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Genetic improvement of livestock has a major impact on animal productivity and its effects are permanent, cumulative and usually highly cost effective. It is also of considerable potential value in countries, mostly in need of increased food supply and security like those in sub-Saharan Africa. However, genetic improvement has not been carried out systematically in most sub-Saharan Africa countries. This is in part because of lack of animal performance recording, insufficient infrastructure, small herd sizes and limited pedigree information. Most genetic improvement initiatives in dairy cattle have often relied on importation of foreign (exotic) breeds. Only a few countries such as South Africa and Kenya have been collecting dairy performance data for national genetic evaluations for some time. Initiatives such as the African Dairy Genetic Gains Programme are helping other countries such as; Tanzania and Ethiopia to develop animal recording systems which will start to provide pre-requisite data for genetic evaluations. Improvements in data recording in multiple countries present an opportunity to develop new approaches to dairy improvement and across-country genetic evaluations. Across-country genetic evaluations would facilitate selection decisions and underpin the fledgling breeding programmes in these countries. Elsewhere, pooling and jointly analysing data across different countries, where common sires are been used, has resulted in more accurate genetic evaluations than using within-country data only. The hypothesis in the present study was that across-country genetic evaluation of dairy cattle in sub-Saharan Africa would result in accurate genetic parameters and estimated breeding values hence, improve genetic progress. In order to test this hypothesis, four objectives were addressed as follows. Firstly, a survey was conducted to investigate the current status and needs of the dairy improvement sector in sub-Saharan Africa. Secondly, existing animal data collated from three countries (Kenya, South Africa and Zimbabwe) from Holstein- Friesian and Jersey breeds were used to determine the level of connectedness among the respective dairy populations. Thirdly, estimates of genetic parameters and breeding values for milk production and fertility traits were derived within and across these countries. Fourthly, the potential genetic gains that could arise from within and across-country genetic selection were estimated. Results from the survey indicated that the main respondent's challenges in sub- Saharan Africa dairy production systems are; poor animal recording, poorly defined animal genetic improvement goals and strategies, inadequate dairy marketing structure and scarce human capacity. The survey identified close collaborations as one of the mitigation measures to these challenges. Results from production and pedigree data for the three countries showed that there were strong links and connectedness in both breeds. Genetic parameter estimation indicated that all three populations would benefit from joint genetic analyses in terms of improved accuracy of estimates. For example, in Holstein-Friesians, heritability (h2) for 305-day milk yield in five lactations (305D MY) across the three countries was 0.11 (s.e=0.014). Within country, estimates for South Africa and Zimbabwe were 0.12 (s.e=0.018) and 0.10 (s.e=0.025), respectively, whereas it was not significantly different from zero for Kenya. In fact in several cases, within-country parameter estimates were either not significantly different from zero or non-estimable. Genetic parameters were always estimable in across-country analyses. In terms of expected genetic progress, the results showed that all three countries would benefit from genetic progress generated from selection in an across country initiative. For production traits, Kenya benefited the most (100% increase in genetic gain from across-country compared to within-country selection) than Zimbabwe (55- 73% increase over within-country) and lowest benefits for South Africa (2-28%). For reproduction traits, Kenya again benefitted the most (100%), as compared to Zimbabwe (59-100%) and South Africa (16-69%). The study suggests that, in general, joint genetic evaluations may support breeding programmes by providing more accurate genetic parameters and estimated breeding values than national initiatives. Furthermore, an across-country breeding programme based on a joint genetic evaluation could provide a platform for shared genetic progress. Such a programme would offer a wider choice of animals for selection than national evaluations. This type of across-country collaboration would facilitate animal trade between countries in terms of both exportations and importations, and would also address some of the key needs identified in the stakeholder survey.

