Methods for mapping QTL are actively used in the chicken to identify chromosomal regions contributing to variation in traits related to growth, disease resistance, egg production, behavior, and metabolic parameters. However, higher-resolution mapping and better knowledge of the genetic architecture underlying QTL are needed for successful application of this information into breeding programs. Therefore, this paper summarizes and integrates original, primary QTL studies in the chicken to identify basic information on the genetic architecture of quantitative traits in chickens. The results of this review show several instances of consensus of QTL locations for similar traits from independent studies. Furthermore, the consensus of QTL location for different traits and evidence for QTL with parent-of-origin effect, transgressive alleles, epistatic QTL, and QTL × sex interaction in chicken are presented and discussed. This information can be helpful in identifying genes or mutations underlying the QTL and in the application of genomic information in marker-assisted breeding programs.

Amino acid supplementation of practical-type rations containing relatively high levels of blood and feather meals, and its effect on broiler chicks' performance were investigated. In experiment 1, four diets were tested: a corn-soybean meal diet and diets containing 10% ring-dried blood meal, 6% hydrolyzed feather meal and a combination of the two. Diets were supplemented with the deficient amino acids. Results showed no significant differences among the four diet treatments with respect to weight gain or feed efficiency of chicks from 1 to 4 weeks of age. In experiment 2, further assessment of amino acid addition to blood-feather meal diets was done. Methionine was added to the basal diet at 0 or 0.21%, lysine at 0 or 0.2% and isoleucine at 0 or 0.33% in a 2 x 2 x 2 factorial arrangement. Growth and feed efficiency of chicks fed the blood-feather meal basal diet were improved by the addition of 0.21% methionine or 0.33% isoleucine. These parameters reached maximums when both methionine and isoleucine were added. Lysine addition at 0.2% had no significant effect on weight gain or feed efficiency. Experiment 3 was conducted to test higher levels of supplemental methionine and isoleucine in blood-feather meal diets. Methionine and isoleucine were added to the basal diet at 0, 0.2 and 0.4% in a 3 x 3 factorial arrangement. The addition of 0.2% methionine improved weight gain and feed efficiency, but 0.4% supplemental methionine resulted in no further improvement. Addition of 0.2% isoleucine improved weight gain and feed efficiency, but 0.4% isoleucine reduced weight gain and feed efficiency. Addition of methionine (the first limiting amino acid) and isoleucine (the second limiting amino acid) reduced the high levels of plasma leucine in chicks fed the basal diet (2.4 to 2.5%);Two additional experiments were conducted to test the effect of sulfur amino acid supplementation to blood-feather meal diets. In the first experiment methionine and cystine were added to the basal diet (0.3% methionine and 0.48% cystine) at 0, 0.1, 0.2, 0.3 and 0.4% and 0 and 0.1%, respectively, in a 2 x 5 factorial arrangement. A corn-soy based diet was used as a positive control diet. In a second experiment 0, 0.1, 0.2, 0.3 and 0.4% supplemental methionine and 0, 0.1 and 0.2% supplemental cystine were added to a milo, blood-feather meal basal diet (0.2% methionine and 0.48% cystine) in a 3 x 5 factorial arrangement. In the first experiment, 0.2% added methionine or 0.1% added cystine improved weight gain and feed efficiency of chicks fed the blood-feather meal diet. In the second experiment, weight gain increased linearly with increasing level of methionine. Maximum weight gain and feed efficiency, however, were observed when 0.1 or 0.2% supplemental cystine were added with 0.4% methionine, and then declined with higher levels of methionine supplementation. Plasma methionine-cystine concentrations in both experiments showed no evidence of a cystine-methionine antagonism.

