. An example is presented in which multiple QTLs for plant height in tomato are mapped in an F(2) progeny, using additional data from the parents and their F(1) progeny.

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				H. Jafary, G. Albertazzi, T. C. Marcel, and R. E. Niks High Diversity of Genes for Nonhost Resistance of Barley to Heterologous Rust Fungi Genetics, April 1, 2008; 178(4): 2327 - 2339. [Abstract] [Full Text] [PDF]

				J. S. Freeman, B. M. Potts, and R. E. Vaillancourt Few Mendelian Genes Underlie the Quantitative Response of a Forest Tree, Eucalyptus globulus, to a Natural Fungal Epidemic Genetics, January 1, 2008; 178(1): 563 - 571. [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]

				S. Isobe, A. Nakaya, and S. Tabata Genotype Matrix Mapping: Searching for Quantitative Trait Loci Interactions in Genetic Variation in Complex Traits DNA Res, November 13, 2007; (2007) dsm020v1. [Abstract] [Full Text] [PDF]

				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]

				B. Kusterer, H.-P. Piepho, H. F. Utz, C. C. Schon, J. Muminovic, R. C. Meyer, T. Altmann, and A. E. Melchinger Heterosis for Biomass-Related Traits in Arabidopsis Investigated by Quantitative Trait Loci Analysis of the Triple Testcross Design With Recombinant Inbred Lines Genetics, November 1, 2007; 177(3): 1839 - 1850. [Abstract] [Full Text] [PDF]

				M. P. Boer, D. Wright, L. Feng, D. W. Podlich, L. Luo, M. Cooper, and F. A. van Eeuwijk A Mixed-Model Quantitative Trait Loci (QTL) Analysis for Multiple-Environment Trial Data Using Environmental Covariables for QTL-by-Environment Interactions, With an Example in Maize Genetics, November 1, 2007; 177(3): 1801 - 1813. [Abstract] [Full Text] [PDF]

				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]

				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]

				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]

				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]

				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]

				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]

				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]

				S. R. Larson, X. Wu, T. A. Jones, K. B. Jensen, N. J. Chatterton, B. L. Waldron, J. G. Robins, B. S. Bushman, and A. J. Palazzo Comparative Mapping of Growth Habit, Plant Height, and Flowering QTLs in Two Interspecific Families of Leymus Crop Sci., November 21, 2006; 46(6): 2526 - 2539. [Abstract] [Full Text] [PDF]

				Z. Hu, X. Wang, and C. Xu A Method for Identification of the Expression Mode and Mapping of QTL Underlying Embryo-Specific Characters J. Hered., September 1, 2006; 97(5): 473 - 482. [Abstract] [Full Text] [PDF]

				L. Chen and J. D. Storey Relaxed Significance Criteria for Linkage Analysis Genetics, August 1, 2006; 173(4): 2371 - 2381. [Abstract] [Full Text] [PDF]

				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]

				J. M. Gleason, J.-M. Jallon, J.-D. Rouault, and M. G. Ritchie Quantitative Trait Loci for Cuticular Hydrocarbons Associated With Sexual Isolation Between Drosophila simulans and D. sechellia Genetics, December 1, 2005; 171(4): 1789 - 1798. [Abstract] [Full Text] [PDF]

				R. L. Malmberg, S. Held, A. Waits, and R. Mauricio Epistasis for Fitness-Related Quantitative Traits in Arabidopsis thaliana Grown in the Field and in the Greenhouse Genetics, December 1, 2005; 171(4): 2013 - 2027. [Abstract] [Full Text] [PDF]

				J. D. Peleman, C. Wye, J. Zethof, A. P. Sorensen, H. Verbakel, J. van Oeveren, T. Gerats, and J. R. van der Voort Quantitative Trait Locus (QTL) Isogenic Recombinant Analysis: A Method for High-Resolution Mapping of QTL Within a Single Population Genetics, November 1, 2005; 171(3): 1341 - 1352. [Abstract] [Full Text] [PDF]

				M. W. ter Steege, F. M. den Ouden, H. Lambers, P. Stam, and A. J.M. Peeters Genetic and Physiological Architecture of Early Vigor in Aegilops tauschii, the D-Genome Donor of Hexaploid Wheat. A Quantitative Trait Loci Analysis Plant Physiology, October 1, 2005; 139(2): 1078 - 1094. [Abstract] [Full Text] [PDF]

				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]

				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]

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				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]

				R. Li, M. A. Lyons, H. Wittenburg, B. Paigen, and G. A. Churchill Combining Data From Multiple Inbred Line Crosses Improves the Power and Resolution of Quantitative Trait Loci Mapping Genetics, March 1, 2005; 169(3): 1699 - 1709. [Abstract] [Full Text] [PDF]

				J.-M. Lacape, T.-B. Nguyen, B. Courtois, J.-L. Belot, M. Giband, J.-P. Gourlot, G. Gawryziak, S. Roques, and B. Hau QTL Analysis of Cotton Fiber Quality Using Multiple Gossypium hirsutum x Gossypium barbadense Backcross Generations Crop Sci., January 1, 2005; 45(1): 123 - 140. [Abstract] [Full Text] [PDF]