Genetic variation between individuals is of great importance for the development of breeding programmes, to select for animals with the most favourable traits. Many production companies routinely measure the feed intake of their animals, in order to calculate efficiency traits such as feed conversion ratio. The development of electronic feeders which automatically record individual intake on a visit-by-visit basis now allows the short-term feeding behaviour of animals to be monitored and analysed as another source of variation between individuals. Due to differences in the resolutions of these feeders as a measurement tool, a standard unit of feeding event needs to be estimated to allow for comparisons between studies. Different models for estimation of the defining value of a meal, the meal criterion, have been used, with the most recent incorporating the change in satiety with time since last feeding as part of the model. In this study I developed a new methodology, based on these models, for use when a within meal population of intervals cannot be easily modelled. I then used this model for application to data from four lines of broiler chickens to estimate meal criteria and compare feeding behaviour within and between the lines. Significant differences were found between fast and slow growing birds, with the faster growing birds having fewer but larger meals than the slower growing birds. However, the lines showed similar structure and bouting of their feeding behaviour, indicating that the fundamental controls of feeding behaviour, such as hunger and satiety, in these lines had been unaltered despite intensive selection for growth. The models were also applied across poultry species, kept in different experimental conditions. A similar structure to the feeding behaviour was found across all these species, with all showing clear separation of feeding events into bouts. In order to estimate the potential use of these behavioural observations in a breeding programme, the heritabilities and genetic correlations with existing performance traits were calculated for the four broiler lines. Heritabilities of all feeding behaviour traits were found to be moderate to high, and very similar across the lines. Correlations with performance traits, however, were low, meaning that there were no clear links of the traits with the current production goals investigated. This indicates that past selection for production has had limited impact on feeding behaviour and also that potential selection for feeding behaviour will have little effect on production gains. To identify the areas of the genome controlling feeding behaviour, traits were associated with a SNP panel. Many regions were found to have highly significant association with feeding behaviour traits, with the most highly correlated traits showing associations with the same regions, suggesting pleiotropic effects of genes in these regions. Future work in this area should include identification of individual genes controlling feeding behaviour to allow prediction of the effects of selection for favourable feeding behaviour on other traits, and comparison of the genotypes of different lines of broilers, to further understand the control of feeding behaviour.

A beef cattle population (n=2,343) was used to assess the impact of variants identified from imputed low-pass sequence (LPS) on the estimation of variance components and genetic parameters of birth weight (BWT) and post weaning gain (PWG). Variants were selected based on functional impact and were partitioned into four groups (Low, Modifier, Moderate, High) based on predicted functional consequences and re-partitioned based on consequence of mutation, such as missense and untranslated region variants, into six groups (G1-G6). Each subset was used to construct a genomic relationship matrix (GRM) for univariate animal models. Multiple analyses were conducted to compare the proportion of additive genetic variation explained by the different subsets individually and collectively, and these estimates were benchmarked against all LPS variants in a single GRM and array (e.g., GeneSeek Genomic Profiler 100K) genotypes. When all variants were included in a single GRM, heritability estimates for BWT and PWG were 0.43±0.05 and 0.38±0.05, respectively. Heritability estimates for BWT ranged from 0.10-0.42 dependent on which variant subsets were included. Similarly, estimates for PWG ranged from 0.05-0.38. Results showed that variants in the subsets Modifier and G1 (untranslated region) yielded similar heritability estimates compared to the inclusion of all variants yielded the highest estimates, while estimates from GRM containing only variants in the categories High, G4 (non-coding transcript exon), and G6 (start and stop loss/gain) were the lowest. All variants combined provided similar heritability estimates to chip genotypes and provided minimal to no additional information when combined with chip data. This suggests that the chip data and the variants from LPS predicted to be less consequential are in relatively high linkage disequilibrium with the underlying causal variants and sufficiently spread throughout the genome to capture larger proportions of additive genetic variation. Advisor: Matthew L. Spangler

