Abstract
Statistical methods for mapping quantitative trait loci (QTLs) in full-sib forest trees, in which the number of alleles and linkage phase can vary from locus to locus, are still not well established. Previous studies assumed that the QTL segregation pattern was fixed throughout the genome in a full-sib family, despite the fact that this pattern can vary among regions of the genome. In this paper, we propose a method for selecting the appropriate model for QTL mapping based on the segregation of different types of markers and QTLs in a full-sib family. The QTL segregation patterns were classified into three types: test cross (1:1 segregation), F2 cross (1:2:1 segregation) and full cross (1:1:1:1 segregation). Akaike’s information criterion (AIC), the Bayesian information criterion (BIC) and the Laplace-empirical criterion (LEC) were used to select the most likely QTL segregation pattern. Simulations were used to evaluate the power of these criteria and the precision of parameter estimates. A Windows-based software was developed to run the selected QTL mapping method. A real example is presented to illustrate QTL mapping in forest trees based on an integrated linkage map with various segregation markers. The implications of this method for accurate QTL mapping in outbred species are discussed.
Highlights
Genetic mapping of quantitative trait loci (QTLs) based on genetic linkage maps is a powerful tool for unraveling the genetic architecture of quantitative trait variation in plants, animals and humans
Bayesian information criterion (BIC) showed a slight advantage over Laplace-empirical criterion (LEC) for selecting the model of test cross and F2 cross, it had drastically lower power than LEC for selecting the model of full cross, especially when the heritability of the QTL was £ 0.20
The applicability of our statistical method for mapping QTLs in a full-sib family was demonstrated for a forest tree, an interspecific F1 hybrid population between Populus deltoides and Populus euramericana in Xuchou, Jiangsu Province, China
Summary
Genetic mapping of quantitative trait loci (QTLs) based on genetic linkage maps is a powerful tool for unraveling the genetic architecture of quantitative trait variation in plants, animals and humans. Since the seminal publication on interval mapping by Lander and Botstein (1989) there has been a tremendous development of statistical methods and algorithms for QTL mapping. For any two inbred lines, there are only two alleles at each locus and in the F1 hybrids that transmit gametes to the generation there is a fixed linkage phase between any two loci. These two features of inbred lines greatly facilitate statistical inference about the QTL location and effects
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