Master of Science / Department of Animal Sciences and Industry / Jim Nelssen / Seven experiments using a total of 3,251 preweaned pigs, nursery pigs, and sows were used to determine the effects of: 1) supplemental vitamin D[subscript]3 on suckling and nursery pig growth, and maternal performance, and 2) high sulfate water, dietary zeolite and humic substance on nursery pig performance. Also, a web-based survey was developed to question pork producers and advisors of the swine industry on their knowledge of feed efficiency. Experiment 1 tested an oral dose of either; none, 40,000 or 80,000 IU vitamin D[subscript]3 given to pigs 24 to 48 h after farrowing. No differences in growth performance or bone mineralization were observed, but vitamin D[subscript]3 supplementation increased serum 25(OH)D[subscript]3 on d 10, 20, and 30, but returned to control values by d 52. Experiments 2 and 3 evaluated an oral dose of vitamin D[subscript]3 to pigs just before weaning, as well as added D[subscript]3 in nursery diets and in drinking water. There were no effects on growth performance; however, serum 25(OH)D[subscript]3 increased with all sources of vitamin D[subscript]3 supplementation. Experiment 4 evaluated if pigs had a preference to 1 of 3 dietary concentrations of vitamin D[subscript]3. Pigs ate less feed from diets containing very high levels of vitamin D[subscript]3 compared to commonly supplemented levels. Experiment 5 evaluated 3 levels of vitamin D[subscript]3 in sow diets. There were no effects on sow productivity, subsequent pig performance, or piglet bone ash content. However, increasing vitamin D[subscript]3 increased sow serum 25(OH)D[subscript]3, milk vitamin D, and pig serum 25(OH)D[subscript]3. Experiment 6 and 7 evaluated the effects of dietary zeolite and humic substances in nursery pigs drinking high sulfate water. Ultimately, pigs drinking high sulfate water had increased fecal moisture content and decreased growth performance, and feed additives evaluated were ineffective in ameliorating these negative effects. Finally, data collected from the feed efficiency survey suggest that there are knowledge gaps about practices that effect feed efficiency. Results from this survey will help extension educators better target specific industry segments with current information and provide more specific areas of future research where lack of information has been identified.

Master of Science / Department of Animal Sciences and Industry / Jennifer M. Bormann / It is important for animals to be feed efficient and reproductively sound to optimize profits for cow- calf producers. The objective of this study was to determine the relationship between feed efficiency and reproductive performance. Feed efficiency measures included residual feed intake (RFI), feed to gain ratio (F:G) and daily dry matter intake (DMI). Reproductive measurements were pregnancy rate, first service conception rate, pregnancy type (AI, natural. open), calving percentage, calving day (CD) and age at first calving. Two data sets which included 136 crossbred Angus females sired by bulls with high or low RFI estimated breeding values (EBV) with multiple parity information and 56 purebred Hereford heifers with their first parity calving information were analyzed. Initially, the crossbred Angus females were analyzed based on their phenotypic RFI values. There was no difference in pregnancy rate between the feed efficiency measures. Second parity pregnant females had lower (F:G) with first service conception (P=0.053), and pregnancy types (P=0.014) than the open (less efficient) females. In parity 5, phenotypically efficient RFI Angus females were pregnant to first service conception versus inefficient RFI Angus females (P=0.052) and those with lower DMI were diagnosed pregnant (P=0.0002). When evaluated as a repeated trait, RFI was not a significant indicator of CD (P=0.514). Crossbred Angus females were analyzed based on their sire’s RFI EBV and grouped accordingly into high (inefficient) or low (efficient) RFI sires. Females sired by high or low RFI (EBV) bulls showed no difference for the reproductive traits, except for a tendency for inefficient sired heifers to have a lower calving percentage in parity 2 (P=0.048). When CD was analyzed as a repeated measure, no difference between sire groups was found (efficient CD of 35.64 d, inefficient CD of 34.23, p = 0.789). In the Hereford heifers, RFI was not an indicator of CD (P = 0.774). There was also no difference in RFI between pregnant and open Hereford females with pregnant females having an LSMean of 0.11 kg/d and the open females having an LSMean of 0.14 kg/d (P = 0.860). Further research needs to be done to confirm any relationships between feed efficiency and reproduction.