Cattle efficiency during the finishing phase is a crucial factor in determining profit in the beef cattle industry. Economically relevant traits associated with efficient production include age at slaughter (AAS) and days to finish (DtF). Selection to reduce the number of days an animal takes to reach a finish endpoint would ultimately reduce production costs, increase net profits, and result in a more sustainable production system. However, most harvested animals are from commercial herds, necessitating the use of indicator traits from seedstock animals for selection. Potential indicator traits include ultrasound measurements that could be genetically correlated to DtF traits. The objectives of the current work were to i) estimate genetic parameters and breed effects for AAS and DtF and their relationships with routine carcass traits, and ii) estimate genetic correlations between AAS or DtF and ultrasound traits (ultrasound intramuscular fat percentage (UIMF), ultrasound rib fat (URF), and ultrasound ribeye area (UREA)). Performance records and pedigree information were obtained from U.S. Meat Animal Research Center (harvest data) and International Genetic Solutions (seedstock data). Univariate and bivariate animal models were fitted with ASREML (version 4.0) to estimate the genetic parameters. Days to finish and AAS are moderately to highly heritable and generally lowly correlated with routine carcass traits. The phenotypic variability in DtF was low. However, there was greater variability in AAS, which was due to differences in date of birth of the animals and thus the ages at weaning. Genetic correlations between AAS or DtF with UIMF were negligible. Genetic correlations were negative and low between DtF and UREA and were positive and moderate between AAS and UREA. Genetic correlations were negative and moderate to high between AAS or DtF and URF. Reducing AAS or DtF in commercial cattle is possible through selection in seedstock for ultrasonically measured fat. Advisor: Matthew L. Spangler

Abstract: Carcass and meat characteristics are of great importance to the pork industry as they determine the ultimate returns from animals produced. Making genetic progress in these traits requires them to be measurable, heritable and have adequate additive genetic variability. Estimates of genetic parameters must therefore be assessed to determine heritability and level of additive genetic variation for use in selection programs. In the first study, phenotypic data from 500 pedigreed crossbred pigs from Duroc sires and hybrid Large White ✕ Landrace sows from two different swine genetics companies were used. Fixed effects (slaughter batch, sex and company), and a random additive effect were fitted in bivariate animal models to estimate phenotypic and genetic parameters in ASReml. Moderate heritabilities were obtained for loin compositional traits ranging from 0.21±0.10 for bone weight to 0.44±0.11 for loin eye weight with low estimates of 0.09±0.08, 0.19±0.08, 0.13±0.09 obtained for bone percent, loin weight and fat trim weight, respectively. Meat quality traits were low to moderately heritable with the highest estimate being found for intramuscular fat (0.42±0.13). The heritability estimates for percentages of heat soluble and insoluble collagen were 0.12±0.09 and 0.15±0.09, respectively, while 0.33±0.12 was found for total collagen content. Moderate heritability implies the possibility of improving these traits through selective breeding. Strong negative genetic correlations between moisture and fat traits and a further negative correlation between fat and muscling traits confirmed that selection for improved muscling over time negatively affects fat traits and may then decrease meat eating quality. The strong genetic correlations of lightness (L*) with soluble collagen (0.68±0.30) and insoluble collagen (-0.71±0.35) suggest possible pleiotropic gene effects on these traits. Warner-Bratzler shear force (WBSF) had moderate genetic correlations with insoluble collagen (0.42±0.16) and soluble collagen (-0.38±0.10), suggesting a potential relationship between some of the genes impacting these traits. Genetic correlations between WBSF and collagen characteristics indicated that despite the relative youthfulness of pigs at slaughter, genetic selection for collagen solubility may decrease WBSF. In the second study, the contributions of company, sex and loin physical and collagen characteristics to measures of pork carcass and meat quality in a Canadian context were examined. Results from this study indicated that intramuscular collagen characteristics influenced loin cooking loss and further revealed that Warner-Bratzler shear force (WBSF) values were driven more by denaturation of myofibrillar proteins than by intramuscular fat content. Means separation analysis also showed WBSF to increase with increased muscularity and reduced backfat which suggests that selection for rapid growth rate with its associated reduction in calpain activity may decrease pork tenderness. This study further implicates pH and intramuscular fat content as part of the traits influencing insoluble collagen percent indicating that deposition of fat in the perimysium may be a potential disruptor of crosslink formation. Step- wise regression indicated that pH is not a reliable sole predictor of meat quality in loin that has been frozen and then thawed and thus other variables in addition to pH are needed to reliably predict frozen/thawed pork quality. Drip loss predicted most of the variation in tenderness which indicated that pork samples in the present study may have undergone myofibrillar protein oxidation during frozen storage or dehydration during cooking. The results indicated that sex has no significant influence (p>0.05) on loin compositional and meat quality traits while source of animal has a significant (p

