Dissertations / Theses on the topic 'Cattle Genetics'

A genetic approach to lowering protease (plasmin) levels in milk, requires the presence of polymorphism of bovine plasminogen. This study was conducted to determine to what extent genetic polymorphism exists in dairy cattle. Bovine plasminogen was first purified from Holstein cow plasma by affinity chromatography on Lysine-Sepharose and antibodies to bovine plasminogen were raised by monthly intramuscular injection of the isolated bovine plasminogen into rabbits. For plasminogen phenotyping, blood samples were collected at random from 50 Holstein and Ayrshire cattle, and plasminogen was isolated from the plasma using lysine-Sepharose and then treated with neuraminidase. After separation by isoelectric focusing (pH 3.5-9.5) in polyacrylamide gels, Plasminogen polymorphs were detected immunologically using rabbit anti-bovine plasminogen antibodies. Additionally, the plasminogen isoforms were evaluated with a functional assay (caseinolytic overlay technique) after activation of the plasminogen with urokinase. Six plasminogen phenotypes were identified which represent products of 5 variant alleles. The 5 plasminogen variants were characterized based on their isoelectric points and designated PLG A$ sb2$ (pI 6.5 and 7.0), B$ sb2$ (pI 7.6 and 7.8), C$ sb1$ (pI 6.8), D$ sb2$ (pI 7.8 and 8.0), and E$ sb2$ (pI 6.8 and 7.0). PLG A$ sb2$ and PLG B$ sb2$ were the most common variants in these cattle. The 6 phenotypes were $ rm A sb2A sb2, B sb2B sb2, A sb2B sb2, B sb2C sb1, A sb2D sb2 and D sb2E sb2$. The phenotypic frequencies in Holstein and Ayrshire were very different, $ rm A sb2A sb2 and B sb2B sb2$ being respectively the most frequent phenotype. In addition, DNA polymorphism at bovine plasminogen gene was detected when genomic DNA was digested with the restriction enzyme Msp I and hybridized with mouse plasminogen cDNA. This is the first description of plasminogen polymorphism reported in dairy cattle. If different variants have altered activity, the detrimental effect

In this study genetic parameters were estimated and the importance of genotype by feeding system interactions investigated for a range of health and fertility traits in dairy cattle. Data were from the Langhill Dairy Cattle Research Centre and two UK recording schemes, one a recording scheme operated by the Scottish Livestock Services Ltd. (SLS) and the other a health and fertility recording and management system, the Dairy Information System (DAISY). Genetic parameters for 305 day yield of milk and its components, health traits (mastitis, somatic cell counts (SCC), lameness and milk fever) and fertility traits (calving interval, days to first service and conception to first service) were estimated using data from DAISY and SLS. Heritabilities and correlations agreed well between the two data sets implying that the nature of the recording scheme had little effect on the parameter estimates obtained. Heritabilities for all health and fertility traits were less than 0.10 with the exception of SCC which had a heritability of 0.15. The genetic correlation between SCC and mastitis was estimated to be 0.65. Genetic correlations of health and fertility traits with production were in all cases unfavourable. Using these estimates, a breeding programme designed to maximise response in production was predicted to increase calving intervals, mastitis and lameness by 0.39, 0.27 and 0.13 genetic standard deviations per unit selection differential. Restricting these traits to zero genetic change was predicted to result in 11% less overall economic response in production than an unrestricted index. Genotype by feeding system interactions were investigated for a wider range of health and fertility traits using data from Langhill. Selection and control line animals housed and managed as one herd were assigned to either a high concentrate or low concentrate feeding system. There were no significant genetic line by feeding system interactions. However, regressions of the traits on pedigree index for fat plus protein yield (PI) were significantly different from zero for six measures of fertility and mastitis. It was concluded that selection for production has led to a deterioration in some health and fertility traits in UK dairy herds. This deterioration could be halted, or the situation improved by direct recording and selection. However, in the absence of a national recording scheme for health and fertility, an alternative would be to use predictor traits, as they are generally easier to measure and record and have higher heritabilities. Results from this study supports the use of SCC as a selection criterion for mastitis (on a small data set), but the regressions on sire predicted transmitting abilities for type were less conclusive. Therefore future research should investigate associations between health, fertility, production, type, SCC and other potential predictor traits more fully and compare the role of direct measurements of these traits or indirect predictions of them in national indices.

For the modern dairy cow, advances in genetics and breeding for productivity has resulted in an increasing incidence of health disorders and reduced longevity. One of the most important health problems is lameness, which has led to significant economic, production and welfare consequences. A reduction in lameness will improve the economic future of the dairy industry through increased profitability and decreased welfare-related problems. Although positive attempts have been made by researchers and the industry towards improving lameness, it has remained a persistent ailment for dairy farmers. Further analysis of the genetic and environmental factors influencing lameness is warranted so that selection indices and management practices can be modified leading to improved health and welfare of the dairy cow. Several factors that cause dairy cow lameness have been implicated. I reviewed previous studies on these causative factors as well as the association between lameness, longevity and fertility. It has also been suggested that lameness affects milk production of dairy cows, but reports on the association between lameness and daily milk yield of cows have varied among researchers. Using locomotion score data on 248 cows from the Langhill herd, I investigated the relationship between locomotion score which has a high genetic correlation with lameness and various explanatory variables and also the association between daily milk yield and lameness. The study revealed that the most significant factors affecting locomotion are management regime (high concentrate feed and all year indoor housing; low concentrate feed and outdoors in summer) and time of year when cows are locomotion scored. It also showed that lameness adversely affects the milk yield of later lactation cows, and that high yielding cows are more susceptible to lameness. Housing environment plays a significant role in the health and welfare of dairy cows. With national type evaluation records, I estimated the association between housing systems and lameness-related type traits as well as genetic parameters for the locomotion traits. The analysis indicated that cows kept at pasture had favourable linear and composite type trait scores compared with cows in cubicles, straw yards and slatted floors or loafing yards. Locomotion score had strong genetic and phenotypic correlations with the leg and feet composite. Bone quality, which is a new trait in the UK type classification scheme, was moderately heritable (0.23) and had a moderate and positive genetic association with locomotion and leg and feet composite. This suggests that breeding for flatter, more refined bones could reduce locomotion disorders and help improve the longevity of the dairy cow. Analysis of national data again showed reduced incidence of digital dermatitis (DD) for cows at pasture and those with flatter, more refined bones, higher locomotion score and better leg and feet composite. Estimates of genetic parameters indicated heritable variation of DD among cows and moderate genetic associations between DD and production traits and longevity. Incorporating DD in future selection indices will be useful for increased productive life. Using random regression, I analysed changes in type traits associated with lameness (locomotion, rear legs, side view, foot angle and leg and feet composite) in relation to time (months) that cows had spent in cubicles before being classified. The general trend supported the fact that cubicle housing is unfavourable to these traits. There was significant evidence of a genotype x environment interaction, suggesting variation between bulls in the sensitivity of their daughters to cubicle housing with time.

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The aim of this study was to estimate genetic parameters between scrotal circumference obtained at 18 months of age (SC) and reproductive traits measured directly in Nellore females, such as number of calvings at 53 months (NC53), heifers rebreeding (HR) and stayability (STAY) in order to investigate the possibility of using traits measured directly in females as a selection criteria in cattle breeding programs, besides, studying and evaluating if number of calvings at 53 months could be used as an alternative way for measuring longevity in cattle herds. Two methods were applied for estimating variance components in order to predict breeding values: restricted maximum likelihood (REML) and Bayesian inference. The average estimates of heritability by bivariate model using REML were equal to 0.013 ± 0.003, 0.057 ± 0.007, 0.039 ± 0.007 and 0.530 ± 0.013 for NC53, STAY, HR and SC, respectively. Using the Bayesian method, the estimates were 0.22 ± 0.009, 0.19 ± 0.025, 0.15 ± 0.021 and 0.52 ± 0.019 for NC53, STAY, HR and SC, respectively. Based on the correlations between reproductive traits measured in females, the selection of animals for NC53 will cause anticipation on genetic evaluation of bulls for longevity, based on the performance of their daughters, from 76 to 53 months

Cattle grazing in extensive open pasture of tropical areas are subjected to several environmental stressors such as heat and humidity, high incidence of disease, cattle ticks and worm infestations. These stressors have major impacts on productivity and animal welfare. The overall focus of this PhD thesis was to conduct classical genetic and modern quantitative genomics analyses for growth and carcass related traits, and disease and parasite tolerance/resistance traits in beef cattle. The specific objectives were: (1) to estimate genetic parameters for growth, carcass related traits, and tropical environment stressors, e.g., infectious bovine keratoconjunctivitis or “pinkeye”, cattle tick counts, and helminth or worm egg counts in Australian tropical adapted beef cattle; (2) to identify genetic markers or gene(s) linked to growth and ultrasound measures of carcass related traits in tropical Australian cattle, and bovine tuberculosis (BTB) traits in African zebu cattle using a genome-wide scan methodology; and (3) to evaluate the feasibility of genome-wide epistasis association for growth and carcass related traits using a two-step two-locus model for Australian tropical beef cattle. Field test data obtained from different sources were used in this thesis. Genetic parameter estimates were computed using mixed models by fitting an additive polygenic animal term as a random effect, whereas in genome association analyses, the genetic markers were fitted as fixed effect and significance of marker effects on the traits were evaluated for association. The heritabilities of tropical stressors traits ranged from low to moderate, suggesting genetic selection is feasible, though the selection response will be slow in this resource population. There was no evidence of unfavourable genetic correlations between environment stressors and growth traits; hence selection against environmental stressors would not have a detrimental effect on production performance. A genome-wide scan identified seven SNP markers on chromosome 14 associated with serum concentration of insulin-like growth factor-1, subcutaneous fat depth, and body condition score measured in Australian Brahman cattle. The rs29020688 marker located in the intronic region of Bos taurus XK, Kell blood group complex subunit-related family, member 4 (XKR4) gene was strongly associated with increased blood levels of insulin-like growth factor-1 (IGF-1), and rs29010471 marker located in the intronic of Bos taurus protein kinase, DNA-activated, catalytic polypeptide (PRKDC) gene was strongly associated with subcutaneous fat deposits. These positional genes could be candidate genes influencing IGF-1 and subcutaneous fat depth, and can potentially be used as biomarkers for these traits. Similarly, this thesis investigated associations between SLC11A1 candidate gene and a panel of microsatellite markers and several diagnostic tests of bovine tuberculosis (BTB) phenotypes. Polymorphisms at SLC11A1 alleles 211, 215 and 217 and alleles in ILSTS006 (Alleles: 286, 288, 290, and 292) and BM2113 (Alleles: 133 and 141) were significantly associated with decreased BTB disease incidence in African zebu cattle; hence these could be considered in a marker assisted selection for screening BTB tolerant animals. This study was able to successfully model epistasis interactions between two-SNP loci using two-step approach. Using experimental field data, it was demonstrated and validated that two-step two-locus epistatic interactions are computationally feasible at a genome-wide scale. If automated recording technology for extensive gazing beef cattle becomes available in the future, this will enable the collection of high dimensional data on animals. In addition large number of animals are expected to be genotyped and imputed up to very high marker densities using imputation techniques. These resources will enable the estimation of genetic parameters more accurately and will allow biomarkers and genes underlying many complex traits in animals in extensive grazing system to be identified.