Fifty mid-lactation Holstein cows were used in a six-week feeding trial to study effects of high-forage, high-fat diets on dry matter intake, milk production, milk composition, and blood constituents. Cows were divided into 10 replicates, each consisting of five cows. Each cow was assigned to one of four experimental diets (high-forage (75%), high-fat (7.5%)(diet 1); high-forage, medium-fat (5.0%)(diet 2); medium forage (65%), high-fat (diet 3); medium-forage, medium-fat (diet 4)), or a control diet containing about 50% forage and 2% fat. All diets were isonitrogenous (17.7% crude protein). The forage mixture consisted of 20% alfalfa hay, 40% alfalfa haylage, and 40% corn silage. Supplemental fat included 80% rumen-protected fat and 20% yellow grease. Dry matter intake was decreased (P < 0.01) in cows fed experimental diets (18.4, 20.9, 19.9, and 22.6 kg for cows fed diets 1-4, respectively vs. 27.5 kg for cows fed the control diet). Daily milk production was lower (P < 0.05) for cows consuming experimental diets (30.5, 31.3, 31.0, and 32.5 kg for cows fed diets 1-4, respectively vs. 34.2 kg for cows fed control diet); however, milk output per unit of dry matter intake was greater for cows consuming experimental diets (1.74, 1.55, 1.60, and 1.53 kg milk/kg dry matter intake for cows fed diets 1-4, respectively, vs. 1.26 kg milk/kg dry matter intake for cows fed the control diet). Milk fat and total solids did not differ significantly; however, milk protein tended to be higher for cows consuming the medium-forage, high-fat diet. A non-significant difference was observed in concentrations of blood glucose for cows on different experimental and control diets. Plasma nonesterified fatty acids (NEFA) were higher in cows consuming experimental diets than those consuming the control diet. However, differences in NEFA concentrations in the plasma of cows consuming diets with different forage and fat levels were not significant. Rumen pH, concentration of volatile fatty acids (VFA) in rumen contents, and dry matter digestibility of control and experimental diets, and diets with different levels of forage and supplemental fat did not differ significantly.

The production system commonly used in the swine industry involves a three-tiered genetic pyramid. The nucleus, where most genetic improvement occurs, is at the top of the pyramid and represents the smallest percentage of total animals in the pyramid. The second tier is called the multiplication level and is where the improvement occurring at the nucleus herd is multiplied or produced in mass. Some genetic improvement can still occur at the multiplication level of the genetic pyramid and this tier generally represents approximately 10 to 15% of the animals in the pyramid. Finally, the third and bottom tier of the genetic pyramid is represented by the commercial level of production. This level of the pyramid represents the largest portion of the system. The genetic improvement occurring in the system is targeted to generate improved production and hence profitability at the commercial level. Genetic lag is the time required for genetic merit or improvement to pass from its source (in this example the nucleus through the multiplication level) to the commercial level of production and it is usually measured in years. 1 Genetic lag is driven by the generation interval (the average age of parents when their offspring are selected to replace them in the nucleus and multiplication levels of production.

Toll-like receptors (TLR) recognize evolutionarily conserved molecular motifs (pathogen-associated molecular patterns) of infectious microbes and initiate innate immune response upon activation with relevant pathogens. This study investigated the acute effect of Salmonella Enteritidis challenge on TLR mRNA expression in cecum and spleen of birds from 3 distinct genetic lines. Chicks from broiler, Leghorn, and Fayoumi lines were inoculated or mock-inoculated with Salmonella Enteritidis. The mRNA expression levels of TLR2, TLR4, and TLR5 genes were assessed by quantitative reverse transcription-PCR of cecum and spleen tissue harvested at 2 or 18 h postinoculation (PI). There were no significant genetic line effects on TLR mRNA expression in spleen or cecum of mock-infected birds, or in the cecum of infected birds. Genetic line effect was significant (P < 0.05) on TLR mRNA expression in the spleen of Salmonella Enteritidis- infected birds. The Fayoumi line had higher TLR2 and TLR4 expression than Leghorn, higher TLR2 mRNA expression than broiler, and the broiler line had higher TLR5 expression than Leghorn and Fayoumi. In Salmonella Enteritidis-infected birds, the TLR2 expression in both cecum and spleen and TLR4 expression in spleen were significantly higher at 18 h PI than 2 h PI. The results demonstrate a significant genetic line effect on TLR expression in the spleen of Salmonella Enteritidis-infected birds, which may partly explain genetic variability in immune response to Salmonella Enteritidis.

