Doctor of Philosophy / Department of Diagnostic Medicine/Pathobiology / David G. Renter / Bradley J. White / The objective of my research was to quantify epidemiologic parameters associated with feedlot mortality and bovine respiratory disease complex (BRDC); the most significant cause of morbidity in U.S. feeder cattle. We conducted four retrospective studies utilizing individual health and cumulative cohort-level feedlot data. We developed a database that represented 33 U.S. feedlots from six states over ten years. Each project used a subset of these data. We found that the timing of BRDC was associated with important performance and health indices. In the first study, we evaluated the effect of the timing of individual BRDC treatments on standardized net returns. We found important performance and health measures (e.g. hot carcass weight and number treatments) driving net return differences associated with the timing of BRDC. For the second cohort-level study, we classified temporal patterns of BRDC, and evaluated associations among temporal patterns and performance and health. Temporal patterns were significantly associated with mean daily weight gain, days on feed, carcass weight, yield grade, quality grade, cumulative mortality, and retreatment risk. We also evaluated combined mortality and culling risks and quantified the effects of risk factors using count models. All risk factors (arrival weight, gender, and arrival month) were significant and the effects were modified by one another; effects of these covariate patterns have been impossible to quantify in smaller studies. Finally, we assessed the ability of regression models to predict cumulative BRDC morbidity based on arrival risk factors; then assessed the additional value of incorporating daily BRDC morbidity and mortality information. The percent of correctly classified cohorts did increase across days, but the effect of day was modified by weight, month, and feedlot. Information on daily morbidity was beneficial in predicting cumulative morbidity, but daily mortality provided little benefit. Our database containing animal health and cohort-level data allowed us to generate novel information on the effects of the timing of BRDC in feedlot populations. We also demonstrated effects of covariate patterns on adverse health outcomes that heretofore had been difficult to quantify. Finally, we showed that a predictive model for BRDC may be useful for the feedlot industry; this model should be further developed with future research.

Typescript (photocopy). / Digitized by Kansas Correctional Industries

Call number: LD2668 .T4 1959 W84

Call number: LD2668 .T4 1979 G462 / Master of Science

Call number: LD2668 .T4 1979 M94 / Master of Science

Master of Science / Department of Animal Sciences and Industry / Twig T. Marston / One hundred ninety-three crossbred steers from two herds were used to determine the association of leptin gene polymorphisms and effects of feedlot management of lean and fat steers on carcass performance. Steers were sorted into FAT and LEAN groups by ultrasound backfat at weaning and randomly assigned to a finishing phase. Steers were assigned to a backgrounding phase (BACK) and were fed a forage-based diet for 90 days or directly entered a feedlot phase (FEED). Genotypes were determined by IGENITY® (Atlanta, GA) for a panel of nine single nucleotide polymorphisms (SNP) in the leptin gene (UASMS1, UASMS2, C963T, E2FB, A1457G, and A252T), leptin receptor (T945M), growth hormone receptor (G200A), and fat metabolism enzyme (K232A). Initial backfat (BF) means for the FAT and LEAN group were 3.4 mm and 1.8 mm, respectively. Mean on-test weight was heavier for FAT (306.5 kg) than LEAN (292.9 kg). Age-adjusted hot carcass weights (HCWT) were heavier for LEAN/BACK when compared to FAT/FEED and FAT/BACK (P<0.05). Dressing percent for the FAT/FEED group tended to be higher (P<0.10) over all groups except LEAN/BACK. Steers that went directly to the feedlot had higher marbling scores than backgrounded groups. FAT/FEED had higher 12th rib BF than the other contemporaries. None of the SNPs were useful for predicting ultrasound BF at weaning. Some association was detected with UASMS2 and HCWT (P<0.10) resulting in an 11 kg difference between genotype CC and CT (P<0.05). Five of the leptin polymorphisms (UASMS1, UASMS2, A1457G, C963T, and E2FB) were associated with adjusted carcass BF (P=0.01, 0.06, 0.01, 0.01, and 0.01, respectively) and calculated yield grade (P<0.01). A252T was associated with REA, and genotype TT was larger than AA and AT (P<0.05). This study suggests that segregation by initial fatness estimates and feedlot management strategies has the opportunity to increase HCWT by 35 kg. Sorting cattle upon feedlot entry by ultrasound BF and segregation using genetic markers are useful tools that can assist in the estimation of carcass composition in the live animal. With additional research, the possibility exists to incorporate genetic markers into feedlot selection to assist in marketing decisions.

