Thesis (Ph. D.)--University of Missouri-Columbia, 2007. / The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on September 18, 2007) Vita. Includes bibliographical references.

Submitted by Ana Cristina Herrera Rios (anacristinah@gmail.com) on 2018-09-06T21:12:03Z No. of bitstreams: 1 Herrera_a_ma_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) / Approved for entry into archive by Neli Silvia Pereira null (nelisps@fcav.unesp.br) on 2018-09-10T16:57:12Z (GMT) No. of bitstreams: 1 herrerarios_ac_dr_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) / Made available in DSpace on 2018-09-10T16:57:12Z (GMT). No. of bitstreams: 1 herrerarios_ac_dr_jabo.pdf: 1549720 bytes, checksum: cc3a9f221086386bf628813bbc967443 (MD5) Previous issue date: 2018-07-30 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / O uso intensivo de biotecnologias reprodutivas tem feito com que se eleve a taxa de nascimento de progênies com maior grau de parentesco (maior taxa de nascimento de meio-irmãos e irmãos completos). Assim, o conhecimento sobre o coeficiente da endogamia média do rebanho torna-se relevante para a eficiência do sistema de produção. Com o advento da genômica, o coeficiente de endogamia (F) pode ser estimado com base na informação de milhares de marcadores do tipo polimorfismos de base única (SNPs), espalhados por todo o genoma. No presente estudo, informações de 3.785 animais da raça Nelore (1,760 machos e 2,025 fêmeas) genotipados para 777.962 SNPs do BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) foram utilizadas com o objetivo de avaliar a taxa de endogamia em rebanhos comerciais da raça Nelore, bem como investigar o seu efeito (depressão endogâmica) sobre a expressão fenotípica de características reprodutivas (idade ao primeiro parto (IPP), ocorrência de prenhez precoce (OPP) e reconcepcão de novilhas (REC)). A estimativa do valor de F, bem como da depressão endogâmica, foi feita utilizando diferentes metodologias: (i) matriz de parentesco genômica com frequências alélicas obtidas da população base (FG); (ii) matriz de parentesco genômica com frequências alélicas fixadas em 0,5 (FGRM); (iii) com base no excesso de SNPs em homozigose (FSNP); e (iv) corrida de homosigose (FROH). Os resultados da corrida de homosigose também foram utilizados para identificar os padrões (tamanho e distribuição) dos segmentos ROH na raça Nelore bem como para identificar ilhas de homosigose (segmentos ROH compartilhados por mais de 50% da população). Foram identificados 210.636 segmentos ROH distribuídos nos 29 autossomos e cinco ilhas de homozigose localizadas nos cromossomos 5, 7, 12, 21 e 26, nas quais 43 genes foram identificados. Alguns destes genes (INHBE, INHBC, STAT6, FGF8 e DPCD) foram previamente associados com caracteristicas reproductivas, de crescimento, resposta inmume e adaptabilidade em bovinos. As médias para o coeficiente de endogamia calculado com base nas diferentes abordagens foram: -0,0006 (FG), 0,4376 (FGRM), 0,5500 (FSNP) e 0,0590 (FROH). As correlações foram ente baixas FG-FSNP (-0,28), FG-FGRM (-0,20), FG-FROH (0,21), a moderadas FROH-FSNP (0,68), FROH-FGRM (0,72) e fortemente alta para FSNP-FGRM (0,99). O valor médio de F variou de acordo com a metodologia utilizada. O valor extremamente alto do FSNP denota que este método tende a superestimar as taxas de endogamia. Independentemente do método utilizado para obter os valores de F, foi verificado que o aumento de 1% no coeficiente de endogamia médio do rebanho influenciou desfavoravelmente a média das características reprodutivas avaliadas. / The intensive use of reproductive biotechnologies has increased the birth rate of progenies with high degree of relationships (higher birth rate of half- and full-sibs). Thus, the control of herd inbreeding becomes relevant for the efficiency of the production system. With genomics, the inbreeding coefficient can be estimated using thousands of single nucleotide polymorphisms (SNPs), spread throughout the genome. In the present study, information of 3,785 Nelore animals (1,760 males and 2,025 females) genotyped with 777,962 SNP markers of BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) was used with the objective of evaluating the inbreeding rates of Nelore commercial herds, as well as to investigate the effects of inbreeding (inbreeding depression) on the phenotypic expression of reproductive traits (age at first calving (AFC), heifer early pregnancy (EP), and heifer rebreeding (HR)). The inbreeding coefficient (F) and inbreeding depression were estimated based on (i) genomic relationship matrix considering allele frequencies estimated from the base population (FG); (ii) genomic relationship matrix considering allele frequencies fixed at 0.5 (FGRM); (iii) excess of homozygous SNPs (FSNP); and (iv) runs of homozygosity (FROH). The runs of homozygosity results were also used to identify the pattern (size and distribution) of ROH segments as well as to identify ROH islands (ROH segments shared by more than 50% of the population). In total, there were identified 210,636 ROH segments and five ROH Islands located on the chromosomes 5, 7, 12, 21 and 26, in which 43 annotated genes were identified. Some of these genes (INHBE, INHBC, STAT6, FGF8 and DPCD) were previously associated with reproduction and growth traits, inmume response and adaptability in cattle. The average inbreeding calculated based on different approaches were -0.0006 (FG), 0.4376 (FGRM), 0.5500 (FSNP) e 0.0590 (FROH). These correlations ranged from low FG-FSNP (-0.28), FG-FGRM (-0.20), FG-FROH (0.21), to moderated FROH-FSNP (0.68), FROH-FGRM (0.72) and extremely high FSNP-FGRM (0.99). The average population inbreeding coefficient ranged according to the method used. The extremely high value of FSNP indicates that this approach tend to overestimate the inbreeding rates. Independently of the method used to obtain the F values, it was verified that the increase of 1% in the average herd inbreeding unfavorably influenced the mean value of the evaluated reproductive traits. / FAPESP#2009/16118-5