Os efeitos maternos e, principalmente, os componentes citoplasmáticos devido sua herança matrilinear, podem influenciar de forma permanente na seleção e no potencial de expressão das características de importância econômica dos bovinos. Como objetivo deste estudo, estimou-se o impacto da inclusão do efeito genético da linhagem citoplasmática sobre estimativas de componente de (co)variância, parâmetros genéticos e sua influência sobre a predição dos valores genéticos para características de crescimento, reprodução e eficiência alimentar de animais da raça Nelore. Para traçar a genealogia, tomando como base a linha materna de cada animal, utilizou-se o software LinMat e arquivo de pedigree contendo 496.190 animais do rebanho de bovinos Nelore pertencentes à Agropecuária CFM e 8.635 animais compondo o arquivo provenientes dos experimentos para eficiência alimentar. Os componentes de (co)variância e parâmetros genéticos foram estimados com base nos registros para peso ao nascimento (PN), peso ao desmame (PD), ganho de peso ajustado para 345 dias de idade (GPSOB), perímetro escrotal aos 18 meses (PE), conformação (CONF), precocidade (PREC), musculosidade (MUSC), ingestão de matéria seca (IMS), consumo residual (CAR), taxa de conversão alimentar (CA) e ganho médio diário (GMD). As análises de componentes de variância foram realizadas no programa computacional BLUPF90 de forma uni-característica com modelo animal pelo método da máxima verossimilhança restrita (REML), e por inferência bayesiana para os indicadores de eficiência alimentar, considerando a linhagem citoplasmática como efeito aleatório. Os resultados obtidos revelam que as características analisadas podem ser utilizadas como critério de seleção pela variabilidade genética e potencial de transmissão. A inclusão do efeito de linhagem citoplasmática foi significativo para PN, CONF, PREC e MUSC. Ao longo prazo, a seleção de linhagens citoplasmáticas com maior efeito genético pode promover o avanço genético para as características de interesse econômico. / Maternal effects and its inheritance have been suggested to have a permanent influence on selection and expression potential traits in cattle. The objectives of this study were to estimate the impact of the inclusion of the cytoplasmic lineage genetic effect on component estimates of (co) variance, genetic parameters and evaluated the influence of this effect on the prediction of breeding values for growth, reproductive and feed efficiency traits of Nellore cattle. Pedigree data from 496,190 Nellore animals belonging to the Agropecuaria CFM and 8,635 animals from feed efficiency traits composing the pedigree file that was used to trace the genealogy, based on the maternal line of each animal by LinMat software. The records for birth weight (BW), weaning weight (WW), weight gain adjusted to 345 days of age (PWG), scrotal circumference at 18 months (SC), conformation (CONF), precocity (PREC), muscularity (MUSC), dry matter intake (DMI), residual feed intake (RFI), feed conversion rate (FCR) and average daily gain (ADG) were evaluated. Analyses were performed by computer program BLUPF90 with an animal model by the method of restricted maximum likelihood (REML) and Bayesian approach to feed efficiency indicators, considering cytoplasmic lineage as a random effect. The results show that the traits analyzed can be used as selection criteria by the genetic variability and the potential for heritability. The inclusion of cytoplasmic lineage effect was significant for BW, CONF, PREC and MUSC. In long-term, the selection of cytoplasmic lines with greater genetic effect may promote genetic progress for economic interest traits.

