Degree Type


Date of Award


Degree Name

Doctor of Philosophy


Animal Science



First Advisor

Jack C. M. Dekkers

Second Advisor

Susan J. Lamont


Identification of genomic regions harboring genes affecting economic traits is the primary step for the improvement of agricultural species through marker-assisted selection. Many important traits are difficult and expensive to measure, and, thus, selection can be improved by selecting directly upon genomic regions affecting these traits (QTL). White meat percentage (WM%) and Marek's disease (MD) resistance are examples of important traits in commercial chickens. One objective of the research presented herein was to identify QTL affecting WM%, other growth-related traits, and MD resistance. Another objective was to compare statistical models for identifying these QTL. Phenotypes and genetic markers on an F2 broiler cross were analyzed using half-sib, line cross, combined, and parent of origin models to identify QTL affecting WM% and other growth related traits. Sixty-eight QTL were identified at the 5% chromosome-wise level, including six QTL affecting WM% and 20 putative imprinted QTL. The use of multiple segregation and expression models proved to be beneficial for identifying QTL. A commercial egg-layer backcross was used to identify QTL affecting MD resistance based on marker genotypes of long and short survivors (selective genotyping). Seventeen markers associated with MD survival were identified at P < 0.10 using linear regression (LR) and Cox proportional hazards (CPH) models. Using simulated data reflecting the MD virus-challenged population, analyses using LR, CPH, and Weibull models were compared. Little difference in power was found between CPH and LR models when few individuals survived to the end of the experimental period (low censoring) and when all or selected individuals were genotyped. Simulated data did not follow a Weibull distribution, and thus the Weibull model generally resulted in less power than the other two models. The LR model was recommended for analyzing survival data when the amount of censoring is low because of ease of implementation of the model and interpretation of estimates. Including non-genotyped individuals in the selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate. The QTL identified in this research can be an integral step for improvement of commercial chickens through marker assisted selection programs or identification of candidate genes.



Digital Repository @ Iowa State University,

Copyright Owner

Joseph Paul McElroy



Proquest ID


File Format


File Size

160 pages