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Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Universidade Estadual Paulista (UNESP)
Foram utilizados dados de 116406 bovinos da raça Nelore, participantes do Programa de Melhoramento Genético da Raça Nelore (PMGRN), nascidos entre 1995 e 2005, com o objetivo de estimar parâmetros genéticos para os pesos padronizados aos 120(P120), 210(P210), 365(P365), 450(P450) e 730(P730) dias de idade e para os ganhos em peso do nascimento aos 120(GP120), dos 120 aos 210 (GP210), dos 210 aos 365(GP365), dos 365 aos 450(GP450) e dos 450 aos 730(G730), além de avaliar a tendência genética das características citadas, tanto para efeito direto como materno. Os componentes de variância foram estimados pelo método de máxima verossimilhança restrita utilizando o programa AIREMLF90, sob modelo animal, o qual incluiu como efeitos fixos, os grupos de contemporâneos e idade da vaca ao parto e como aleatórios, efeito genético aditivo direto para todas as características estudadas e efeito genético materno para P120, P210, P365, GP120, GP210 e GP365. As estimativas de herdabilidade direta foram 0,21, 0,22, 0,22, 0,34, 0,28, para cada peso, respectivamente, e 0,19, 0,20, 0,18, 0,18 e 0,20, para os respectivos ganhos em peso. As herdabilidades maternas foram 0,26, 0,25 e 0,12, para P120, P210 e P365 e 0,23, 0,17, 0,12 para GP120, GP210 e GP365. As correlações direto-maternas foram todas negativas, exceto para P365 (0,06). As tendências genéticas diretas foram todas positivas. As tendências maternas foram quase nulas para todas as características. As estimativas de herdabilidade para os pesos padronizados e para os ganhos em peso indicam que a seleção pode promover mudanças genéticas. As herdabilidades maternas para P120, P210, P365 e GP365 indicam que a seleção nestas características pode contribuir para melhorar a habilidade materna do rebanho. Os ganhos genéticos diretos observados, para todas as características estão aquém dos ganhos potenciais da raça Nelore...
Data of 116406 bovines of the Nellore beef cattle, participants of the Programa de Melhoramento Genético da Raça Nelore (PMGRN), been born between 1995 and 2005 were used with the objective to estimate genetic parameters for the 120-days weight (P120), 210-days weight (P210), 365-days weight (P365), 450-days weight (P450) and 730-days weight (P730) and for the weight gain from birth to 120(GP120), from 120 to 210(GP210), from 210 to 365(GP365), from 365 to 450(GP450) and from 450 to 730 days weight(GP730), besides evaluating the genetic trends of the traits, so much for the direct effect as for the maternal. The variance components were estimated by the restricted maximum likelihood method using the program AIREMLF90. The animal model included fixed effects for contemporary groups and age of the dam at calving, and also included random effects for genetic direct effects for all the studied traits and genetic maternal effect for P120, P210, P365, GP120, GP210 and GP365. The estimative of direct heritability were 0,21, 0,22, 0,22, 0,34, 0,28, for each weight, respectively and 0,19, 0,20, 0,18, 0,18 and 0,20, for the respective weight gains. The maternal heritability were 0,26, 0,25 and 0,12, for P120, P210 and P365 and 0,23, 0,17, 0,12 for GP120, GP210 and GP365. The direct-maternal correlations were all negatives except for P365 (0,06). The direct genetic trends were all positive ones. The maternal trends were almost null for all the traits. The estimative of heritability for the adjusted weights and for the weight gains indicated that the selection could promote genetic changes. The maternal heritability for P120, P210, P365 and GP365 indicated that the selection in these traits could contribute to improve the maternal ability of the herd. The direct genetic gain observed, for all the traits were on this side of the potential gain of the Nellore beef cattle... (Complete abstract click electronic access below)

The main objective of this work was to undertake analyses which would lead to an improvement in the accuracy of production and type breeding value predictions for Holstein-Friesian dairy cattle and to investigate the relationship between production and type traits and herd life. Production records were obtained from the National Milk Records files and linear type records from the Holstein Friesian Society. An animal model estimation of heterosis and recombination loss between North American Holstein and European cattle for first lactation milk, fat and protein yield showed that the omission of these effects in breeding value prediction would bias the results. Including both these effects in the breeding value estimation increased the predicated sire proof for fat plus protein yield of a typical F1 Holstein X Friessian sire by 3kg. An analysis of approximately 275 000 first lactation records and the 2^nd to 5^th lactation records of survivors found the regression coefficients of yield in lactations 1 to 5 on heterosis and recombination loss to be fairly consistent over lactations. After fitting first lactation yield in the model and compared to a pure Friesian, there is an increased chance of survival to third lactation of 3.6% for a pure Holstein, 3.8% for an F1 and an F2, and 2.4% for a Friesian backcross. In the investigation of herd life, defined as the completion of a specified number of lactations, in relation to linear type traits and production, results were not completely consistent either over lactations or over different subsets of the population. In general, there was a significant positive association between survival and angularity, fore udder attachment and udder depth and a negative association with chest width, rump width and teat length. Regressions on yield were positive, while those on fat and protein content were usually negative.

Thesis (M.Sc. (Agric.)) --University of Limpopo, 2010
The objectives of the study were to estimate genetic parameters for tick resistance and to evaluate the effect of the level of tick infestation on the estimates of genetic parameters in South African Bonsmara cattle. Field data of repeated tick count records (n = 11 280) on 1 176 animals were collected between 1993 and 2005 by ten breeders participating in the National Beef Recording and Improvement Scheme. The distribution of tick count records were normalized using a Box-Cox transformation. Data were divided into 7 sub-data sets based on the mean tick count per contemporary group, to facilitate the investigation of the effect of level of tick infestation on the derived genetic parameters. A repeatability animal model including the fixed effects of contemporary group and age of animal at tick counting and random effects of the direct additive genetic, permanent environmental and residual effects was used to estimate genetic parameters using REML procedures. The additive genetic variances for tick count ranged from 0.01 to 0.08. Variances for the permanent environment ranged from 0.00 to 0.03. Phenotypic variance decreased with increasing mean tick count level while additive genetic variance increased with increasing mean tick count level. The heritability also increased with mean tick count level until a mean tick count level of ≥30. The highest heritability estimate obtained in the current study was 0.17 for data with mean tick count level ≥25. These results suggest that sufficient genetic variation for tick count exists in the Bonsmara cattle. Therefore genetic selection for tick resistance is feasible even though genetic progress may be slow.
the Limpopo Department of Agriculture (LDA) and the Department of Science and Technology (DST)

Includes bibliographical references (leaves 178-194). Genetic and non-genetic factors affecting fat colour in cattle were examined in biopsy and carcass samples of Jersey and Limousin cattle in their F1 and backcross progeny.

Includes bibliograpical references (leaves 119-134). The most common chromosome abnormalities in live cattle are various Robertsonian translocations (centric fusions). Two hypotheses have been used to explain how monocentric Robersonian translocation chromosomes are generated: either direct formation, or evolution from dicentic chromosomes. Four main cattle procentric Satellite sequences were used as single and two-colour fluorescence in situ hybridization probes for studying the centromere organisation of cattle autosomes and the rearrangement in two cattle Robertsonian translocation chromosomes, the t(1:29) which is monocentric and found in numerous breeds, and the t(14:20) which is dicentric and found in 2 breeds.

Single-strand conformation polymorphism analysis (SSCP) and restriction fragment length polymorphism analysis (RFLP) were used to determine the genotype of Holsteins at the $ kappa$-casein ($ kappa$-CN) locus. A 432-bp fragment within exon IV containing nucleotide substitutions diagnostic of the A- and B-variants of $ kappa$-CN was amplified using the polymerase chain reaction (PCR). The sires from the earliest years of the AI industry had a significantly higher (p $<$ 0.01) frequency of allele than sires in modern usage. These data indicate that selection or milk production parameters may discriminate against the B-allele. SSCP analysis was also used for detecting polymorphisms within the regulatory region of $ kappa$-CN gene. A 640-bp fragment within the 5$ sp prime$-flanking region of bovine $ kappa$-CN gene which contained the TATA box, CAAT box, and exon I was amplified using PCR. The SSCP analysis of this fragment revealed no variation, possibly due to the lower detection efficiency of SSCP with large fragment size. Nested primers were, therefore, designed to amplify fragments of 234- and 486-bp. Polymorphism was detected only in the 486-bp fragment and the two variants were designated M$ sb1$ and M$ sb2.$ The allelic frequencies of M$ sb1$ and M$ sb2$ in bulls used by AI industry before 1970 were 0.67 and 0.33, and in bulls used by AI industry after 1980 the frequencies were 0.68 and 0.32, respectively. The frequency of these alleles were not significantly different in Holsteins used by AI industry before 1970 and after 1980. Unlike the apparent change in frequency of the A- and B-variants noted within exon IV, this polymorphism seems to have not responded to selection. However, a higher frequency of M$ sb1$ allele appeared to be associated with B-variant (exon IV) genotypes. The presence of these variants within the regulatory region may possibly be involved in the quantitative expression of $ kappa$-CN gene. (Abstract shortened by UMI.)