No description available.

Enterohemorrhagic Escherichia coli (EHEC) are important foodborne pathogens with a bovine reservoir. For many years, research and regulations have focused on the EHEC serogroup most commonly associated with severe human illness, EHEC O157. However, six additional EHEC serogroups have been identified as important human foodborne pathogens and have been declared adulterants in raw, non-intact ground beef by the United States Department of Agriculture’s Food Safety Inspection Service. Collectively these seven organisms are referred to as EHEC-7. With the addition of these six pathogens, epidemiological studies are needed to estimate the probability for cattle to carry them and to identify risk factors associated with their presence in samples of bovine origin. In addition, the potential for pre-harvest control of EHEC-7 in feedlot cattle, particularly by dietary intervention, is a knowledge gap that needs to be addressed. Finally, detection methods of EHEC-7 have not been validated, and there is no “gold-standard” test. The first study included in this dissertation was a cross-sectional study estimating the prevalence and risk factors associated with hide contamination by EHEC-7 on the hides of market beef cows at slaughter. The second study was a longitudinal analysis of EHEC-7 from fecal samples from cow-calf herds in Mississippi and Nebraska. The third study was a randomized controlled trial evaluating the effects of fiber from distillers grains on the probability to detect EHEC-7 in samples from the rectoanal mucosa of feedlot steers. The fourth study included in this dissertation was a Bayesian latent class analysis estimating the diagnostic performance of three EHEC-7 detection methods, specifically modeling the performance and prevalence of EHEC O157 in fecal samples from beef cow-calf herds.

Two studies were conducted to evaluate cotton gin mote as a forage replacement by determining nutrient digestibility and nitrogen and energy retention. Three diets were used: 0%, 50%, and 100% mote. Dry matter intake was greatest for steers consuming 100% mote. Digestibility of DM, OM, CP, and energy was least for steers consuming 50% mote and greatest for those consuming 0% mote. Digestibility of NDF and ADF was greatest for steers consuming 0% mote. Fat digestibility was greatest by steers consuming 0% mote and least by steers consuming 100% mote, with those consuming 50% mote being intermediate. Steers consuming 0 and 50% mote retained less protein and energy than those consuming 100% mote. In trial 2, IVDMD of cotton gin mote was evaluated to determine rate of disappearance of DM, CP, NDF, and ADF. The 0% mote diet revealed the greatest rate of disappearance for DM, CP, NDF, and ADF, followed by the 50% and 100% mote diet, respectively.

No description available.