The objective of this dissertation was to evaluate multiple approaches to incorporating sow longevity or lifetime sow productivity into a selection program. Sow longevity can be selected for using indicator traits, such as structural soundness and lameness. In the first study, objective measurements to detect sow lameness were examined. Lameness was chemically induced for a short time period in multiparous sows and their weight distribution and walking gait were objectively measured in the days following lameness induction. Using a classification tree analysis, it was determined that the mean weight being placed on each leg was the most predictive measurement when determining whether the leg was sound or lame after injection. The weight distribution measures had a greater predictive ability compared to the walking gait indicators. These measures could be used to select sows that are less likely to become lame and be removed from the breeding herd. While reducing the lameness instances in a herd would improve sow longevity, direct selection for longevity would be desirable. In the second study, genetic correlations between purebred and crossbred sow longevity were estimated. Most genetic improvement programs are based on an assumed relationship between purebred performance in a nucleus herd and their relatives' crossbred performance in a commercial herd; however, this study found that there was little to no genetic correlation between purebred and crossbred sow longevity for this population. While longevity is heritable at both the nucleus and commercial levels, results from this study indicate that little improvement would be made in crossbred longevity if selection relies solely on purebred information. One way to select for sow longevity would be to estimate purebred genomic breeding values using records from a related crossbred population. A spreadsheet for estimating the total costs associated with incorporating genome-enabled selection into a swine breeding program was developed as the final part of this dissertation. This tool will aid producers in estimating the economic viability of incorporating genome-enabled selection into their specific breeding program. Based on the results from these projects, it is recommended that a commercial test herd be implemented as part of a selection program to improve longevity or sow productive lifetime. If a genetic company can succeed in improving sow longevity through an effective breeding program, production efficiency and profitability can be improved for commercial swine operations.

The genome sequence and a high-density SNP map are now available for the chicken and can be used to identify genetic markers for use in marker-assisted selection (MAS). Effective MAS requires high linkage disequilibrium (LD) between markers and quantitative trait loci (QTL), and sustained marker-QTL LD over generations. This study used data from a 3,000 SNP panel to assess the level and consistency of LD between single nucleotide polymorphisms (SNPs) over consecutive years in two egg-layer chicken lines, and analyzed one line by two methods (SNP-wise association and genome-wise Bayesian analysis) to identify markers associated with egg-quality and egg-production phenotypes. The LD between markers pairs was high at short distances (r² > 0.2 at < 2 Mb) and remained high after one generation (correlations of 0.80 to 0.92 at < 5 Mb) in both lines. Single- and 3-SNP regression analyses using a mixed model with SNP as fixed effect resulted in 159 and 76 significant tests (P < 0.01), respectively, across 12 traits. A Bayesian analysis called BayesB, that fits all SNPs simultaneously as random effects and uses model averaging procedures, identified 33 SNPs that were included in the model >20% of the time (φ > 0.2) and an additional ten 3-SNP windows that had a sum of φ greater than 0.35. Generally, SNPs included in the Bayesian model also had a small P-value in the 1-SNP analyses. High LD correlations between markers at short distances across two generations indicate that such markers will retain high LD with linked QTL and be effective for MAS. The different association analysis methods used provided consistent results. Multiple single SNPs and 3-SNP windows were significantly associated with egg-related traits, providing genomic positions of QTL that can be useful for both MAS and to identify causal mutations.

The benefit of using QTL information in dairy cattle breeding schemes by means of computer simulation is investigated. In addition, algorithms to overcome computational problems arising when marker data are included in mixed linear models were proposed.;Computer simulation was conducted with parameters relative to the Holstein population of the United States. Superiority of QTL-assisted selection (QAS) over QTL-free selection was studied in four pathways of selection, namely active sires, young bulls, bull dams, and cows, for cumulative genetic response, accuracy of evaluation, and selection pressure on the QTL.;Further, breeding scheme as a factor was studied. The breeding scheme was the most effective factor in increasing the superiority of QAS. As it agreed with many previous studies, nucleus breeding schemes were found to be promising systems to implement QTL information. On the other hand, benefits of QAS in conventional two stage selection programs were limited.;The interaction between the type of QTL information available and the breeding system was found important. Using a highly polymorphic QTL in nucleus schemes was found very effective. Effects of different number of alleles per locus and different number of loci on the superiority of QAS were studied.;An algorithm to directly build the inverse of a conditional gametic relationship matrix, given marker data, was developed. The inverse algorithm is based on matrix decomposition instead of partitioned matrix theory. Numerical techniques that greatly improved computing performance were introduced.;Appropriate modifications to the conventional breeding schemes that are currently in use are highly recommended. Further, attention should be paid to the characteristics of the QTL and how they may interact with the breeding system, e.g., number of loci and alleles. Finally, the study found that the use of marked or known QTL information in genetic evaluation is computationally possible and generally useful.

