Combining Different Line Crosses for Mapping Quantitative Trait Loci Using the Identical by Descent-Based Variance Component Method

Corresponding author: Shizhong Xu, Department of Botany and Plant Sciences, University of California, Riverside, CA 92521-0124, xu{at}genetics.ucr.edu (E-mail).

Communicating editor: T. F. C. MACKAY

Mapping quantitative trait loci (QTLs) is usually conducted with a single line cross. The power of such QTL mapping depends highly on the two parental lines. If the two lines are fixed for the same allele at a putative QTL, the QTL is undetectable. On the other hand, if a QTL is segregating in the line cross and is detected, the estimated variance of the QTL cannot be extrapolated beyond the statistical inference space of the two parental lines. To reduce the likelihood of missing a QTL and to increase the statistical inference space of the estimated QTL variance, we present a consensus QTL mapping strategy. We adopt the identical by descent (IBD)-based variance component method originally applied to human linkage analysis by combining multiple line crosses as independent families. We explore the properties of consensus QTL mapping and demonstrate the method with F₂, backcross (BC), and full-sib (FS) families. In addition, we examine the effects of the QTL heritability, marker informativeness, QTL position, the number of families, and family size. We show that F₂ families notably outperform BC and FS families in detecting a QTL. There is a substantial reduction in the standard deviation of the estimated QTL position and the separation of the QTL and polygenic variance. Finally, we show that the power to detect a QTL is greater when using a small number of large families than a large number of small families.

This article has been cited by other articles:

				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]

				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]

				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]

				M.-F.ço. Jourjon, S. Jasson, J. Marcel, B. Ngom, and B. Mangin MCQTL: multi-allelic QTL mapping in multi-cross design Bioinformatics, January 1, 2005; 21(1): 128 - 130. [Abstract] [Full Text] [PDF]

				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, November 1, 2004; 168(3): 1737 - 1749. [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]

				Y. M. Parsons and K. L. Shaw Mapping Unexplored Genomes: A Genetic Linkage Map of the Hawaiian Cricket Laupala Genetics, November 1, 2002; 162(3): 1275 - 1282. [Abstract] [Full Text] [PDF]

				J.-L. Jannink and R. Jansen Mapping Epistatic Quantitative Trait Loci With One-Dimensional Genome Searches Genetics, January 1, 2001; 157(1): 445 - 454. [Abstract] [Full Text]

				A. W. George, P. M. Visscher, and C. S. Haley Mapping Quantitative Trait Loci in Complex Pedigrees: A Two-Step Variance Component Approach Genetics, December 1, 2000; 156(4): 2081 - 2092. [Abstract] [Full Text]

				N. Yi and S. Xu A Random Model Approach to Mapping Quantitative Trait Loci for Complex Binary Traits in Outbred Populations Genetics, October 1, 1999; 153(2): 1029 - 1040. [Abstract] [Full Text] [PDF]