Thesis (Ph.D.)--George Mason University, 2009.
Vita: p. 123. Thesis director: John J. Grefenstette. Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Bioinformatics and Computational Biology. Title from PDF t.p. (viewed Sept. 8, 2009). Includes bibliographical references (p. 114-122). Also issued in print.

The objective of this study was to estimate the relationship between survival at various stages of productive life (17, 30, 43, 55 and 96 months of productive life) and type traits in Quebec Holstein and Ayrshire cows. The original data set from the Programme d'Analyse des Troupeaux Laitiers du Quebec contained 559,203 lifetime records calculated from 2,237,081 lactation records including calvings from 1979 to 1995. Lifetime records containing type classification information provided by the respective breed associations were used to study true survival variables (opportunity to survive to 17, 302 43, 55 and 96 months) and functional survival variables opportunity to survive to the same ages, independently of the level of production). K. Meyer's EQREML program was used to analyse these data by fitting a sire model. Heritabilities varied between 0.03 and 0.11 for both breeds. Final score and rear udder were two of the traits most highly correlated with survival. Specifically, in Holsteins, mammary system and fore udder showed the highest genetic correlation with functional survival, and dairy character showed the highest genetic correlation with true survival. In Ayrshires, final score, breed character, dairy quality, style and fore udder had the highest genetic correlations with both true and functional survival across all survival stages. In a second study, lifetime records not having type information and type records without lifetime information were analysed with D. L. Johnson and R. Thompson's AIREML program which enabled linking of sires in common between type and lifetime data sets. Only survival to 96 months was studied here, but the effect of supervised and non-supervised records was considered. In Holstein supervised records, body traits were more highly correlated with survival, whereas udder traits were more highly correlated in the non-supervised records. Ayrshire results were not conclusive.

Orientador: Sandra Aidar de Queiroz
Banca: Roberto Carvalheiro
Banca: Vânia Cardoso
Resumo: Não disponível
Abstract: The aim of this study was to estimate genetic parameters between scrotal circumference obtained at 18 months of age (SC) and reproductive traits measured directly in Nellore females, such as number of calvings at 53 months (NC53), heifers rebreeding (HR) and stayability (STAY) in order to investigate the possibility of using traits measured directly in females as a selection criteria in cattle breeding programs, besides, studying and evaluating if number of calvings at 53 months could be used as an alternative way for measuring longevity in cattle herds. Two methods were applied for estimating variance components in order to predict breeding values: restricted maximum likelihood (REML) and Bayesian inference. The average estimates of heritability by bivariate model using REML were equal to 0.013 ± 0.003, 0.057 ± 0.007, 0.039 ± 0.007 and 0.530 ± 0.013 for NC53, STAY, HR and SC, respectively. Using the Bayesian method, the estimates were 0.22 ± 0.009, 0.19 ± 0.025, 0.15 ± 0.021 and 0.52 ± 0.019 for NC53, STAY, HR and SC, respectively. Based on the correlations between reproductive traits measured in females, the selection of animals for NC53 will cause anticipation on genetic evaluation of bulls for longevity, based on the performance of their daughters, from 76 to 53 months
Mestre

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Este experimento objetivou analisar o padrão de expressão do mRNA de SOX2, STAT3 e GBX2 em embriões bovinos produzidos in vitro nos estádios de blastocisto (E7) e blastocisto eclodido (E10). O RNA foi extraído de embriões em cada fase do desenvolvimento embrionário (n=7) e da massa celular interna (MCI) e epiblasto isolados por imunocirurgia de 20 embriões (n=20). A expressão do mRNA foi obtida por transcriptase reversa seguida da reação em cadeia da polimerase em tempo real (RT-qPCR), quantificada pelo método da curva padrão e normalizada pela média geométrica de GAPDH, YWHAZ e SDHA. Os dados de cinco replicatas foram analisados por ANOVA seguido de comparações, aos pares, pelo teste de Tukey. A expressão relativa do mRNA de SOX2 foi significativamente maior em blastocistos (E7) do que em blastocistos eclodidos (E10) (P<0,05), sendo que a expressão na MCI foi 40X maior do que a obtida no blastocisto inteiro (P<0,05). A expressão relativa do mRNA de STAT3 3 não diferiu entre blastocistos (E7) e blastocistos eclodidos (E 10) (P>0,05). Não houve diferença entre blastocisto eclodido (E10) e epiblasto para SOX2 e STAT3 (P>0,05). Comparando-se o nível relativo de mRNA de GBX2 entre blastocistos (E7) e MCI e blastocisto eclodido (E10) e epiblasto não foi detectada diferença (P>0,05), sendo que MCI e epiblasto corresponderam a aproximadamente 90% da expressão observada nos embriões em suas respectivas fases de desenvolvimento. Portanto, com o desenvolvimento do blastocisto, há a tendência do aumento dos níveis de mRNA de STAT3 e SOX2 nas células pluripotentes do epiblasto; o nível de mRNA de GBX2 se mantém constante em blastocistos, com alta expressão em células pluripotentes
This experiment aimed to analyze the pattern of expression of the mRNA of SOX2, STAT3 and GBX2 in in vitro produced bovine embryos at stages of blastocyst (E7) and hatched blastocyst (E10). The RNA was extracted from embryos at each stage of embryonic development (n= 7) and from the inner cell mass (ICM) and epiblasts isolated from 20 embryos by immunosurgery. The expression of mRNA was obtained by reverse transcriptase-polymerase chain reaction (real-time qPCR), quantified by the standard curve method and normalized by geometric mean of genes YWHAZ, SDHA and GAPDH. The data from five replicates were analyzed by ANOVA followed by comparisons, in pairs by Tukey test. The relative expression levels of SOX2 mRNA was significantly higher in blastocysts (E7) than in hatched blastocysts (E10) (P<0.05), whereas that the expression in MCI was 40X greater than the expression obtained in blastocyst (P< 0.05). The relative expression of STAT3 mRNA did not differ between blastocysts (E7) and hatched blastocysts (E 10) (p>0.05). There was no difference between blastocyst hatched (E10) and epiblasts for SOX2 and STAT3. By Comparing the relative level of GBX2 mRNA between blastocysts (E7) and ICM and blastocyst hatched (E10) and epiblasts no difference was detected (P>0.05), ICM and epiblasts corresponded to approximately 90% of expression observed in embryos in their respective stages of development. Therefore, with the development of the blastocyst, there is a tendency for increased levels of STAT3 and SOX2 mRNA in the pluripotent cells of epiblasts; the level of GBX2 mRNA is constant in blastocysts with high expression in pluripotent cells

Orientador: Fernanda da Cruz Landim
Coorientador: João Pessoa Araujo Junior
Banca: Sony Dimas Bicudo
Banca: Fabiana Ferreira Sousa
Banca: Felipe Perecin
Banca: Cláudia Barbosa Fernandes
Resumo: Este experimento objetivou analisar o padrão de expressão do mRNA de SOX2, STAT3 e GBX2 em embriões bovinos produzidos in vitro nos estádios de blastocisto (E7) e blastocisto eclodido (E10). O RNA foi extraído de embriões em cada fase do desenvolvimento embrionário (n=7) e da massa celular interna (MCI) e epiblasto isolados por imunocirurgia de 20 embriões (n=20). A expressão do mRNA foi obtida por transcriptase reversa seguida da reação em cadeia da polimerase em tempo real (RT-qPCR), quantificada pelo método da curva padrão e normalizada pela média geométrica de GAPDH, YWHAZ e SDHA. Os dados de cinco replicatas foram analisados por ANOVA seguido de comparações, aos pares, pelo teste de Tukey. A expressão relativa do mRNA de SOX2 foi significativamente maior em blastocistos (E7) do que em blastocistos eclodidos (E10) (P<0,05), sendo que a expressão na MCI foi 40X maior do que a obtida no blastocisto inteiro (P<0,05). A expressão relativa do mRNA de STAT3 3 não diferiu entre blastocistos (E7) e blastocistos eclodidos (E 10) (P>0,05). Não houve diferença entre blastocisto eclodido (E10) e epiblasto para SOX2 e STAT3 (P>0,05). Comparando-se o nível relativo de mRNA de GBX2 entre blastocistos (E7) e MCI e blastocisto eclodido (E10) e epiblasto não foi detectada diferença (P>0,05), sendo que MCI e epiblasto corresponderam a aproximadamente 90% da expressão observada nos embriões em suas respectivas fases de desenvolvimento. Portanto, com o desenvolvimento do blastocisto, há a tendência do aumento dos níveis de mRNA de STAT3 e SOX2 nas células pluripotentes do epiblasto; o nível de mRNA de GBX2 se mantém constante em blastocistos, com alta expressão em células pluripotentes
Abstract: This experiment aimed to analyze the pattern of expression of the mRNA of SOX2, STAT3 and GBX2 in in vitro produced bovine embryos at stages of blastocyst (E7) and hatched blastocyst (E10). The RNA was extracted from embryos at each stage of embryonic development (n= 7) and from the inner cell mass (ICM) and epiblasts isolated from 20 embryos by immunosurgery. The expression of mRNA was obtained by reverse transcriptase-polymerase chain reaction (real-time qPCR), quantified by the standard curve method and normalized by geometric mean of genes YWHAZ, SDHA and GAPDH. The data from five replicates were analyzed by ANOVA followed by comparisons, in pairs by Tukey test. The relative expression levels of SOX2 mRNA was significantly higher in blastocysts (E7) than in hatched blastocysts (E10) (P<0.05), whereas that the expression in MCI was 40X greater than the expression obtained in blastocyst (P< 0.05). The relative expression of STAT3 mRNA did not differ between blastocysts (E7) and hatched blastocysts (E 10) (p>0.05). There was no difference between blastocyst hatched (E10) and epiblasts for SOX2 and STAT3. By Comparing the relative level of GBX2 mRNA between blastocysts (E7) and ICM and blastocyst hatched (E10) and epiblasts no difference was detected (P>0.05), ICM and epiblasts corresponded to approximately 90% of expression observed in embryos in their respective stages of development. Therefore, with the development of the blastocyst, there is a tendency for increased levels of STAT3 and SOX2 mRNA in the pluripotent cells of epiblasts; the level of GBX2 mRNA is constant in blastocysts with high expression in pluripotent cells
Doutor