The quality of early milk produced by dams is affected by various factors (i.e. breed, age, parity, environment, nutrition, management). The impact of these factors on the quality of milk then have subsequent effects on calf health and development. Producers are responsible for following guidelines in order to ensure that they feed calves optimal quality milk in order to produce a healthy animal. They can also regulate factors such as environment and nutrition of the dam in order to produce better quality early milk. However, even after maximizing these factors there is still high mortality rate among pre-weaned calves, therefore, other factors such as mode of birth and genetics need to be studied to determine impacts on early milk quality and make further improvements to calf health and decrease mortality. Two experiments were conducted in order to study the effects of maternal and genetic factors on early milk production and to determine relationships that exist with calf health. The objective of the first study was to determine the effects that the mode of delivery had on early milk composition, and on the rumen microbiome of calves. We hypothesized that mode of birth would impact early milk composition, and, in turn, influence the microbial phyla in the calf gut. The second study had three objectives: 1) establish phenotypic relationships between colostrum composition traits, milk production traits, and calf health, 2) determine impact of breed and season on colostrum production and 3) ) elucidate the genetic parameters (i.e. heritability, genotypic, and phenotypic correlations) among colostrum production and milk production We hypothesized that colostrum composition and production differ among breeds and by season and that individual components influence calf health. Additionally, we hypothesized that colostrum quality traits (i.e. Brix score and volume) are heritable. For the first study Charolaise (CHAR; n = 23) and Angus (ANG; n = 15) dams were divided into two experimental groups; dams underwent vaginal (VD; n= 25) or cesarean (CD; n= 13) deliveries. Early milk samples were collected and quantified for protein, lactose, somatic cell count, and fatty acid concentrations. After parturition calves were separated based on dams experimental group. Rumen fluid was collected from calves on d 1, 3, and 28 post-partum. Extracted DNA from fluid were used for metagenomic sequencing (ANG calves, n=11; CHAR calves, n=13). Samples were run on the HiSeq 2500 platform as paired end reads according to Ilumina's standard sequencing protocol. A regression analysis was done in SAS using PROC GLM and regressing mode of birth on milk components for d 1,3, and 28. After, milk components found to be significantly impacted by mode of birth were regressed against microbial counts. Results showed that VD dams were more likely to have increased (P  0.05) protein, solids non-fat, and lactose on d 1 and 3, but decreased (P < 0.05) urea concentrations. Similarly, short, medium, and long-chain fatty acids were increased (P  0.05) in VD d 3 milk. Changes in true protein elicited a decrease (P  0.05) in rumen fluid Actinobacteria and Proteobacteria; whereas, both solids non-fat and lactose were associated with an increased (P  0.05) response in d 1 transition milk. No significant results for d 28 of sampling were observed. Based on our results we suggest that mode of birth influences protein concentrations in early milk. However, only a slight impact on the overall dynamics of the calf rumen was observed with the microbiome remaining relatively stable on the phyla level in response to changes in protein concentration. The second study looked into relationships between colostrum composition traits, management practices, and calf health, as well as determined heritability and genetic correlations for colostrum quality traits. Values for test-day milk, protein, fat, and somatic cell count (SCS) for Holstein (HO, n= 250) and Jersey (JE, n=289) cows were obtained from the Animal Genomic and Improvement laboratory server at the USDA. Brix score, colostrum weight, dam age, parity, and 3-month season of calving were also recorded. After, colostrum samples from JE cows were sent to DHIA where compositional measurements were obtained (i.e. true protein, fat, lactose, SCS, solid non-fats). Lactoferrin concentration for JE colostrum samples was also determined via ELISA. Calf blood samples were collected within 72 h post-partum and total serum protein (TSP) quantified to determine success of passive immunity transfer. Additionally, farm staff were instructed to record colostrum source for 1st feeding (i.e. dam, mix, other), freshness for 1st feeding (frozen vs fresh), Brix score of colostrum fed, volume of colostrum fed, and birth weight. A PROC Mixed with LSMEANS was performed in SAS to determine relationships between colostrum components, test day components, and quality traits for season, breed, and the interaction between season and breed. Also, PROC Mixed with LSMEANS was used to determine relationships of calf health with environment, management, and colostrum components. Additionally, a Pearson correlation was used to determine relationships between colostrum components and quality traits. Results for Holstein and Jersey showed that both colostrum Brix and volume (P < 0.001) differed by breed. Colostrum volume (P < 0.001), lactose (P < 0.001), and lactoferrin (P = 0.002) varied significantly by season. Additionally, test day milk (P = 0.046), fat (P = 0.012), and protein (P = 0.003) varied significantly by season. Moreover, a significant season and breed interaction (P = 0.028) was observed solely for colostrum volume. Calf health models indicated that TSP, colostrum total protein and solid non-fats impacted incidence of respiratory illness, but no factor significantly impacted incidence of scours. Results for Pearson correlation indicated strong correlations between true protein and solid non-fats and Brix (r = 0.99; 0.86). Lactoferrin also had moderate negative correlations with volume and lactose (r = -0.35; -0.33). Heritability and repeatability's were calculated using BLUPF90 family of programs. A single-trait repeatability animal model was used and included a 1-vector phenotype (Brix or Colostrum weight), fixed effects (i.e. calving year, parity, 3-month season of calving, and age at calving), additive genetic variance, random permanent environment effects, and random residual effects. A series of bivariate models were used to calculate