Marker Pair Selection for Mapping Quantitative Trait Loci

Corresponding author: Hans-Peter Piepho, Institut für Nutzpflanzenkunde, Universität Kassel, Steinstrasse 19, 37213 Witzenhausen, Germany., piepho{at}wiz.uni-kassel.de (E-mail)

Communicating editor: C. HALEY

Mapping of quantitative trait loci (QTL) for backcross and F₂ populations may be set up as a multiple linear regression problem, where marker types are the regressor variables. It has been shown previously that flanking markers absorb all information on isolated QTL. Therefore, selection of pairs of markers flanking QTL is useful as a direct approach to QTL detection. Alternatively, selected pairs of flanking markers can be used as cofactors in composite interval mapping (CIM). Overfitting is a serious problem, especially if the number of regressor variables is large. We suggest a procedure denoted as marker pair selection (MPS) that uses model selection criteria for multiple linear regression. Markers enter the model in pairs, which reduces the number of models to be considered, thus alleviating the problem of overfitting and increasing the chances of detecting QTL. MPS entails an exhaustive search per chromosome to maximize the chance of finding the best-fitting models. A simulation study is conducted to study the merits of different model selection criteria for MPS. On the basis of our results, we recommend the Schwarz Bayesian criterion (SBC) for use in practice.

This article has been cited by other articles:

				H. P. Piepho Ridge Regression and Extensions for Genomewide Selection in Maize Crop Sci., June 26, 2009; 49(4): 1165 - 1176. [Abstract] [Full Text] [PDF]

				L. Zhang, H. Li, Z. Li, and J. Wang Interactions Between Markers Can Be Caused by the Dominance Effect of Quantitative Trait Loci Genetics, October 1, 2008; 180(2): 1177 - 1190. [Abstract] [Full Text] [PDF]

				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]

				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]

				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]

				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]

				B. Stich, J. Yu, A. E. Melchinger, H.-P. Piepho, H. F. Utz, H. P. Maurer, and E. S. Buckler Power to Detect Higher-Order Epistatic Interactions in a Metabolic Pathway Using a New Mapping Strategy Genetics, May 1, 2007; 176(1): 563 - 570. [Abstract] [Full Text] [PDF]

				P. J. Balint-Kurti, J. C. Zwonitzer, R. J. Wisser, M. L. Carson, M. A. Oropeza-Rosas, J. B. Holland, and S. J. Szalma Precise Mapping of Quantitative Trait Loci for Resistance to Southern Leaf Blight, Caused by Cochliobolus heterostrophus Race O, and Flowering Time Using Advanced Intercross Maize Lines Genetics, May 1, 2007; 176(1): 645 - 657. [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]

				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]

				L. A. Robertson-Hoyt, M. P. Jines, P. J. Balint-Kurti, C. E. Kleinschmidt, D. G. White, G. A. Payne, C. M. Maragos, T. L. Molnar, and J. B. Holland QTL Mapping for Fusarium Ear Rot and Fumonisin Contamination Resistance in Two Maize Populations Crop Sci., June 20, 2006; 46(4): 1734 - 1743. [Abstract] [Full Text] [PDF]

				R. Mihaljevic, H. F. Utz, and A. E. Melchinger No Evidence for Epistasis in Hybrid and Per Se Performance of Elite European Flint Maize Inbreds from Generation Means and QTL Analyses Crop Sci., October 27, 2005; 45(6): 2605 - 2613. [Abstract] [Full Text] [PDF]

				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]

				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]

				M. J. Sillanpaa and M. Bhattacharjee Bayesian Association-Based Fine Mapping in Small Chromosomal Segments Genetics, January 1, 2005; 169(1): 427 - 439. [Abstract] [Full Text] [PDF]

				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]

				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. [Abstract] [Full Text] [PDF]

				J. T. G. Hwang and D. Nettleton Investigating the Probability of Sign Inconsistency in the Regression Coefficients of Markers Flanking Quantitative Trait Loci Genetics, April 1, 2002; 160(4): 1697 - 1705. [Abstract] [Full Text] [PDF]