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O objetivo deste estudo foi estimar os componentes de variância para a característica aprumo em bovinos da raça Nelore, e realizar estudos de associação genômica ampla para identificar possíveis regiões genômicas relacionadas com sua expressão. Os registros de aprumo foram obtidos pela atribuição de escores visuais em dois momentos diferentes: FL1) característica binária medida ao sobreano, com o objetivo de identificar se o animal apresenta (FL1=1) ou não (FL1=0) defeito de aprumo; FL2) escores de aprumo variando de 1 (menos desejável) a 5 (mais desejável), foram designados aos animais top 20% para o índice de seleção adotado pelo programa de melhoramento genético de bovinos de corte PAINT (CRV Lagoa), e foram medidos em torno de 2 a 5 meses após a avaliação de sobreano. As características FL1 e FL2 foram avaliadas em conjunto com peso ao sobreano (YW). Os componentes de variância e covariância e os valores genéticos foram estimados por inferência Bayesiana, por meio de modelo animal bi-característica (três análises: FL1-FL2, YW-FL1 e YW-FL2). O estudo de associação genômica ampla (GWAS) para FL1 e FL2 foi realizado utilizando o método weighted single-step GBLUP, a partir do qual foram estimados os efeitos dos SNPs. As janelas top 10 de 1 Mb que explicam a maior proporção da variância genética foram observadas para cada característica. As médias (erros padrão) a posteriori das estimativas de herdabilidade foram iguais a 0,18 (0,04) e 0,39 (0,07), para FL1 e FL2, respectivamente. A estimativa de correlação genética entre FL1 e FL2 (-0,47) foi de moderada magnitude e negativa, conforme esperado, considerando que o escore de classificação que favorece cada característica corresponde a valores numéricos atribuídos em sentidos opostos. A correlação genética estimada entre FL2 e YW (0,39) sugere que a média do peso ao sobreano da população em estudo não é alta a ponto de causar ...
The aim of this study was to estimate variance components of two traits associated to feet and legs in Nelore cattle and identify putative genomic regions underlying the expression of these traits through genome-wide association (GWA) analyses. Feet and legs was evaluated by the assignment of visual scores at two different moments: FL1) binary trait measured at yearling (about 550 days of age), aimed to identify whether an animal had defects related to feet and legs (FL1=1) or not (FL1=0); FL2) feet and legs score ranging from 1 (less desirable) to 5 (more desirable) was assigned to the top 20% animals for the selection index adopted by the beef cattle breeding program PAINT (CRV Lagoa), which were measured around 2-5 months after the evaluation of yearling. The FL1 and FL2 traits were evaluated together with yearling weight (YW). The components of variance and covariance and breeding values were estimated by Bayesian inference, using two-trait animal models (three analyses: FL1-FL2, YW-FL1 and YW-FL2). The genome-wide association (GWA) analyses for FL1 and FL2 was performed using the weighted single-step GBLUP method, from which were estimated the SNP effects. Functional annotation was focused on the ten 1Mb windows explaining the largest fraction of the genetic variance for each trait. Posterior means (standard errors) of heritability estimates were equal to 0.18 (0.04) and 0.39 (0.07), for FL1 and FL2, respectively. The estimate of genetic correlation between FL1 and FL2 (-0.47) was of moderate magnitude and negative, as expected considering that the classification score that favors each trait represents numerical values assigned in opposite directions. The genetic correlation estimated between FL2 and YW (0.39) suggests that the average yearling weight of the studied population is currently not high enough to cause a negative association with feet and legs problems. The genetic trends estimated for FL1 and FL2 (-0.043 and ...

This study, being part of a larger project - "Canadian/New Zealand GxE Interaction Trial" - is comparing Canadian and New Zealand sired heifers for growth traits within Canada, since differences for growth traits were found in the Polish strain comparison (Jasiorowski et al., 1987) and due to selection programs in the two countries. Twenty Canadian Holstein and twenty New Zealand Friesian progeny tested, A.I. bulls were randomly mated to over 1,000 cows in 10 Canadian herds. 3,539 records of weight and wither height from 475 heifers (i.e. 241 Canadian and 234 New Zealand sired) were generated. Subsets of the data for different stages of heifer maturity were analyzed separately. Herd and strain effects least squares means were estimated using analysis of variance. Genetic and phenotypic and correlations and heritability for weight and wither height were estimated by a Derivative-Free Restricted Maximum Likelihood (DFREML) algorithm and an animal model (AM). No differences were found between sire strains for weight except at 15 and 18 months where sib groups of Canadian (CN) sires were heavier than their New Zealand (NZ) contemporaries (393 vs 386 kg and 447 vs 445 kg, respectively). CN sired heifers were taller at all ages except at birth, 3 and 9 months of age. At 24 months CN heifers were 136 cm while NZ heifers were 133 cm. Heritability estimates for weight at birth was 0.62 for the CN strain and 0.59 for the NZ strain. CN estimates (3 to 6 months) and NZ estimates (3 to 9 months) were close to zero. Between 9 to 24 months CN strain estimates ranged from 0.44 to 0.69 while NZ estimates were 0.17 to 0.51. The joint estimates ranged from 0.10 to 0.66. Heritability estimates for wither height for CN strain at birth and between 9 to 21 months were between 0.34 to 0.66 and close to zero between 3 to 6 and at 24 months. The NZ estimates at birth, 18, 21 and 24 months were between 0.36 to 0.93 but close to zero between 3 to 15 months. The joint estimates ranged from 0.32 to 0.75 between 12 to 24 months. Genetic correlations between weight and wither height ranged from 0.62 to 1.0 for CN strain and from -0.04 to 0.91 for NZ strain between 4.5 to 21 months. At six months of age the genetic correlation for CN strain was -0.01 and NZ strain was 0.54. At birth, both sire groups had a genetic correlation of 1.0. At 24 months NZ strain had a genetic correlation of 0.84 while that of the CN strain was 0. Genetic correlations for the joint analysis ranged from 0.61 to 1.0 for all ages except at 6 months (0.18). Phenotypic correlations between weight and wither height were between 0.33 to 0.60 for CN group and 0.33 to 0.62 for NZ group. The joint estimates were 0.36 to 0.61. There were no differences in the phenotypic variances except at 9, 12 and 15 months. Genetic variances were different at all ages except at birth for weight.
Land and Food Systems, Faculty of
Graduate

Laboratory scale Cheddar type cheese were made from 411 milk samples originating from Ayrshire, Brown Swiss, Canadienne and Jersey with different phenotypes of kappa-casein (kappa-CN) and beta-lactoglobulin (beta-LG). From the milk input, cheese and whey outputs, the cheese yield, cheese composition and cheesemaking efficiency and other parameters were determined. The overall 37% moisture adjusted cheese yield and cheese yield efficiency were 11.19g, 10.19g, 11.97g, 11.46g and 98.91%, 90.10%, 90.76% and 90.92% for Ayrshire, Brown Swiss, Canadienne and Jersey respectively. The milk of the four respective breeds contained 12.91, 12.69, 13.50, 14.57% total solids; 3.97, 3.58, 4.40, 4.61% fat; 3.61, 3.73, 3.81, 4.00% protein. In Ayrshire, the combination BB/BB and BB/AA (kappa-CN/beta-LG) were associated with higher 37% moisture adjusted cheese yield with the values of 12.51 and 12.83 g/100 g milk respectively. The cheese composition for these two types of milk were 62.28 and 63.96% total solids, 24.22 and 20.40% protein; 32.75 and 37.92% fat. For Brown Swiss, type AA/BB was associated with higher cheese yield (11.18g) with composition of 62.15% total solids, 22.54% protein, 33.23% fat. The phenotype with the highest cheese yield for Canadienne is BB/AB (12.45g) with cheese composition of 63.61% total solids, 23.27% protein and 63.61% fat. In Jersey, the phenotype combination with higher cheese yield (14.59g) is BB/BB. The cheese composition corresponding to this phenotype was 58.64% total solids, 22.96% protein and 29.59% fat. Phenotypes associated with better coagulating properties for Ayrshire, Brown Swiss, Canadienne and Jersey were BB/AB, BB/BB, BB/BB and BB/BB for kappa-CN/beta-LG respectively.

DNA methylation has been shown to be involved in switching a number of genes on or off in particular cells. The relationship between DNA methylation and $ beta$-casein gene expression in the mammary tissue of lactating cows and mammary epithelial cells was examined. A positive correlation existed between hypomethylation of two MspI/HpaII sites in the body and one MspI/HpaII site in the 3$ sp prime$ end of the $ beta$-casein gene and its expression. In addition to these sites, hypomethylation of a distal MspI/HpaII site and HindIII sensitivity at a HindIII site also correlated with gene expression. Five DNase I hypersensitive sites were located within a 8 kb fragment. These sites designated as H1 to H5 were mapped approximately $-5, -1.3, -0.2,$ 1.7 and 2.5 kb with respect to the start site of transcription, respectively. The H2 and H3 sites were within a 1790 bp sequence that has been reported to contain a responsive element for prolactin and extracellular matrix dependent regulation and the binding site for mammary gland specific factor.
To study the dynamic changes in hypomenthylation at the MspI/HpaII sites and HindIII sensitivity, mammary tissues from pregnant heifers were evaluated. Site specific demethylation was observed depending on the stage of gestation. Demethylation of two MspI/HpaII sites (denoted M2 and M4) occurred during the early gestation, progressed slowly until mid-pregnancy, and rapidly during the last part of pregnancy. During the early stages of gestation, changes in the HindIII sensitivity in the coding domain of the $ beta$-casein gene also took place. Despite changes in HindIII sensitivity, the second HindIII site remained resistant to HindIII. By the fifth stage of gestation, the third MspI/HpaII site (M3) became less methylated and during this time the H2 site became more sensitive to HindIII. Northern analysis confirmed that demethylation of the M3 site and the acquisition of HindIII sensitivity at the H2 site was correlated with $ beta$-casein transcription.
Although $ alpha$-lactalbumin and $ beta$-casein genes are structurally and evolutionarily unrelated, they likely share common regulatory features, since both are expressed in the mammary gland during lactation. To investigate this possibility, methylation of the $ alpha$-lactalbumin gene was examined. In vivo studies revealed hypomethylation of the bovine $ alpha$-lactalbumin gene at two MspI sites and a cluster of two HhaI sites during the first and second stage of gestation, respectively. Furthermore, hypomethylation events occured only in the functional gene and not in pseudogenes, and the hypomethylation pattern was established prior to gene expression.
Taken together, the present finding suggest that DNA hypomethylation is necessary for the expression of two mammary-specific milk protein genes, $ beta$-casein and $ alpha$-lactalbumin. Hypermethylation within the body of these genes may silence these genes in non-expressing tissues and in non-epithelial cells within the mammary gland during lactation.