Master of Science / Department of Agricultural Economics / Kevin C. Dhuyvetter / When purchasing feeder calves, bulls are typically discounted relative to steers. Most would agree that a discount is warranted but determining the appropriate discount to apply is considerably more difficult. Being able to calculate this discount under varying conditions would help stock operators maintain a certain level of profitability or recognize opportunities to make more profit when excessive discounts are being applied. The goals of this study were to determine how castration timing affects performance (as measured by average daily gain), morbidity, and carcass quality and how morbidity affects performance and carcass quality. Ordinary Least Squares regression and logit models were estimated to quantify the effects of various management and environmental factors on performance, morbidity, and carcass quality. These model estimates of production variables along with price and cost assumptions were used to calculate breakeven purchase prices and price discounts for bulls relative to steers, accounting for the possibility of contracting bovine respiratory disease, if owned for a short background period or if ownership is retained through slaughter. Model results confirm that late-castrated steers do indeed exhibit diminished performance and increased morbidity probabilities relative to early-castrated steers. Increased morbidity also decreases average daily gain. However, this study found that castration timing and morbidity during the backgrounding period have minimal effects on carcass quality, with morbidity only impacting hot carcass weight and castration timing significantly affecting days to market and only tending to impact hot carcass weight. Ultimately, based on 2009 market conditions, bulls should be discounted at feeder calf sales compared to steers. The average calf arrived at 459 pounds, and at this weight bulls should be discounted $4.69/cwt relative to the same weight steers. The discount increases to $5.37/cwt for 400 pound calves and drops to $4.20/cwt for 500 pound calves. If ownership is retained through slaughter, required discounts will change to $6.77/cwt, $4.91/cwt, and $7.55/cwt, respectively.

BACKGROUND:General, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.RESULTS:For the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value<0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value<0.001) including, 9nucleotide binding / ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.CONCLUSIONS:The general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.

The relationship between measures of temperament, growth performance, and social hierarchy in finishing beef cattle were explored in two experiments. In experiment 1, high OCS (objective chute score) steers had periods of significantly higher ADG (P < 0.01), but OCS had no relationship with dominance ranking (P > 0.47). Conversely, slow exit velocity (EV) correlated with higher ranking (P ≤ 0.06), but EV had no relationship with performance (P > 0.37) in a competitive environment. Rank showed no relationship with performance (P > .58). In experiment 2, steers with fast EV had periods of decreased growth (P ≤ .06), intake (P ≤ .06), and gain:feed (G:F; P = 0.02). There were no interactions between EV, OCS, and monensin or between EV and monensin. Monensin and EV together, however, significantly impacted overall (days 0 – end) G:F (P = 0.02) and gain (P = 0.05). Overall, these studies further confirm the idea that EV affects performance as does OCS in concert with monensin. Moreover, it further confirms that different measures of temperament correlated to different aspects of performance and should not be lumped together under the general term “temperament” when describing its relationship with performance.