Selection of pigs has focussed on the improvement of lean growth with simultaneous reduction in fat tissue, due to the high economic importance of these traits. As a consequence, a large number of quantitative trait loci (QTL) have been reported for these traits. In contrast, very few QTL have been reported for chemical body composition (protein and lipid). Knowledge about the deposition rates of these components is important to accurately predict the nutritional requirements of pigs and to determine selection objectives for optimal development of body tissues and feed intake capacity. Therefore, the principle aims of this thesis were to investigate the genomic regulation of physical and chemical body composition as well as feed intake, feed efficiency and meat quality in a commercial pig population. Data for all analyses were derived from a three generation full-sib design created by crossing Pietrain sires with a crossbred dam line. In total, 386 animals were genotyped for 96 molecular markers covering 11 chromosomes. Phenotypic data were available for 315 F2 animals for carcass characteristics measured at slaughter weight, chemical body composition measured at different target weights throughout growth, feed intake measured throughout growth, and meat quality traits collected post-slaughter. Individual QTL analyses of several autosomes and chromosome X uncovered a large number of QTL in different regions of the genome for physical body composition traits as well as novel QTL for chemical body composition and deposition. Associations between QTL for chemical and physical body composition were also detected. The results highlighted that different stages of growth are under different genomic regulation. Further QTL were detected for feed intake and feed efficiency and interesting causative biological reasons for QTL of feed efficiency were derived in associations with QTL for body composition and growth. Epistatic QTL analyses were performed to investigate the contribution of interactions (epistasis) to the genomic regulation of physical and chemical body composition as well as growth and feed intake. Epistasis was found to contribute to the entire growth period, however, different epistatic QTL pairs contributed to different stages of growth. Epistatic QTL pairs mostly accounted for higher proportions of the phenotypic variance than QTL detected from individual QTL analyses. A large number of QTL were identified, which could not be detected from individual QTL analyses, mainly because these QTL did not express individually significant additive or dominance effects and only expressed their effects through interactions with other QTL. Individual and epistatic QTL analyses uncovered numerous QTL as well as epistatic interactions influencing meat quality traits, including pH, meat colour and conductivity, traits which influence the quality of pork. The work of this thesis gives substantial insight into the genomic regulation of economically important traits of pigs. The research highlights that the genomic regulation of growth and body composition, feed intake and meat quality is complex, involving numerous QTL located in different regions of the genome, controlled partly by imprinting effects, as well as a complex network of interactions between QTL. The results obtained in this study can be used in pig breeding to optimise breeding programmes and for marker assisted selection.

Objectives were to characterize residual feed intake (RFI) and determine the phenotypic correlation between performance, feed efficiency, and other biological measurements in Brahman heifers, as well as the relationship between RFI determined in confinement and measurements of grazing activity on pasture. Three separate 70 d feeding trials were performed, and RFI was determined as the residual between actual and predicted dry matter intake (DMI) for a given level of production. Brahman heifers (n = 103; 5-to-9 mo of age) were individually limit-fed a pelleted 12% CP complete ration daily in Calan gates. Weekly body weight (BW) and DMI data were collected, and predicted DMI was determined by linear regression of actual DMI on mid-test metabolic BW. Ytterbium chloride was used to evaluate digestive kinetics, and fecal samples were collected to determine fecal volatile fatty acids (VFA) concentration and determine apparent dry matter digestibility (DMD) utilizing acid insoluble ash as an internal marker. Measurements of temperament were evaluated on all heifers at weaning. High (n = 6) and low (n = 6) RFI heifers (Exp. I) grazed fescue and ryegrass to determine variation in grazing behavior, DMI, and apparent DMD. Data from all three experiments were pooled, and RFI was not correlated with average daily gain (ADG), DMI, BW, partial efficiency of gain, feed conversion ration, fecal VFA concentration, or any measures of temperament. There were no significant differences in digestive kinetics between the RFI efficiency groups. Fecal samples taken for acid detergent insoluble ash (ADIA) determination were not collected at frequent enough intervals to account for weekly variation in fecal ADIA concentration. Pasture measurements were not different between the efficiency groups for heifers evaluated for grazing behavior, as well as estimated intake as a proportion of BW, or apparent DMD. Results of this study suggest that Bos indicus cattle appear to have similar efficiency traits as Bos taurus and Bos indicus influenced cattle, making this measure of efficiency equally as valid for use in both types of cattle. This indicates that selection based on RFI can be made to increase feed efficiency without affecting ADG or BW in Brahman cattle.