The objective of this study was to evaluate the variability of growth curves of dairy heifers and estimate genetic parameters. 15066 records taken from birth until 26 months (808 days) on 2754 heifers of Quebec were considered. The pedigree file comprised 10123 animals. The Mixed procedure of SAS with ordinary polynomials was used for simple phenotypic analyses, fitting fixed linear, quadratic and cubic regressions of body weight (in kilograms) on age (in months) as well as random intercept, and random linear and quadratic regressions for each animal. The Wombat program (Meyer, 2007), with Legendre polynomials was used to estimate the genetic parameters by fitting fixed herd-year-season of birth and quartic regression of body weight on age in days, as well as random regressions for quadratic additive genetic and cubic permanent environmental effects. Heritability estimates of body weight ranged from 0.22 at around 70 days to 0.45 at around 210 days. Heritabilities of body weight at birth and 808 days were 0.35 and 0.32, respectively. The additive genetic correlations between body weights at different ages ranged from -0.37 to 1.00. In general, the genetic correlations were higher than the permanent environmental and phenotypic correlations.

All contemporary taurine cattle originated some 10,000 years ago when their wild ancestor, the aurochs, was domesticated in the Near East. Although the aurochs was widespread also in Europe, there is no evidence for a local domestication. The aurochs has been extinct since 1627 and therefore little is known about its biology. Following domestication, cattle were selected for traits of interest to humans. All modern cattle breeds were developed in the 19th century and the only sources of information about prehistoric breeding practices, and breeds, come from a few ancient Roman Empire and medieval European written accounts. The aim for this thesis was to investigate the effects early selection may have had on the cattle genome and to investigate genetic variation in European aurochs. Using second-generation sequencing and coalescent simulation analyses of aurochs Y chromosomal DNA, I estimated effective population size to between 20,000-80,000 aurochs bulls, indicating that a large population was present when domestic cattle entered Europe. A Y chromosomal SNP revealed that the two male lineages present in modern cattle were also present in European aurochs, and that the frequency of these lineages in domestic cattle fluctuated over time. This indicates that cattle were mobile and that bottlenecks, possibly due to selective breeding, occurred. I used nuclear SNPs to trace genetic variation in North European cattle through time and show that when genetics is combined with archaeology and osteology, even small but notable changes in the use of cattle can be detected. There has been a significant decrease in genetic variation over time, with the most dramatic changes associated with the formation of breeds during the 19th century.

Orientador: Roberto Carvalheiro
Coorientador: Danísio Prado Munari
Coorientador: Haroldo Henrique de Rezende Neves
Banca: Fernando Sebastián Baldi Rey
Banca: Idalmo Garcia Pereira
Resumo: O objetivo deste estudo foi estimar os componentes de variância para a característica aprumo em bovinos da raça Nelore, e realizar estudos de associação genômica ampla para identificar possíveis regiões genômicas relacionadas com sua expressão. Os registros de aprumo foram obtidos pela atribuição de escores visuais em dois momentos diferentes: FL1) característica binária medida ao sobreano, com o objetivo de identificar se o animal apresenta (FL1=1) ou não (FL1=0) defeito de aprumo; FL2) escores de aprumo variando de 1 (menos desejável) a 5 (mais desejável), foram designados aos animais top 20% para o índice de seleção adotado pelo programa de melhoramento genético de bovinos de corte PAINT (CRV Lagoa), e foram medidos em torno de 2 a 5 meses após a avaliação de sobreano. As características FL1 e FL2 foram avaliadas em conjunto com peso ao sobreano (YW). Os componentes de variância e covariância e os valores genéticos foram estimados por inferência Bayesiana, por meio de modelo animal bi-característica (três análises: FL1-FL2, YW-FL1 e YW-FL2). O estudo de associação genômica ampla (GWAS) para FL1 e FL2 foi realizado utilizando o método weighted single-step GBLUP, a partir do qual foram estimados os efeitos dos SNPs. As janelas top 10 de 1 Mb que explicam a maior proporção da variância genética foram observadas para cada característica. As médias (erros padrão) a posteriori das estimativas de herdabilidade foram iguais a 0,18 (0,04) e 0,39 (0,07), para FL1 e FL2, respectivamente. A estimativa de correlação genética entre FL1 e FL2 (-0,47) foi de moderada magnitude e negativa, conforme esperado, considerando que o escore de classificação que favorece cada característica corresponde a valores numéricos atribuídos em sentidos opostos. A correlação genética estimada entre FL2 e YW (0,39) sugere que a média do peso ao sobreano da população em estudo não é alta a ponto de causar...
Abstract: The aim of this study was to estimate variance components of two traits associated to feet and legs in Nelore cattle and identify putative genomic regions underlying the expression of these traits through genome-wide association (GWA) analyses. Feet and legs was evaluated by the assignment of visual scores at two different moments: FL1) binary trait measured at yearling (about 550 days of age), aimed to identify whether an animal had defects related to feet and legs (FL1=1) or not (FL1=0); FL2) feet and legs score ranging from 1 (less desirable) to 5 (more desirable) was assigned to the top 20% animals for the selection index adopted by the beef cattle breeding program PAINT (CRV Lagoa), which were measured around 2-5 months after the evaluation of yearling. The FL1 and FL2 traits were evaluated together with yearling weight (YW). The components of variance and covariance and breeding values were estimated by Bayesian inference, using two-trait animal models (three analyses: FL1-FL2, YW-FL1 and YW-FL2). The genome-wide association (GWA) analyses for FL1 and FL2 was performed using the weighted single-step GBLUP method, from which were estimated the SNP effects. Functional annotation was focused on the ten 1Mb windows explaining the largest fraction of the genetic variance for each trait. Posterior means (standard errors) of heritability estimates were equal to 0.18 (0.04) and 0.39 (0.07), for FL1 and FL2, respectively. The estimate of genetic correlation between FL1 and FL2 (-0.47) was of moderate magnitude and negative, as expected considering that the classification score that favors each trait represents numerical values assigned in opposite directions. The genetic correlation estimated between FL2 and YW (0.39) suggests that the average yearling weight of the studied population is currently not high enough to cause a negative association with feet and legs problems. The genetic trends estimated for FL1 and FL2 (-0.043 and ...
Mestre

Master of Science
Department of Animal Sciences and Industry
Robert L. Weaber
Feet and leg soundness is an important trait for beef producers as it has an impact on cow longevity and animal well-being. The objective of this study was to investigate genetic parameter estimates for feet and leg traits, understand the relationship between feet and leg traits and Stayability EPD, and develop a scoring method for feet and leg traits in Red Angus cattle. Cattle were scored on 14 subjective traits: Body Condition Score (BCS), Front Hoof Angle (FA), Front Heel Depth (FHD), Front Hoof Claw Shape (FC), Rear Hoof Angle (RA), Rear Heel Depth (RHD), Rear Hoof Claw Shape (RC), Foot Size (FS), Hoof Orientation (HO), Knee Orientation (KO), Front Side View (FSV), Rear Leg Side View (RS), Rear Leg Hind View (RH), Composite Score (CS). Red Angus cattle (n=1885) were scored for all 14 traits by trained evaluators. All traits except CS were scored with the assumed optimum level being in the middle with undesirable scores being located on the extremes. Scores were observed on a scale of 1-100 and analyzed, then scores were simplified to 1-9 where scores were collapsed by 10’s into bins, starting at 10 since there were no scores observed below that point and the rubric used did not have an associated phenotype below that point. A three-generation pedigree file was obtained from the Red Angus Association of America (RAAA) that contained 13,306 animals, as well as a performance file on all animals observed in the study. Data were modeled using multiple linear bivariate animal models with additive and residual random effects, and age and contemporary group (herd-year) as fixed effects. Genetic parameters were estimated with ASREML4.0. Heritability estimates on the 1-9 scale for BCS, FA, FHD, FC, RA, RHD, RC, FS, HO, KO, FSV, RS, RH, and CS were 0.13, 0.18, 0.12, 0.08, 0.17, 0.24, 0.15, 0.29, 0.15, 0.15, 0.11, 0.29, 0.11, and 0.09 respectively. In general, feet and leg traits were lowly to moderately heritable, and are similar when compared to estimates for the same traits scored on a 1-100 scale. This informs a less granular and more simplified scale of measurement can be an appropriate method of feet and leg trait classification. Front hoof angle, FHD, RA, and RHD were all highly genetically correlated (r = 0.83 - 0.97), suggesting that angle and heel depth are controlled by many of the same genes. Front claw shape and RC were highly genetically correlated (r = 0.80) with each other but were not as significantly correlated with FA, FHD, RA, RHD (r = -0.43 to 0.38). This suggests that hoof angle/depth should be measured separately from claw shape. Rear leg side view, and RH had a strong correlation (r = 0.69). Strong correlations between FSV, HO, and KO also existed, yet there was noticeable variation among point estimates and standard error. Six traits on the 1-9 scale were selected to generate estimated breeding values (EBV’s) based on their heritability and correlation with other traits; BCS RHD, RC, FS, RSV, RH. A linear model was used to determine breeding values for BCS, RHD, RC, FS, FSV and RH. Those breeding values were regressed on Stayability EPD. When fixed effects of herd, age and year born were accounted for, RC (P < 0.0001), RSV (P = 0.0517), and FS (P = 0.086) had relationships as predictor variables for Stayability EPD. The use of feet and leg traits as predictor variables for improved Stayability EPD can be achieved with a simplified scoring system (1-9 vs. 1-100) in Red Angus cattle. By narrowing the number of traits needed to measure with a more simplified scoring method should allow for more rapid adoption among current beef cattle producers. A greater number of observations could be useful to validate these results and provide more accurate point estimates for feet and leg trait heritabilities and correlations.