The purpose of this project was to determine the value of implementing litters per sow per year (LSY) into a selection program. Two studies were conducted to achieve this objective. The goal of one study was to determining the genetic and phenotypic relationships between LSY and other economically important reproductive and post-weaning traits from a commercial swine breeding company. Determining the genetic and phenotypic correlations among traits can help breeders evaluate the expected impacts their selection decisions have on other economically important production traits. These other economically important traits may or may not be included in the selection criteria. This is particularly important when considering reproductive and post-weaning traits because of the undesirable genetic relationships that typically exist between reproductive and post-weaning traits. The traits collected included number born alive (NBA), wean to estrus (W2E), adjusted back fat (BF), percent lean (PCL), and days to 100 kg (D100). Litters per sow per year (LSY) was calculated based on recorded information. Genetic parameter estimates were calculated using ASREML. The heritability estimates for NBA, LSY, W2E, BF, D100, and PCL were 0.15, 0.03, 0.03, 0.52, 0.33, and 0.36, respectively. The genetic correlation between LSY and W2E was large and favorable. The genetic correlations between LSY and the three post-weaning traits (BF, D100, and PCL) have large standard errors and are unclear in direction. Some economically important traits can be favorably changed indirectly with selection on LSY; however, a selection index will be needed to ensure that post-weaning growth traits are not adversely affected by selection for LSY in a maternal line breeding program. The goal of the second study was to determine the relationship between individual sire breeding values (BV) for LSY and progeny means for farrowing rate, removal parity, and lifetime born alive. Landrace, Large White, and F1 (YyL or LyY) crossbred females were included in the analyses. Estimated breeding values (EBV) for LSY were calculated using ASREML. The heritability estimate for LSY was 0.11. Sire progeny (daughter) farrowing rate means were calculated as total number of services of the sire's daughters divided by the total litters farrowed from the sire's daughters. Similar values were calculated for daughter average removal parity, and daughter average lifetime born alive. The Spearman rank correlation between the LSY EBV and the progeny farrowing rate of the sires was calculated using SAS software. When all sires with 10 or more daughters were included in the analysis, the Spearman rank correlations between the sire's LSY EBV and daughter means for farrowing rate, removal parity, and lifetime born alive were 0.49, 0.23, and 0.25 (P<0.01). The LSY EBV was favorably correlated with the daughter means for all three traits. This provides evidence that selecting sires with high LSY EBV to improve the LSY could also improve the herd farrowing rate, removal parity, and lifetime born alive. Sires ranked in the top 25% for LSY EBV had a 15.3% higher average farrowing rate compared to sires in the bottom 25%. Daughters from the top sire had a one parity greater average removal parity than daughters from the other sire group. This extra litter corresponded to an average of 8.9 more pigs produced in a sow's lifetime. Based on the results of this project, LSY is heritable. There is a genetic component of LSY and there is sufficient biological variation of the trait for traditional selection methods to be efficient and effective. There are little to no antagonistic relationships between LSY and the other economically important traits considered in this study. A selection index must be employed to ensure that there is no adverse effect on other economically important traits when selecting for LSY. There is evidence to suggest that a desirable relationship exists between LSY and farrowing rate, removal parity, and lifetime born alive. Improving farrowing rate through improving LSY can reduce the number of costly non-productive sow days in the herd. Improving removal parity and lifetime born alive through increasing LSY could improve sow longevity.