Dissertation (PhD(Agric))--University of Stellenbosch, 2007. / ENGLISH ABSTRACT: This study is a search for a quantifiable measure which estimates the genetic merit of female animals’ breeding efficiency. For practical reasons, such a measure must be both simple and inexpensive to record, irrespective of the herd management strategy. A literature investigation was undertaken to summarize breeding objectives for reproduction efficiency and to review different ways of expressing genetic reproduction efficiency. Traits to assess these in terms of the breeding objective, merits and requirements in terms of data collection are discussed. During the lifetime of a cow events occur which influence her fertility. A distinction is made between component traits and aggregate traits: a component trait points to one event, while aggregate traits are composites of more than one event. Although all the traits discussed seem relevant for breeding value estimation, the practical application depends on the herd management system in use. Age at first calving and days to calving are component traits that are easily and inexpensively measurable. Heritability estimates for the age at first calving were moderate. The heritability estimated for days to calving was 0.09. Calving rate comes close to the overall breeding objective. The estimated heritability of calving rate is low (0.04), resulting in slow genetic improvement. Calving success was defined and investigated even though some constraints exist. A sire model proved that genetic variation exists for calving success on the underlying scale. The corresponding heritability estimate was 0.27. Three categorical traits were defined. For stayability a sire variance of 0.41 was estimated with a heritabitity on the underlying scale of 0.27. The sire variances and heritabilities estimated for retention and calf tempo were high. Of the three traits, calf tempo is the one that reflects the true fertility of the bull’s female progeny. Calf tempo was redefined as net breeding merit, a trait describing the retention of male animals and the reproductive performance of their female offspring. The obtained sire variances show that the trait is heritable and can be improved by selection. Net breeding merit gives an indication of the ‘success’ of sires in a given population. A heritability estimate of 0.20 was estimated on a data set comprising offspring of bulls older than nine years, but when offspring of all sires were included, heritability estimates of 0.08 and 0.11 for the Afrikaner and Bonsmara, respectively, were found. Adjusting for young females was investigated by using the best linear unbiased estimate (BLUE) deviations to derive adjustment factors for herd level in order to predict performance for net breeding merit. Variation in the BLUE deviations occurred between all age class groups for the Afrikaner, whereas for the Bonsmara the variation between the BLUE deviations for the 3 year olds seems greater than the variation in the other age groups. It is suggested that the standardized curve for herd performance level derived from the BLUE deviations be used to adjust the phenotypic values of younger animals. This way the comparison between older and younger animals should be more valid. In conclusion, reproductive traits are heritable and genetic improvement can be achieved through selection. Any economical viable beef enterprise should include at least one trait in their selection criteria that will improve the reproductive efficiency. / AFRIKAANSE OPSOMMING: Hierdie studie is ‘n ondersoek na ‘n kwantifiseerbare maatstaf wat die genetiese meriete van vroulike diere se teeldoeltreffendheid beraam. Om praktiese redes moet so ‘n beraming sowel eenvoudig as goedkoop wees om te bepaal, onafhanklik van die kudde bestuurstrategie. ‘n Literatuurstudie is onderneem om die teeldoeleindes vir reproduktiewe doeltreffendheid op te som, sowel as om die verskillende wyses van genetiese reproduksiedoeltreffendheid beskrywing onder oë te neem. Verskeie eienskappe om hierdie beskrywings in terme van teeldoeleindes, meriete en dataversamelings-vereistes te raam, word bespreek. Gedurende ‘n koei se leeftyd kom gebeurtenisse voor wat haar vrugbaarheid beïnvloed. Daar word onderskei tussen komponenteienskappe en aggregaateienskappe: ‘n komponenteienskap verwys na een gebeurtenis, terwyl aggregaateienskappe na samestellings van meer as een gebeurtenis verwys. Hoewel al die eienskappe wat bespreek word relevant voorkom, sal die praktiese toepassing afhang van die kuddebestuurstelsel in gebruik. Ouderdom by eerste kalwing en dae tot kalwing is komponenteienskappe wat maklik en goedkoop bepaal kan word. Oorerflikheidsramings vir die ouderdom van eerste kalwing was matig. Die oorerflikheidsraming vir dae tot kalwing was 0.09. Kalffrekwensie is baie na aan die oorkoepelende teeldoelwit. Die geraamde oorerflikheid vir kalffrekwensie is laag (0.04), wat stadige genetiese verbetering tot gevolg het. Kalfsukses is gedefinieer en ondersoek, hoewel enkele beperkings bestaan het. ‘n Vaar-model het aangetoon dat genetiese variasie ten opsigte van kalfsukses op die onderliggende skaal bestaan. Die ooreenkomstige oorerflikheidsraming was 0.27. Drie kategoriese eienskappe is gedefinieer. Vir blyvermoë in die kudde is ‘n vaar-variansie van 0.41 geraam, met ‘n oorerflikheid van 0.27 op die onderliggende skaal. Die vaar-variansies en oorerflikhede wat vir retensie en kalftempo bereken is, was hoog. Van die drie eienskappe is kalftempo die een wat die ware vrugbaarheid van die bul se vroulike nageslag reflekteer. Kalftempo is herdefinieer as netto teelmeriete, ‘n eienskap wat die retensie van manlike diere en die reproduktiewe prestasie van hulle vroulike nasate beskryf. Die verkreë vaar-variasies wys dat die eienskap oorerflik is en verbeter kan word met seleksie. Netto teelmeriete gee ‘n aanduiding van die “sukses” van ‘n vaar in ‘n gegewe populasie. ‘n Oorerflikheidsraming van 0.30 is verkry op ‘n datastel bestaande uit die nageslag van bulle ouer as nege jaar, maar as die nageslag van alle vaars ingesluit is, was die oorerflikheidsraming onderskeidelik 0.08 en 0.11 vir die Afrikaner en Bonsmara. Aanpassing vir jong vroulike diere is ondersoek deur gebruik te maak van die beste lineêre onpartydige beramings (BLUE) om korreksiefaktore vir die kuddevlak te verkry, ten einde die prestasie ten opsigte van netto teelmeriete te voorspel. Variasies in die BLUE afwykings het voorgekom tussen alle ouderdomsgroepe vir die Afrikaner, terwyl vir die Bonsmara die variasie tussen BLUE afwykings vir die 3-jaar oud diere groter was as vir die ander ouderdomsgroepe. Dit word voorgestel dat die gestandardiseerde kurwe vir kuddeprestasievlak wat afgelei word van BLUE afwykings gebruik word om die fenotipiesewaardes van jonger diere aan te pas. Op hierdie wyse behoort die vergelyking tussen ouer en jonger diere meer geldig te wees. Ten slotte, reproduktiewe eienskappe is oorerfbaar en genetiese vordering is moontlik deur seleksie. Enige ekonomies lewensvatbare vleisbees-onderneming behoort ten minste een eienskap wat die reproduktiewe doeltreffendhied sal verbeter, in te sluit in seleksie kriteria.