Stearoyl-CoA desaturase1 (SCD1) catalyzes the synthesis of conjugated linoleic acid (CLA) and mono-unsaturated fatty acids (MUFA) in the mammary gland of ruminant animals. We hypothesized that single nucleotide polymorphisms (SNPs) in the coding region, 5' and 3' untranslted regions (UTRs) of the SCD1 gene would influence the activity of SCD1 enzyme and consequently account for some within-breed variations in milk CLA and MUFA. Sequence analysis of the coding region of the SCD1 gene of Jerseys and Holsteins revealed c.702A→G, c.762T→C and c.878C→T SNPs in exon 5 in both breeds and c.435G→A in exon 3 in Holsteins. The SNPs resulted in: A (G435A702T 762C878), A1 (A435A702T 762C878), B (G435G702C 762T878) and B1 (A435G702C 762T878) coding variants in Holsteins and only variants A and B in Jerseys. Only SNP 878C→T resulted in a non-synonymous codon change resulting in p.293Ala and p.293Val protein variants or alleles at the SCD1 locus. Subsequent association studies found significantly higher C10 index, C12 index and C14 index and consequently higher concentrations of C10:1 and C12:1 in p.293AA cows compared to the p.293VV cows in both breeds. The SCD1 genotype had no influence on concentrations of C141, C16:1, C18:1 and CLA in both breeds.
Sequence analysis of the 5' and 3' UTRs revealed no SNPs in the 5'UTR and a total of 14 SNPs in the 3'UTR of both breeds. The SNPs were in complete linkage disequilibrium resulting in 3 haplotypes or regulatory variants: H1 (G1571G1644C1763C2053A2584 A3007C3107G3208 T3290G 3497G3682A4399C4533G4881), H2 (G1571G1644A1763C2053A 2584G3007 C3107G3208T3290G3497G 3682A4399C4533G4881) and H3 (T 1571C1644A1763 T2053G2584G3007T 3107A3208C3290A3497A3682T 4399T4533A4881) in Holsteins and only H1 and H3 variants in Jerseys. A subsequent association study involving 862 Holstein cows, found the H1 regulatory variant to be associated with higher C10 and C12 desaturase indices and consequently with higher concentrations of C10:1 and C12:1 compared with the H3 variant. The effects of the H2 variant were intermediate to those of H1 and H3. 3'UTR genotype had no influence on the concentrations of C14:1, C16:1, C18:1 and CLA. The concentrations of C10:1 and C12:1 in milk fat could therefore be due to effects of SNPs in the open reading frame and the 3'UTR regions of the SCD1 gene. These results indicate that SNPs in the coding and 3'UTR regions of the SCD1 gene could be used as markers for genetic selection for increased C10:1 and C12:1 contents of milk.

It is well known that DNA methylation in gene promoter regions inhibits gene transcription and that tissue-specific gene expression is partially under the control of this transcription regulatory mechanism. In this study, bovine mammary gland tissues were collected from individual animals in lactating and non-lactating stages to investigate the DNA methylation patterns in the kappa-casein gene and alpha-lactalbumin gene core promoter regions using the bisulphite treatment in combination with polymerase chain reaction (PCR) sequencing. Different methylation status of each sample was classified into three categories, namely methylation at known transcription factor binding domains, methylation at core promoter non-binding domains and the absence of cytosine methylation. Real-time quantitative PCR was used to quantify the transcription levels of the kappa-casein and alpha-lactalbumin genes from the collected samples. A comparative method was used and fold-change values were calculated based on the comparison of the normalized threshold values of samples from different physiological stages as well as on various methylation patterns observed in their core promoter regions. Statistical analyses showed that the expressions of the kappa-casein and alpha-lactalbumin genes were significantly different in lactating and non-lactating mammary gland tissues. The methylation observed in the core promoter region of bovine alpha-lactalbumin gene was found to be associated with its gene expression. On the other hand, the methylation found in the core promoter region of bovine kappa-casein gene did not have any effect on its gene transcript levels.

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.

Data for this study were 79,997 evaluations for 12 individual body and udder traits of Holstein cows. Type scores were subjectively assigned by trained personnel of Select Sires, Inc., Plain City, OH, through their corrective mating and young sire evaluation programs. After editing data to remove incomplete, erroneous and duplicate records, 56,642 records were used to calculate overall and regional age adjustment factors. Genetic parameters were estimated. Heritabilities ranged from .40 for stature to .14 for fore udder. Standard errors ranged from .039 for stature to .018 for fore udder. Genetic correlations ranged from +.75 between teats and udder support to -.61 between feet and legs. Phenotypic correlations were generally smaller than genetic correlations, ranging from .56 between udder support and teats to -.23 for dairyness and strength. These findings were in general agreement with previous research. Genetic evaluations for the 12 individual linear traits were made using Herdmate Comparison (HC) and Best Linear Unbiased Prediction (BLUP) methods. Mean evaluations by HC were near zero, and ranged from .026 for stature to -.027 for teats. Mean repeatability also showed very little variation, ranging from .404 for stature to .241 for teats. BLUP evaluations were similar to HC evaluations, with mean evaluation ranging from .121 for feet to -.183 for dairyness. Direct correlations between BLUP and HC evaluations ranged from .90 for stature to .74 for dairyness. Forty-eight different combinations of minimum daughter numbers and model variables were tested to predict sires' overall evaluations for type from linear trait evaluations using regression analysis. Results indicate that with 5 or more daughters per sire, all predictions tested were similar in accuracy for Predicted Difference for Type.
M.S.

Thesis (MScAgric )--University of Stellenbosch, 2001.
ENGLISH ABSTRACT: The main object of this study was to estimate heritabilities and possible genetic correlations for and between reproductive traits in a composite multi breed beef cattle herd. Reproduction is a complex process with many components. Due to the nature of the data, obtained from the two farms of the Johannesburg Metropolitan Council from 1974 to 1993, only calving date (CD), calving date with a penalty score (CDP), calving success (CS), calving interval (CI), age at first calving (AFC), longevity and stayability at 36, 48, 60, 72 and 84 months were investigated. A GFCAT set of programmes was used and fitted on a sire model to analyse all the categorical traits. Heritabilities and product moment correlations between predicted breeding values for stayability at 36, 48, 60, 72, 84 months, calving success (CS) and longevity, were estimated. The estimated heritabilities on the underlying scale for these traits were 0.06, 0.10, 0.06, 0.03, 0.11, 0.03 and 0.08, respectively. Product moment correlations between breeding values for stayability traits were very low. The highest correlation of 0.22 was obtained between 36 and 48 months. Heritability estimates and correlations between traits appear to be of such a low magnitude that selection for these characteristics would result in limited improvement and indicate that the sire had little influence on his daughter's stayability, longevity and CS. For the analyses oflinear traits (CI, CD, CDP and AFC), a REML procedure fitting a multitrait animal model (using REML VCE 4.2.5 package of Groeneveld, 1998) was used. Heritabilities and geneticcorrelations for and between calving interval (CI), calving date (CD), calving date with a penalty score (CDP) and age at first calving (AFC) were estimated as traits of the dam. The estimated heritabilities for CI, CD, CDP and AFC obtained in this study were 0.01, 0.04, 0.06 and 0.40, respectively with a repeatability of 0.07, 0.12 and 0.13 for CI, CD and CDP, respectively. Genetic correlations between traits obtained varied from low to moderate, except for the high correlations between CD and CDP (0.98), CI and CD (0.75) and CI and CDP (0.79). Heritabilities, genetic correlations and repeatabilities of CD and CDP obtained in this study suggest that CD and CDP are the same traits and that selection for CDP rather than for CD does not have any additional advantage. Due to the additional advantages of CD over CI and the fact that CD is a less biased measurement of the female reproductive complex, CD appears to be of genetic value and should.be considered-as a possible selection criterion to ensure genetic improvement for reproduction in a beef cattle herd.
AFRIKAANSE OPSOMMING: Die doeI met hierdie studie was om oorerflikhede vir en moontlike genetiese korrelasies tussen verskillende reproduksiekenmerke in 'n meerras vleisbeeskudde te bepaal. Reproduksie is 'n komplekse proses en bestaan uit veelvuldige komponente. Weens die aard van die data, verkry vanaf die Johannesburg Metropolitaanse Raad se twee plase (vanaf 1974 tot 1993), is slegs kalfdatum (CD), kalf datum met 'n verswaringswaarde (CDP), kalwingsukses (CS), kalfinterval (CI), ouderdom met eerste kalwing (AFC), langlewendheid en volhoubaarheid van die moeders om reproduktief in die kudde tot op onderskeidelik 36, 48, 60, 72 en 84 maande te bly, bestudeer. Kategoriese kenmerke is deur middel van 'n GFCAT stel programme, wat op 'n vadermodel gepas is, geanaliseer. Oorerflikhede vir en die produkmoment korrelasies tussen die voorspelde teelwaardes vir CS, langlewendheid en volhoubaarheid op onderskeidelik 36, 48, 60, 72 en 84 maande, is bereken. Die oorerflikhede vir bogenoemde kenmerke was onderskeidelik 0.03, 0.08, 0.06, 0.10, 0.06, 0.03 en 0.11. Die korrelasie tussen die voorspelde teelwaardes vir die verskillende volhoubaarheidskenmerke was laag. Die hoogste korrelasie, n1. 0.22, is tussen 36 en 84 maande verkry. Die oorerflikhede en korrelasies tussen die kenmerke blyk van so 'n lae omvang te wees dat direkte seleksie vir die kenmerke slegs tot 'n beperkte genetiese verbetering sal lei en dui daarop dat die vader slegs 'n beperkte invloed op CS, volhoubaarheid en die langlewendheid van sy dogters het. Vir die analise van die lineere kenmerke (CI, CD, CDP en AFC), is 'n REML-prosedure gebruik wat op 'n multikenmerk dieremodel gepas is (deur die gebruik van die REML VCE 4.2.5 pakket van Groeneveld, 1998). Oorerflikhede vir en genetiese korrelasies tussen CI, CD, CDP en AFC is bereken as kenmerke van die moeder. In hierdie studie is die beraamde oorerflikhede vir CI, CD, CDP en AFC as onderskeidelik 0.01, 0.04, 0.06 en 0.40 bepaal, met herhaalbaarhede van onderskeidelik 0.07, 0.l2 en 0.13 vir CI, CD en CDP. Genetiese korrelasies tussen die kenmerke het van laag tot matig gevarieer, behalwe vir die hoe korrelasies tussen CD en CDP (0.98), CI en CD (0.75) en CI en CDP (0.79). Die oorerflikhede en herhaalbaarhede vir en genetiese korrelasie tussen CI en CDP verkry in hierdie studie, veronderstel dat CD en CDP in wese dieselfde kenmerk is en dat seleksie vir CDP in plaas van CD geen addisionele voordele inhou nie. Weens die addisionele voordele wat CD inhou, bo die van CI, en die feit dat CD 'n minder sydige bepaling van die vroulike reproduksiekompleks is, blyk CD van genetiese waarde te wees en moet dit as 'n moontlike seleksie kriterium, om genetiese verbetering in 'n vleisbeeskudde te verseker, oorweeg word.