Objectives were to characterize residual feed intake (RFI) and determine the phenotypic correlation between performance, feed efficiency, and other biological measurements in Brahman heifers, as well as the relationship between RFI determined in confinement and measurements of grazing activity on pasture. Three separate 70 d feeding trials were performed, and RFI was determined as the residual between actual and predicted dry matter intake (DMI) for a given level of production. Brahman heifers (n = 103; 5-to-9 mo of age) were individually limit-fed a pelleted 12% CP complete ration daily in Calan gates. Weekly body weight (BW) and DMI data were collected, and predicted DMI was determined by linear regression of actual DMI on mid-test metabolic BW. Ytterbium chloride was used to evaluate digestive kinetics, and fecal samples were collected to determine fecal volatile fatty acids (VFA) concentration and determine apparent dry matter digestibility (DMD) utilizing acid insoluble ash as an internal marker. Measurements of temperament were evaluated on all heifers at weaning. High (n = 6) and low (n = 6) RFI heifers (Exp. I) grazed fescue and ryegrass to determine variation in grazing behavior, DMI, and apparent DMD. Data from all three experiments were pooled, and RFI was not correlated with average daily gain (ADG), DMI, BW, partial efficiency of gain, feed conversion ration, fecal VFA concentration, or any measures of temperament. There were no significant differences in digestive kinetics between the RFI efficiency groups. Fecal samples taken for acid detergent insoluble ash (ADIA) determination were not collected at frequent enough intervals to account for weekly variation in fecal ADIA concentration. Pasture measurements were not different between the efficiency groups for heifers evaluated for grazing behavior, as well as estimated intake as a proportion of BW, or apparent DMD. Results of this study suggest that Bos indicus cattle appear to have similar efficiency traits as Bos taurus and Bos indicus influenced cattle, making this measure of efficiency equally as valid for use in both types of cattle. This indicates that selection based on RFI can be made to increase feed efficiency without affecting ADG or BW in Brahman cattle.

The cost of feed remains an important factor affecting the profitability of beef production, and the difficulty of recording feed intake is a major limitation in an industry-wide selection program. Novel genomics approaches offer opportunities to select for efficient cattle. Therefore, the main objective of this work was to identify genetic markers responsible for genetic variation in feed efficiency traits as well as to understand the molecular basis of feed efficiency traits. The candidate gene approach revealed new single nucleotide polymorphisms (SNPs) in the Cholecystokinin B receptor (CCKBR) and pancreatic anionic trypsinogen (TRYP8) genes that showed strong evidence of association with feed efficiency traits. An in silico approach was proposed as a cost-effective method for SNP discovery. SNPs within genes Pyruvate carboxylase, ATPaseH+, UBQEI, UCP2, and PTI showed evidence of association with carcass traits without negatively affecting feed efficiency traits. The polymorphisms within genes CCKBR and TRYP8 were associated with pancreas mass and pancreatic exocrine secretion. A fine-mapping study on 1,879 SNPs revealed 807 SNPs with significant associations corresponding to 1,012 genes. These 807 SNPs represented a genomic heritability of 0.32 and 89% of the genetic variance of residual feed intake (RFI). Genomic breeding values estimated from the SNP set (807) were highly correlated (0.96) to the breeding values estimated from a mixed animal model. The 10 most influential SNPs were located in chromosomes 16, 17, 9, 11, 12, 20, 15, and 19. Enrichment analysis for the identified genes (1,012) suggested 110 biological processes and 141 pathways contributed to variation in RFI. The 339 newly identified SNPs corresponding to 180 genes identified by fine-mapping were tested for association with feed efficiency, growth, and carcass traits. Strong evidence of associations for RFI was located on chromosomes 8, 15, 16, 18, 19, 21, and 28. Combing validated SNPs from fine-mapping and the candidate gene approach may help develop a DNA test panel for commercial use and increase our understanding of the biological basis of feed efficiency in beef cattle. / The Ministry of Higher Education of Egypt