genetic correlations of Brix score and colostrum weight with test-day compositional traits. Heritability estimates results for Holstein cow Brix and colostrum weight, were 0.25 and 0.15. Jersey cow heritability estimates were 0.36 and 0.47 respectively. We also observed some significant genetic correlations with Holstein Brix score and test-day milk (-0.23), fat (0.54), and SCS (0.29) having moderate correlations. Holstein colostrum weight had a strong correlation with test-day milk (0.96). Jerseys had strong genetic correlation of Brix score with colostrum weight (-0.98). Low to moderately heritability was observed for Brix score and colostrum weight in both breeds making them receptive to genetic selection in order to improve breeding programs. In conclusion, mode of birth significantly impacted colostrum composition which had subsequent effects on abundance of rumen microbiota. Colostrum Brix and volume were impacted by breed, season, and interaction, and calf incidence of disease was impacted by colostrum composition and environment. Additionally, two factors influencing colostrum quality (Brix score and colostrum weight) were found to be low to moderately heritable and have moderate to strong genetic correlations to compositional traits. Strong significant relationships were also found between colostrum compositional traits and colostrum quality traits. Therefore, incorporating quality traits into breeding programs has the potential to influence compositional traits which, in turn, can impact calf health and development by the interactions that exist between composition and microbial abundance in the rumen. / Master of Science in Life Sciences / Factors like breed, age, parity, nutrition, environment, and management can affect the quality of early milk produced. Many of these factors have been studied and guidelines developed in order to ensure producers feed the best quality milk to their calves which will allow for calves to develop properly. However, there is still a high mortality rate in pre-weaned calves and factors like mode of birth and genetics have not been readily studied. The purpose of our studies were to determine mode of birth impacts on composition of early milk and establish relationships between composition and rumen microbial phyla abundance. Additionally, establish relationships between colostrum composition traits, management practices, and calf health, and determine heritability and genetic correlations of colostrum quality traits to test-day composition traits. Our hypothesis was that colostrum quality traits such as Brix score and colostrum weight are heritable. We also hypothesized that mode of birth influences early milk composition and changes to composition has secondary effects to calf rumen microbial abundance. Charolaise (CHAR; n = 23) and Angus (ANG; n = 15) dams were divided into two experimental groups; dams underwent vaginal (VD; n= 25) or cesarean (CD; n= 13) delivery. Early milk samples were collected and sent to DHIA to quantify components. After parturition calves were separated based on dam's experimental group. Rumen fluid was collected from calves on d 1, 3, 28 post-partum and DNA extracted from fluid (ANG calves, n=11; CHAR calves, n=13). Results showed that VD significant differences in composition of VD and CD cows. Dams in VD group were more likely to have increased (P  0.05) protein, solids non-fat, and lactose but decreased (P < 0.05) urea concentrations. Similarly, short, medium, and long-chain fatty acids were increased (P  0.05) in VD. Changes in true protein elicited a decrease (P  0.05) in rumen fluid Actinobacteria and Proteobacteria. Results suggest that mode of birth influences protein concentrations in early milk and induces a slight impact on the overall dynamics of the calf rumen microbiome. A second study was conducted to establish relationships between colostrum components, management and calf health as well as determine genetic parameters of colostrum quality traits. Holstein (HO, n= 250) and Jersey (JE, n=289) cow test-day data was obtained from the Animal Genomic and Improvement laboratory server at the USDA. Brix score, colostrum weight, dam age, parity, and 3-month season of calving were also recorded. Colostrum samples from JE cows were sent to DHIA where compositional measurements were obtained (i.e. true protein, fat, lactose, SCS, solid non-fats). Lactoferrin concentration for JE cow colostrum samples was also determined via ELISA. Calf blood samples were collected within 72 h post-partum and TSP quantified. Farm staff recorded colostrum source for 1st feeding and colostrum freshness for 1st and feeding. A PROC Mixed was performed to determine impact of test-day milk composition traits on colostrum quality traits by breed, PROC Mixed with LSMEANS was used to determine relationships of environment, colostrum management, and colostrum components with incidence of scours and respiratory disease in calves. A Pearson correlation was used to determine relationships between colostrum components and quality traits Heritability and repeatability's were calculated using BLUPF90 family of programs. A series of bivariate models were used to calculate genetic correlations of Brix score and colostrum weight with test-day compositional traits. Results indicated that colostrum Brix and volume were impacted by season, breed, and the interaction of breed and season. Calf incidence of disease was impacted by colostrum components and total serum protein levels. Results for Pearson correlation indicated strong correlations between true protein and solid non-fats and Brix (r = 0.99; 0.86). Lactoferrin also had moderate negative correlations with volume and lactose (r = -0.35; -0.33). Heritability estimates results for Holstein Brix and colostrum weight were 0.25 and 0.15. Jersey cow heritability estimates were 0.36 and 0.47, respectively. We also observed some significant genetic correlations with Holstein Brix score and test-day milk (-0.23), fat (0.54), and SCS (0.29) having moderate correlations. Holstein colostrum weight had a strong correlation with test-day milk (0.96). Jerseys had strong genetic correlation of Brix score with colostrum weight (-0.98). Results indicated a low to moderately heritability for Brix score and colostrum weight in both breeds making them receptive to genetic selection in order to improve breeding programs. Strong significant relationships were also found between colostrum compositional traits and colostrum quality traits.