The Middle Holocene (8,000-2,000 BC) was a period of immense socioeconomic and technological transformation. This thesis examines the development and impact of the combination of cattle, mobility, and pastoralism, together comprising a Mobile Pastoralism Package. Since data on mobile pastoralism are exceptionally fragmented and ‘disorderly’, independent lines of evidence: comparands, zooarchaeological, archaeological, human and cattle genetic data are used to test a set of hypotheses. Published data are used to investigate the origin of cattle and the MPP, and the MPP’s development and adoption by mobile hunter-gatherers and dispersal across West Asia and adjacent regions. The results support the presence of a sustained, predominantly mobile pastoralist economy with widespread but unstable sedentism, high-density settlement, agropastoralism and impermanent sedentary cultivation sectors. West Asia and surrounding regions were universally characterised by widespread mobile pastoralism. This ubiquity was driven by the development of cattle and the MPP c. 8,500-7,000 BC. Farming first developed in the Southern Levant and the Upper Tigris/ Euphrates. Hunter-gatherers in the Southern Levant PPNB developed a sedentary form of farming based on crops, goats and, later, imported sheep. Its failure resulted in regional depopulation, while subsequent importation of cattle and the MPP was likely responsible for a revival. In contrast, hunter-gatherers in the Upper Tigris/Euphrates domesticated auroch and developed cattle pastoralism and the MPP, which was immensely successful and rapidly exported across West Asia and into Africa, Europe, Eurasia and eventually South Asia. The economic success and wealth creation of the MPP provided the economic underpinnings of subsequent developments in sedentary agropastoralism and centralised/urban societies.

The growth hormone receptor gene (GHR) has been previously documented to be a good candidate gene for detection of a quantitative trait locus (QTL) which influences milk production in Holstein cattle. In this study, the promoter region of the GHR gene and microsatellite markers AGAL29 and BM5004 were studied. Their effects on milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FP) and protein percentage (PP) were examined. DNA was isolated from 1746 used by the artificial insemination (AI) industry representing 26 half-sibling families. Three polymorphisms in the GHR gene were genotyped (GHRAlu, GHRAcc and GHR Stu) along with both microsatellites. The markers were analyzed in a cross-family analysis. The model included a population mean, a fixed grandsire effect, a fixed allele effect and a random residual error. The data was also analyzed using a nested model in a granddaughter design to investigate a possible consistency in the allelic effect in individual families. Lastly, the data was analyzed using the haplotypes of GHRAlu and GHR Acc, using the same model as the cross-family analysis. It included an analysis of a fixed haplotype effect instead of a fixed allele effect. (Abstract shortened by UMI.)

The influences of some environmental and genetic factors on the incidence of abnormal test-days in milk-recorded cows enrolled in the Quebec Dairy Herd Analysis Service (QDHAS) was determined in this study. Conditions Affecting Records (CAR) codes, collected monthly by QDHAS's supervisors, are possible explanation for a reduced production in the day of test. For the purpose of this study, CAR codes were used to analyze the incidence of health problems under generalized linear models methodology. Poisson and logistic regression model analyses were able to model the number of cases of abnormal test-days and health problems per lactation. Herd, testing program, parity number, and stage of lactation were important systematic effects included in the analysis. However, calving year, season of calving, and herd production level were not statistically significant in most analysis. Sires significantly differed in the incidence of some health problems of their daughters. Low heritability values, between 0.02 and 0.05, were found showing that most variability was explained by non-genetic factors. Regardless of the low heritability, the genetic variability has been shown to be considerable, suggesting that a significant genetic improvement of the disease resistance is achievable if proper procedures are adopted.

Methodologies have been devised to genotype the $ kappa$-casein ($ kappa$-CN) and $ beta$-lactoglobulin ($ beta$-LG) loci using the polymerase chain reaction (PCR) and restriction fragment length polymorphisms (RFLPs) analysis. A fragment of 432 base pair from the $ kappa$-CN gene which contains the nucleotide substitutions diagnostic of the A- and B-alleles of $ kappa$-CN was amplified. DNA amplified from the A-variant contained a unique HinfI restriction site, whereas DNA amplified from the B-variant contained a unique TaqI site. Thus, the genotype of the animal could be determined by restriction enzyme analysis. A region extending from exon IV to V of the $ beta$-LG gene was also amplified using PCR. In this region, the B-allele contains 2 HaeIII restriction sites which are not present in DNA amplified from the A-allele. The digestion of the PCR product with HaeIII thus allowed discrimination between the A- and B-alleles. Analysis of bulls (n = 68) used by artificial insemination (AI) centres after 1980, bulls (n = 27) used before 1960, a random sample of male calves (n = 102) and cows (n = 123) revealed a frequency of the B allele of $ kappa$-CN as 0.13, 0.37, 0.22 and 0.19 in these populations, respectively. In the populations of bulls (n = 69) used by AI centres after 1980, bulls (n = 27) used before 1960, a random sample of male calves (n = 99), and cows (n = 129), the B-allele of $ beta$-LG was present at frequencies of 0.60, 0.52, 0.67, and 0.65, respectively. Statistical analysis of these data shows the frequency of the B-allele of $ kappa$-CN was significantly higher in sires (n = 27) which were used by the AI centre before 1960 compared to more modern proven sires (n = 68) (P $<$ 0.01).

The effect of composite and descriptive linear type traits on Functional Herd Life in Holstein cows was studied by means of Survival Analysis (Ducrocq and Solkner, 1998a). The original data set contained 331,105 lifetime records from the Programme d'Analyse des Troupeaux Laitiers du Quebec, from January 1980 to March 1995. Only 191,167 records (or cows) had type information. Mixed Weibull models were fitted to analyse the data; the probability of being culled (hazard) was defined as a product of a baseline Weibull hazard function and explanatory variables. The heritability estimates for Functional Herd Life were 0.07 in the log scale and 0.15 in the original scale. Sire Estimated Transmitting Ability for FHL, expressed as relative culling rate, ranged from 0.6 to 1.4 for all models. Solutions for fixed effects (all significant) indicated a higher probability of being culled for primiparous cows calving at older ages, for cows producing below herd average, for first lactation cows in the first and last stage of lactation and for older cows at the end of lactation. The risk of being culled did not change for cows in herds decreasing or increasing in size. Cows classified with a high score for Final Score were less likely to be culled; Final Score seems to be an important selection criteria among Quebec producers. Feet and Legs, Rump and Mammary System are traits that producers consider in their culling policies; cows classified with a high score had more chance of surviving. Among the linear type traits, the 5 traits with the highest impact on productive life, were Rear Attachment Height, Fore Attachment, Bone Quality, Stature and Fore Teat Placement; Quebec producers seem to consider these traits when they make their culling decisions.

