Combined line-cross and half-sib QTL analysis of crosses between outbred lines

Abstract

Data from an F 2 cross between breeds of livestock are typically analysed by least squares line-cross or half-sib models to detect quantitative trait loci (QTL) that differ between or segregate within breeds. These models can also be combined to increase power to detect QTL, while maintaining the computational efficiency of least squares. Tests between models allow QTL to be characterized into those that are fixed (LC QTL), or segregating at similar (HS QTL) or different (CB QTL) frequencies in parental breeds. To evaluate power of the combined model, data wih various differences in QTL allele frequencies (FD) between parental breeds were simulated. Use of all models increased power to detect QTL. The line-cross model was the most powerful model to detect QTL for FD>0.6. The combined and half-sib models had similar power for FD<0.4. The proportion of detected QTL declared as LC QTL decreased with FD. The opposite was observed for HS QTL. The proportion of CB QTL decreased as FD deviated from 0.5. Accuracy of map position tended to be greatest for CB QTL. Models were applied to a cross of Berkshire and Yorkshire pig breeds and revealed 160 (40) QTL at the 5% chromosome (genome)-wise level for the 39 growth, carcass composition and quality traits, of which 72, 54, and 34 were declared as LC, HS and CB QTL. Fourteen CB QTL were detected only by the combined model. Thus, the combined model can increase power to detect QTL and mapping accuracy and enable characterization of QTL that segregate within breeds.

Characterization of the porcine differentially expressed PDK4 gene and association with meat quality

“…Alignment between pig chromosome 9 on RH map and human maps on USDA-MARC Pig Database [23], we found some QTLs associated with meat quality and production traits in this region such as body weight at 10 weeks of age (87 cM) [24], average backfat thickness (79.3-90 cM) [25], total saturated fatty acids (61.5-83.3 cM) [26], backfat at tenth rib (96-79 cM) [27]. Also, PDK4 had thought to be a key regulatory enzyme involved in switching the energy source from glucose to fatty acids in response to physiological conditions [17].…”

Mapping quantitative trait loci for economic traits in chickens

“…For all models, fixed effects were F1 sire (n = 7), sex (n = 2), and hatch (n = 3). Group 1 models consisted of three models, as described by Kim et al (2005a) and Kim et al (2005b): a line-cross (LC) model, a half-sib (HS) model, and a combined (CB) model that included coefficients from both the LC and HS models. These models were based on the least-squares regression models of and .…”

“…These models were based on the least-squares regression models of and . Following Kim et al (2005a) and Kim et al (2005b) and Pd(ij) are the line-origin coefficients for each animal at a given position conditional on flanking marker genotypes. Following , P a (ij) for an individual is the difference between the probabilities of being homozygous for the QTL allele that originated from Line 1 versus Line 2, and fa# is the probability of an individual being heterozygous for line origin QTL alleles.…”

“…When at least one of the models was significant (chromosome-wise P = 0.05), a decision tree was used to define the segregation type of the QTL, following Kim et al (2005a) and Kim et al (2005b): the QTL is fixed for alternate alleles in the two parental lines (LC QTL); the QTL is not fixed in the parental lines but has similar allele frequencies in the two parental lines (HS QTL); or the QTL is not fixed in the parental lines, but has different allele frequencies between the parental lines (CB QTL). The decision tree was as follows:…”

“…The overall significance level reached by a QTL was determined using the model that corresponded to the classification of the QTL, i.e. Mend, Full, Pat, orMat.For all models, the estimated proportion of phenotypic variance explained by a detected QTL was calculated, following Kim et al (2005a), by comparing the reduction of the residual sums of squares with and without fitting the QTL in the model. The Z chromosome 70 was analyzed only with the half-sib model using QTL Express , and followed only the effects of the alleles inherited from the F1 sires averaged over the Z or W alleles inherited from the dams.…”