Temperament in cattle can be described as the reactivity or fear response to human handling, and it is important to beef cattle producers not only from a human safety but also due to potential correlations with other economically traits. Before a docility selection metric can be added to a genetic evaluation, any potential antagonisms with economically relevant traits should be quantified. The objective was to estimate genetic parameters, including genetic correlations, for chute score (CS), weaning weight (WW), yearling weight (YW), and intramuscular fat percentage (IMF) in Hereford cattle. Single-trait and bivariate animal models were used to estimate heritabilities and genetic correlations. Models included fixed effects of sex and contemporary group, defined as herd–year–season. Direct genetic and residual components were included as random effects. For CS and WW, also additional random effects of maternal genetic and maternal permanent environment were fitted. For CS, WW, YW, and IMF, heritability estimates were 0.27 ± 0.02, 0.35 ± 0.03, 0.36 ± 0.02, and 0.27 ± 0.02, respectively. Genetic correlations between CS and WW, CS and YW, CS and IMF, WW and YW, WW and IMF, and YW and IMF were –0.12 ± 0.06, –0.10 ± 0.05, –0.08 ± 0.06, 0.47 ± 0.05, –0.19 ± 0.09, and –0.41 ± 0.05, respectively. Heritability estimates for all traits suggest that they would respond favorably to selection, although the selection for increased WW or YW could decrease marbling, which is often associated with favorable meat quality. Genetic correlations between CS and WW, YW, and IMF were all favorable but weak, suggesting that selection for improved docility will not have negative consequences on growth or meat quality. Maternal additive and maternal permanent environmental variances for CS were close to zero, suggesting that their inclusion in National Cattle Evaluations is not warranted. Advisor: Matthew Spangler

Abstract: Pork quality and carcass characteristics are now being integrated into swine breeding objectives because of their economic value. Understanding the genetic basis for these traits is necessary for this to be accomplished. The main objective of this study was to improve pork quality traits in two Canadian swine populations. Data from 6,408 commercial crossbred pigs with performance traits recorded in production systems with 2,100 of them having meat quality and carcass measurements. These pigs were progeny from 139 Duroc boars bred to 429 F1 hybrid Landrace × Large White sows. In the first study, phenotypic and genetic parameters for meat quality and carcass traits were estimated. Heritability estimates (± SE) for carcass traits were moderate to high and ranged from 0.22 ± 0.08 for longissimus dorsi muscle area to 0.63 ± 0.04 for trimmed ham weight, except for firmness that was low. Heritability estimates (± SE) for meat quality traits varied from 0.10 ± 0.04 to 0.39 ± 0.06, for the Minolta b* of ham quadriceps femoris muscle and shear force, respectively. There were high negative genetic correlations between drip loss with pH and shear force and a positive correlation with cooking loss. Genetic correlation between carcass weight with carcass marbling was highly positive. It was concluded that selection for increasing primal and subprimal cut weights with better pork quality may be possible. Furthermore, the use of pH is confirmed as an indicator for pork water-holding capacity and cooking loss. In the second study, heritability, phenotypic, and genetic correlations between performance traits (n=9) with meat quality (n=25) and carcass (n=19) traits were estimated. Performance traits had low-to-moderate heritabilities (±SE), ranged from 0.07±0.13 to 0.45±0.07 for weaning weight, and ultrasound backfat depth, respectively. The results indicate that: (a) selection for birth weight may increase drip loss, lightness of longissimus dorsi, and gluteus medius muscles but may reduce fat depth; (b) selection for nursery weight can be valuable for increasing both quantity and quality traits; (c) selection for increased daily gain may increase the carcass weight and most of the primal cuts. These findings suggest that deterioration of pork quality may have occurred over many generations through the selection for less backfat thickness, and feed efficiency, but selection for growth had no adverse effects on pork quality. The heritabilities of carcass and pork quality traits indicated that they can be improved through traditional selection and genomic selection, respectively. The estimated genetic parameters for performance, carcass and meat quality traits can be incorporated into the breeding programs that emphasize product quality in these Canadian swine populations. In the third study, a genomic selection was performed for meat quality and carcass traits in 2,100 commercial pigs and 107 Duroc purebred pigs using Illumina’s PorcineSNP60 BeadChip and single-step BLUP (ssBLUP). It was concluded that genomic predictions models developed using ssBLUP could predict the parental purebreds without substantial loss of prediction accuracy compared to their crossbred progenies to improve carcass and pork quality traits. The prediction accuracies for the purebred parental resulted from the ssBLUP evaluation were also compared with the accuracies from the traditional parental average. The results showed that the prediction accuracies resulted from the ssBLUP had average improvements of 17% and 16% for pork quality and carcass, respectively. In conclusion, this study confirmed that genomics could improve pork quality through genomic selection from commercial crossbred pigs to meet the demands by consumers, packers and processors.

