Abstract
The aim of this study was to compare the variance component approach for QTL linkage mapping in half-sib designs to the simple regression method. Empirical power was determined by Monte Carlo simulation in granddaughter designs. The factors studied (base values in parentheses) included the number of sires (5) and sons per sire (80), ratio of QTL variance to total genetic variance (λ = 0.1), marker spacing (10 cM), and QTL allele frequency (0.5). A single bi-allelic QTL and six equally spaced markers with six alleles each were simulated. Empirical power using the regression method was 0.80, 0.92 and 0.98 for 5, 10, and 20 sires, respectively, versus 0.88, 0.98 and 0.99 using the variance component method. Power was 0.74, 0.80, 0.93, and 0.95 using regression versus 0.77, 0.88, 0.94, and 0.97 using the variance component method for QTL variance ratios (λ) of 0.05, 0.1, 0.2, and 0.3, respectively. Power was 0.79, 0.85, 0.80 and 0.87 using regression versus 0.80, 0.86, 0.88, and 0.85 using the variance component method for QTL allele frequencies of 0.1, 0.3, 0.5, and 0.8, respectively. The log10 of type I error profiles were quite flat at close marker spacing (1 cM), confirming the inability to fine-map QTL by linkage analysis in half-sib designs. The variance component method showed slightly more potential than the regression method in QTL mapping.
Highlights
Fernando and Grossman [5] presented a methodology for the application of BLUP to marker-assisted selection (MAS) in which QTL alleles were considered random in the context of the mixed model terminology
Alternative methods for computing identity by descent (IBD) probability are a correlation based algorithm and a segregation algorithm [2, 3, 6, 20]. Both methods are based on the IBD probability matrix between all individuals at the putative QTL position obtained using the markers to trace the inheritance of the QTL
The variance component approach using restricted maximum likelihood (REML) is an approach derived to estimate the position of the QTL
Summary
The variance component approach is based on a mixed inheritance linear model and the QTL is treated as a random effect This method is based on an identity by descent (IBD) probability matrix between all individuals at the putative QTL position. Fernando and Grossman [5] presented a methodology for the application of BLUP to marker-assisted selection (MAS) in which QTL alleles were considered random in the context of the mixed model terminology They presented recursive algorithms to calculate IBD probabilities for a QTL as a gametic relationship matrix. These approaches are possible for pedigrees with incomplete marker information, unknown linkage phase and multiple linked markers. The likelihood is maximized over the parameters at each position and the position with the largest maximized likelihood is selected [6, 9, 21]
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