Biological factors regulating feed efficiency were investigated in replacement beef heifers to establish factors that differ between efficient and less efficient animals. Feed efficiency, measured as residual feed intake (RFI) adjusted for body ultrasound measurements, was determined in forty-seven cross-bred heifers. Reproductive differences between efficient (low RFI) and less efficient (high RFI) heifers were examined. Low RFI heifers had an earlier age at both sexual maturity (P=0.08) and conception (P=0.08), and delivered heavier calves (P=0.006). The potential of fecal progesterone metabolites (FP4M) as an indicator of sexual maturity was examined. Measurements of FP4M present a promising non-invasive alternative technique for determining the onset of sexual maturity. A subset of 36 heifers was used to determine if plasma triiodothyronine (T3) concentrations could be used to predict feed efficiency. Triiodothyronine concentrations a correlation of 0.58 (P=0.001) to those from a quadratic prediction model of RFI in heifers sampled as yearlings. / Research into reproductive characteristics associated with residual feed intake, and to determine the effectiveness of the thyroid hormones as a screening tool for feed efficient animals. / OMAFRA (Ontario Ministry of Agriculture, Food, and Rural Affairs) through the Farm Innovation Program, Agriculture Canada through the Growing Forward Project, the Canadian Cattlemen’s Association through the Beef Cattle Research Council, and the Ontario Cattlemen’s Association.

Identifying molecular mechanisms regulating cellular energy utilization may lead to increased understanding of maintenance energy cost and improved feed efficiency in beef cows. Three experiments were conducted to characterize measures of residual feed intake (RFI) in pregnant beef cows; to examine the effects of moderate dietary restriction on visceral organ mass and proteins relating to energy metabolism; and to investigate the influence of pregnancy on visceral organ mass and proteins relating to energy metabolism. The first experiment combined data from five experiments using 321 pregnant Angus × Simmental cows. Including ultrasound fat measures and diet/management information increased the feed intake prediction model R2 by 7.3% and > 20%, respectively. Individual experiment RFI models varied greatly in accuracy. In the second experiment, 22 pregnant beef cows were fed at 85% (LOW; n=11) or 140% (HIGH; n=11) of net energy requirements during mid- to late-gestation. Tissue samples from liver, kidney, muscle, ruminal papillae, pancreas, and small intestinal muscosa were collected. Western blots were conducted to quantify abundance of: proliferating cell nuclear antigen, ATP synthase, ubiquitin, and Na/K+ ATPase for all tissues; peroxisome proliferator-activated receptor gamma, peroxisome proliferator-activated receptor gamma coactivator 1 alpha (PGC-1α), and 5’-adenosine monophosphate-activated protein kinase and phosphorylated-AMPK (pAMPK) for liver, muscle, and rumen; phosphoenolpyruvate carboxykinase for liver and kidney; and uncoupling protein 2 for liver. Cows fed HIGH had greater (P ≤ 0.04) ADG and final BW than cows fed LOW. Ubiquitin abundance in muscle was greater (P = 0.009) in cows fed LOW, and PCG-1α in liver was greater (P = 0.03) in cows fed HIGH. In the third experiment, 18 pregnant (PREG; n =9) or non-pregnant (OPEN; n=9) Angus × Simmental cows were fed for ad libitum intake during mid- to late-gestation. Tissues were weighed and collected and analyzed for protein abundance as described in the second experiment. Liver mass was lower (P ≤ 0.02), abundance of Na+/K+-ATPase was greater (P =0.04) and rumen pAMPK abundance was increased (P = 0.006) in PREG cows. These experiments indicate that measuring RFI in pregnant cows may pose some challenges, and nutrient restriction and pregnancy can influence molecular factors influencing feed efficiency. / Financial support was provided by Canadian Beef Cattle Industry Science Cluster, through funding provided by the Beef Cattle Research Council and Agriculture and Agri-Food Canada, Agriculture Adaptation Council-Farm Innovation Program, Ontario Ministry of Agriculture, Food and Rural Affairs, and the Ontario Cattleman’s Association.

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