Pork quality is a composite trait that is not readily and accurately assessed with any one or few simple measures. Additionally, it is a relative concept that takes on different meanings to different segments of the pork production chain. Ultimately, the end consumer will define those attributes of pork quality responsible for maintaining pork as an attractive dietary protein and nutrient source. However, those quality attributes (i.e. efficiency, leanness, technological quality) deemed important by other segments of the pork production chain cannot be disregarded. Regardless of the definition, the swine industry has been plagued with pork of inferior and variable quality and has focused much attention to improving the levels and consistency of quality. Variation in pork quality is, to a large degree, attributable to genetic factors. In order to be utilized as selection criteria in genetic improvement programs, traits must I.) exhibit variation, II.) allow for accurate assessment, III.) be heritable, and IV.) be economically important. The objectives of the current research were to estimate genetic parameters of performance, composition, and meat quality traits in pigs and to partially evaluate measures of myofiber and extracellular matrix characteristics and myosin heavy chain isoform composition as potential selection criteria for genetic improvement programs. This research reports on differences between Berkshire and Landrace purebred pigs for performance, composition, and meat quality traits and reports estimates of heritabilities for and genetic correlations between these traits. This research also reports on the proportions of variation in performance, composition, and meat quality traits that are attributable to variation in myofiber, extracellular matrix, and myosin heavy chain isoform compositions. Outcomes of this research suggest that variation in meat quality is moderately to lowly heritable and should respond favorably to selection. However, antagonistic genetic correlations between composition and meat quality traits exist and present challenges to simultaneous improvement in both trait types. While variation in meat quality can be explained, in part, by variation at the cellular and protein levels, these relationships warrant validation prior to utilization as selection criteria. This research provides insight into potential mechanisms involved in the conversion of muscle to meat.

Wood samples were collected from 10-year-old loblolly pine (Pinus taeda L.) rooted cuttings and seedlings from nine full-sib families resulting from a 3x3 factorial mating design. The field design consisted of two sites with six blocks per site in a randomized complete block design. In the spring of 2001, 12 mm increment cores were taken from approximately 1600 trees, and measurements of height and diameter were taken at the age of 10 ½ years. No significant differences were found between rooted cuttings and seedlings for specific gravity or growth traits, but sites significantly differed for growth traits. Significant family variation was found for both growth and specific gravity. Genetic parameters were estimated for wood specific gravity and growth traits for both seedlings and rooted cuttings. Heritabilities for specific gravity were generally high, and estimates from rooted cuttings were higher than from seedlings. Specific gravity was found to be negatively correlated with height. Clones were less variable than full-sib seedlings for specific gravity. These results suggest that gains in specific gravity could be made in breeding programs through the use of clonal testing during breeding and the deployment of superior clones. Wood strips from the increment cores were then measured using x-ray densitometry. Seedlings and rooted cuttings did not differ significantly for overall latewood density, earlywood density or latewood percentage of the whole core, but overall wood density did differ significantly based on seven growth rings. Half-sib and full-sib loblolly pine families did not display significant variation, but clones within families differed significantly in wood density, latewood density, and latewood percentage, indicating the greater potential for gains from clonal selection. Heritabilities for composite ring density traits were found to be moderate to high, indicating the potential for gains in wood density through selection of families or clones. Individual ring analysis revealed that the wood density of rings 1-4 was highly correlated with wood density through ring 7, suggesting that selection of juvenile wood density could be made at an early age.

