Multiple trait analysis for genetic mapping of quantitative trait loci for carcass and beef quality

The use of molecular markers to identify quantitative trait loci ( QTL ) affecting economically important traits has become a key approach in animal genetics, both for understanding the genetic basis of these traits and to help design novel breeding programs. The general goal of the present work was to map QTL for economically important traits in beef cattle. Because of the practical limitations of phenotypic selection for meat quality, these traits are ideal candidates for the use of marker - assisted selection. Thus, the thesis specifically focused on carcass and beef quality traits. Six half - sib families were generated by mating six Limousin x Jersey crossbred sires to purebred Jersey or Limousin cows, producing 784 backcross progeny ( 366 and 418 progeny in Australia and New Zealand, respectively ). The six crossbred sires and all the backcross progeny were genotyped for 285 microsatellite markers ( on average 189 informative loci per sire family ) spread across the 29 bovine autosomes. A large number of traits were recorded on backcross progeny. In the first phase of the research, a single - QTL model based on regression interval mapping was used to map QTL for a wide range of economically important traits in the beef industry. Chromosome - wise significant evidence for linkage was found on BTA12 ( P < 0.01 ) and BTA16 ( P < 0.05 ) for age at puberty. Thirteen QTL were found to affect calving ease related traits ( birth weight, pelvic area and gestation length ). BTA11, 14 and 22 were most significant linkage groups affecting calving ease traits. Several genomic regions were linked to the carcass and beef quality traits. The results revealed a major QTL on BTA2 close to the map position of myostatin gene, affecting yield, carcass fatness and beef quality traits. In the second phase, the pleiotropic effects of a myostatin functional SNP on beef traits were studied. There was no association between this myostatin variant and birth weight and growth traits. However, the variant decreased overall fatness, increased muscle mass and improved meat tenderness, thus providing an intermediate and more useful phenotype than the more severe double - muscling phenotype caused by a major deletion in the myostatin gene described by others. In the third phase, a multiple marker analysis approach in the framework of the mixed - effects model was developed, allowing all markers of the entire genome to be included in the analysis simultaneously. Further, exploiting a factor analytic covariance structure for modeling trait by marker or family by marker interaction terms, the approach was extended to the multi - trait and multiple family situations. The simulation study showed that modeling multiple phenotypes and multiple families in a single linkage analysis simultaneously can markedly increase the power to detect QTL, compared to modeling each phenotype or family separately. Finally, the multi - trait multiple QTL approach developed herein was applied to map QTL influencing carcass and meat quality traits. Several pleoitropic QTL and also traitspecific QTL affecting beef traits were mapped, resulting in a useful resource from which fine mapping can be launched for subsequent gene discovery and marker - assisted selection.Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2007