The purpose of this study was to determine the most accurate method of calculating the most probable producing ability (MPPA) of beef cows based on one, two or three records. A preliminary analysis of preweaning records on 9,515 calves from 4 Angus herds enrolled in the Virginia Beef Cattle Improvement Association program was conducted on average daily gain, 205-day weight and index value. Adjusted 205-day weight was selected for further study. To obtain a realistic repeatability value of adjusted 205-day calf weight, needed for calculating MPPA, separate estimates were first obtained for each herd by intraclass correlation. These values were 0.34, 0.00, 0.35 and 0.14. The individual herd sums of squares and degrees of freedom were then pooled to obtain an overall estimate of 0.31. Repeatability was also calculated by the correlation of adjacent records (r = 0.48) and by the regression of the second record on the first (b = 0.51). The pooled intraclass correlation coefficient (0.31) was selected as the best for the calculation of all MPPAs. MPPAs were calculated by the method of Lush (1949), using the dam's progeny record: (1) as a deviation from the herd-year average, and (2) as a deviation from the sire progeny average within years. MPPAs were calculated by both methods based on each of one, tuo and three records and each of these correlated with the average of all subsequent records (maximum of six). The first, second and third MPPA values by the herd-year method yielded correlation coefficients of 0.18, 0.10 and 0.04 with the average of all subsequent records, respectively. Corresponding sire-year correlation coefficients were 0.23, 0.31 and 0.36, respectively. The differences between the correlation coefficients obtained by the two methods for MPPA one, two and three were significant at the level of P < .10, P < .05 and P < .0005, respectively, indicating that the sire-year method is more accurate. The variance was also lower for the sire-year method (427 ± 44.2 pounds) than for the herd-year method (428 ± 55.2 pounds). Thus, the author has concluded from these results that the sire-year method of calculating most probable producing ability is a more accurate measure of the true productivity of beef cows. / Ph. D.

The counties involved in this study belong to the Piedmont Plateau. Soils are largely from crystalline rock and except for small areas of Davidson and Lloyd types, the soils are derived from acidic rock. The soils of this area are deficient in phosphorus but are fairly well supplied with potassium. In most cases lime and phosphate are the limiting factors in securing high yields of pasture and forage crops, and in getting stands of certain legumes. / Master of Science

The data for this study were taken from the calf crops born from 1950 through 1958 at the Beef (Battle Research Station, Front Royal, Virginia. These included 556 Angus, 556 Hereford, and 590 Shorthorn calves. / Master of Science