During the last half of the 20th century, the world pork industry has achieved astonishing developments in pig breeding. Now swine farms are larger, ownership more concentrated, and farms have become more industrialized. Artificial insemination (AI) plays an important role in animal breeding increasing utilization of genetically superior sires. Currently boars selected for commercial use as AI sires are evaluated on grow-finish performance and carcass characteristics. The objectives of this study were to (A) estimate genetic correlations between production and semen traits in the boar; average daily gain (ADG), back fat thickness (BF) and muscle depth (MD) as production traits, and total sperm cells (TSC), total concentration (TC), volume collected (SV), number of extended doses (ND), and acceptance rate of ejaculates (AR) as semen traits; (B) to model the variances and covariances of total sperm cells (x 10⁹) over the active lifetime of AI boars; and (C) to compare multiple traits and random regression analyses applied to total sperm cells (TSC). Average heritability estimates were 0.39 for ADG, 0.32 for BF, 0.15 for MD, and repeatability estimates were 0.38 for SV, 0.37 for TSC, 0.09 for TC, 0.39 for ND, and 0.16 for AR. Semen traits showed negative genetic correlations with MD. Genetic correlations would indicate that current selection objectives are having a negative effect on semen traits. Therefore, current AI boar selection practices may be having a detrimental effect on semen production. In random regression analysis for total sperm cells, maximum log likelihood value was observed for sixth, fifth, and seventh order polynomials for fixed, additive genetic and permanent environmental effects, respectively. Best fit as determined by Akaike's Information Criterion was based on a model with sixth, fourth, and seventh order polynomials for fixed, additive genetic and permanent environmental effects, respectively. Best fit as determined by Schwarz Criterion was by fitting fourth, second, and seventh order polynomials for fixed, additive genetic and permanent environmental effects, respectively. Heritability estimates for total sperm cells ranged from 0.27 to 0.61 across age of boar classifications. Heritability for total sperm cells tended to increase with age of boar classification. The cyclic nature of heritability for total sperm cells that was observed over the active lifetime of boars may be due in part to number of observations across seasons limiting our ability to correct for seasonal effects on sperm production. In MTDFREML analysis, heritability estimates of 9, 12, 15, 18, 21, 24, and 27 months of age were, respectively, 0.28, 0.29, 0.26, 0.27, 0.30, 0.79, and 0.41. The results from MTDFREML seemed to be overestimated when compared to random regression. Therefore, random regression methods are the most appropriate to analyze semen traits as they are longitudinal data measured over the boars lifetime.

Genetic parameters for live weight and velvet antler production in red deer were estimated using two data sources. One contained performance records of 194 progeny of ten red deer stags of European and English Park origin used in a progeny test. The second data set contained performance and pedigree records of 1989 commercially farmed red deer by 68 sires and was used to investigate more thoroughly fixed effects of year, sex and age of dam influencing weaning and yearling weights and to estimate genetic parameters for these traits. Heritability estimates obtained from analysis of the progeny test data were 0.92 (0.37), 0.16 (0.17) and 0.04 (0.13) for weaning, yearling and 15 month weights respectively. Velvet antler traits heritability estimates were 1.04 (0.48), 0.55 (0.40), 1.02 (0.48), for two year old velvet weight, grade and value and 0.67 (0.48), 0.50 (0.45), 0.67 (0.48) for three year old velvet weight, grade and velvet. Estimated heritability of weaning weight obtained from analysis of the second data set was 0.80 (0.07), while yearling weight heritability estimated from 270 records was 0.70 (0.17). Genetic and phenotypic correlations between live weight traits were similar to values for sheep and cattle in both studies. Results are discussed in relation to estimation techniques and practical application to breeding programs.