Thesis (MScAgric)--Stellenbosch University, 2008.
ENGLISH ABSTRACT: Research conducted on beef cattle in Botswana investigated both growth and reproduction. These studies however, did not specifically determine the influence of the different environmental factors on growth in the Tswana and Composite beef cattle breeds. The establishment of a national beef herd recording and performance testing scheme requires knowledge on the appropriate adjustment methods of field data for the fixed effects such as sex of calf and age of dam. A fair comparison of birth and weaning weights between male and female calves, and calves born from young, mature and old dams will be derived from these adjustment factors. There is no information on adjustment factors for the Tswana and Composite cattle breeds in the country. Genetic parameters for growth traits in these breeds are not known and are needed for the implementation of the performance scheme in Botswana. The Composite breed resulted from a controlled crossbreeding programme using the Simmental, Brahman, Tswana, Tuli and the Bonsmara breeds. The Tswana animals are indigenous to the country and were sourced locally at the beginning of the growth evaluation trial in the two breeds. The objectives of the study were to use data collected from Tswana and Composite cattle breeds to estimate the influence of non-genetic factors on growth traits in the two breeds; to develop adjustment factors for the effects of sex of calf and age of dam; and to estimate genetic parameters (heritabilities and genetic correlations) for future genetic evaluations in both breeds. Data were collected over the period 1988 to 2006. A total of 2 257 records for the Composite breed and 5 923 records for the Tswana breed were available for analyses. Growth characteristics of interest in this study were birth weight (BW), weaning weight (WW), pre-weaning average daily gain (ADG1), 18 months weight (18MW) and post-weaning average daily gain (ADG2). Study 1 indicated that non-genetic effects of breed of calf, sex of calf, month and year of birth, previous parous state, weight of cow at parturition, age of dam, and age of calf at weaning significantly affected BW, WW, 18MW, ADG1 and ADG2 in both breeds. The Composite breed had higher BW, ADG1 and WW whereas the Tswana had higher ADG2 and 18MW. Pre-weaning growth rate increased with an increase in the age of the dam, reaching a peak in mature (5-12 years) cows and declined in cows 13 years and older. Conversely, post-weaning growth rates declined as age of dam advanced but increased in old (13 years and older) dams. Male calves were heavier than female calves for all the growth traits. Birth weight increased as calving season progressed whilst a decrease in WW was observed over the same period. Heifers gave birth to lighter calves when compared to mature multiparous dams. The Composite breed can therefore be considered for weaner production under ranch conditions while the Tswana can be reared under extensive systems due to its adaptability to the environment. Additive correction factors for effects of sex of calf and age of dam on BW and WW were studied separately for the Tswana and Composite in study 2. The least squares means procedure was used to derive age groups and the adjustment factors. The three age groups were young (4 years and below) dams, mature (5-12 years) dams and older (13 years and above) dams. Male calves were heavier than their female counterparts. The sex of calf adjustments for BW and WW were 2.75 and 8.21 kg in the Tswana, and corresponding values for the Composite 2.84 and 10.11 kg, respectively. Birth weight and WW increased as age of dam increased, reached maximum in mature dams and declined in older dams. Age of dam adjustment factors for BW in the 3, 4 and 13+ years age groups for the Tswana were 1.74, 0.96 and 1.87 kg, respectively. The corresponding values for the Composite were 2.28, 0.94 and 2.06 kg, respectively. Age of dam adjustment factors for weaning weight in the Tswana were 10.36 and 5.46 kg for age groups 3-4 and 13+ years, respectively. Adjustment factors for WW in the Composite were 13.84, 3.20 and 9.58 kg for age groups 3, 4 and 13+ years. The differences in adjustment factors obtained between the two breeds emphasize the need to compute and apply these factors within breed. Study 3 involved the estimation of genetic parameters for BW, WW, ADG1, 18MW and ADG2. Single-trait and multi-trait analyses were used in the estimation of (co)variance components by fitting an individual animal model (AM) and the animal maternal model (AMM) for the two breeds. Direct heritabilities for BW, WW, ADG1, 18MW and ADG2 in the Tswana were 0.45, 0.32, 0.37, 0.31 and 0.31, respectively from a single-trait AM analysis. Fitting the AMM resulted in direct heritabilities of 0.31, 0.20 and 0.16 for BW, WW and ADG1, respectively, while the maternal heritabilities were 0.11, 0.15 and 0.21, respectively. For the Composite the direct heritabilities for BW, WW and ADG1 were 0.58, 0.32 and 0.30, respectively with single-trait AM. Partitioning using the AMM resulted in the direct heritabilities for BW, WW and ADG1 of 0.55, 0.17 and 0.14, respectively, while corresponding maternal effects were 0.09, 0.15 and 0.15, respectively. The genetic correlations between direct and maternal effects were positive and ranged from 0.20 to 0.89. When using the multi-trait analysis and fitting the AM, the direct heritabilities for the Tswana were 0.45, 0.37, 0.34, 0.39 and 0.31 for BW, WW, ADG1, 18MW and ADG2, respectively. Genetic correlations between the growth traits ranged from 0.16 to 0.97. Direct (and maternal) heritabilities for BW, WW and ADG1 were 0.31(0.11), 0.19(0.15) and 0.14(0.17), respectively, in the Tswana. Correlations between direct heritabilities for BW, WW and ADG1 ranged from 0.45 to 0.95, while maternal effects ranged from 0.12 to 0.99. The magnitude of the heritabilities indicates an existence of the opportunity to make genetic progress through selection in both breeds. Selection based on WW seems to be the ideal procedure to bring genetic improvement in the Tswana without detrimental long term effects.
AFRIKAANSE OPSOMMING: Navorsing wat op die vleisbeesrasse in Botswana gedoen is, het hoofsaaklik op beide groei en reproduksie gehandel. Hierdie studies het egter nie spesifieke gefokus op die bepaling van die invloed wat verskillende omgewingsfaktore op die groei van saamgestelde (d.i. Composite) en die Tswana vleisbeesrasse het nie. Die bepaling van ʼn nasionale vleisbees rekordhouding- en prestasietoetsskema verg kennis van die mees gepaste metode om velddata vir vaste effekte soos geslag van die kalf en ouderdom van die moeder aan te pas. Hierdie aanpassingsmetodes sal lei tot die regverdige vergelyking van geboorte- en speengewigte tussen manlike en vroulike diere, sowel as van kalwers gebore van jong, volwasse of ou moeders. Tans is daar geen inligting oor aanpassingfaktore vir die Tswana en saamgestelde vleisbeesrasse in Botswana bekend nie. Geen genetiese parameters vir groei-eienskappe vir geeneen van die rasse is beskikbaar nie en word benodig vir die implementering van die prestasie skema in Botswana. Die saamgestelde ras is die produk van ʼn beheerde kruisteeltprogram, wat onderskeidelik die Simmental, Brahman, Tswana, Tuli en die Bonsmara beesrasse ingesluit het. Die Tswana ras is inheems aan Botswana en vanaf plaaslike bronne vir die groei evaluasie studie bekom. Die doelwitte van die studie was eerstens die analisering van data wat van beide die Tswana en saamgestelde rasse ingesamel is, om die invloed van nie-genetiese faktore op die groei eienskappe te bepaal om ten einde aanpassingsfaktore vir die effek van geslag van die kalf en ouderdom van die moederdier te ontwikkel. ʼn Tweede doelwit was die bepaling van genetiese parameters (oorerflikhede en genetiese korrelasies) vir die gebruik in toekomstige genetiese evaluering van beide rasse. Data is vanaf 1988 tot 2006 ingesamel. ʼn Totaal van 2 257 waarnemings vir die saamgestelde ras en 5 923 waarnemings vir die Tswana ras is ontleed. Groei eienskappe wat in die studie ondersoek is, het geboortegewig (BW), speengewig (WW), voorspeen gemiddelde daaglikse toename (ADG1), 18-maand gewig (18MW) en naspeense gemiddelde daaglikse toename (ADG2) ingesluit. Studie een het aangedui dat nie-genetiese effekte van die ras van die kalf, die geslag van die kalf, maand en jaar van geboorte, vorige dragtigheidsstatus, koei se gewig met geboorte van kalf, ouderdom van die moederdier en die speenouderdom van die kalf het ʼn betekenisvolle invloed op BW, WW, 18MW, ADG1 en ADG2 van beide rasse gehad. Die saamgestelde ras het hoër waardes vir BW, ADG1 en WW gehad, terwyl die Tswana ras hoër waardes vir ADG2 en 18MW geopenbaar het. Voorspeense groeitempo het toegeneem met ʼn toename in die ouderdom van die moederdier, met ʼn piek in volwasse (d.i. 5-12 jaar ouderdom) moeders en ʼn afname in koeie 13 jaar en ouer. Omgekeerd het naspeen groeitempo afgeneem met ʼn toename in die ouderdom van die moederdier en weer begin toeneem vir ou (d.i. 13 jaar en ouer) koeie. Geboortegewig het toegeneem met die verloop van die kalfseisoen, terwyl ʼn afname in WW vir dieselfde periode aangeteken is. Verse het, wanneer hulle met volwasse koeie vergelyk is, het geboorte aan ligter kalwers gegee. Die saamgestelde ras kan dus oorweeg word vir die produksie van speenkalwers onder kommersiële intensiewe toestande, terwyl die Tswana ras, op grond van sy beter aanpassing by ekstensiewe omstandighede waar die moederlike invloed nie voorkom nie, vir produksie onder ekstensiewe omstandighede gebruik kan word. In studie 2 is die additiewe korreksie faktore vir die invloed van geslag van die kalf en moederouderdom op BW en WW apart vir die twee rasse bestudeer. Die geslag van die kalf x ouderdom van die moederdier interaksie was nie betekenisvol vir enige van die rasse nie. Dus kan geen aanpassing vir die ouderdom van die moeder binne geslagte vir enige van die twee rasse gemaak word nie. Die kleinste kwadraat gemiddeldes metode is gebruik om die ouderdomsgroepe en aanpassingsfaktore te bepaal. Die drie ouderdomsgroepe was jong (d.i. 4 jaar en jonger) koeie, volwasse (d.i. 5-12 jaar ouderdom) en ouer (d.i. 13 jaar en ouer) koeie. Daar is gevind dat manlike kalwers swaarders as hulle vroulike eweknieë is. Die aanpassingswaarde vir die geslag van die kalf vir BW en WW was 2.75 kg en 8.21 kg in die Tswana en 2.84 kg en 10.11kg vir die saamgestelde ras. Geboortegewig en WW het toegeneem met ʼn toename in die ouderdom van die moeder. Dit het ʼn maksimum bereik in volwasse koeie en afgeneem vir koeie ouer as 13 jaar. Die aanpassingsfaktore vir die ouderdom van die moederdier vir BW in die 3, 4 and 13+ jarige ouderdomsgroepe vir die Tswana ras was onderskeidelik 1.74 kg, 0.96 kg en 1.87 kg. Die ooreenstemmende waardes vir die saamgestelde ras was onderskeidelik 2.28 kg, 0.94 kg en 2.06 kg. Aanpassingsfaktore vir WW vir die Tswana ras was 10.36 kg en 5.46 kg vir onderskeidelik die 3-4 jaar en 13+ jaar en ouer ouderdomsgroepe. Aanpassingsfaktore vir WW in die Composite ras was 13.84 kg, 3.20 kg en 9.58 kg vir onderskeidelik die 3 jaar, 4 jaar en 13 jaar en ouer ouderdomsgroepe. Verskille in die onderskeie parameters vir die twee rasse beklemtoon die noodsaaklikheid vir die berekening en toepassing van die onderskeie aanpassingfaktore vir en binne elke ras. Studie 3 het die bepaling van die genetiese parameters vir BW, WW, ADG1, 18MW en ADG2 behels. Enkel- en multivariaat analises is gebruik vir die skatting van die (ko)variansie komponente deur ʼn direkte diermodel (AM) en ʼn dier-maternale model (AMM) vir die twee rasse te pas. Direkte oorerflikhede vir BW, WW, ADG1, 18MW en ADG2 vir die Tswana ras was onderskeidelik 0.45, 0.32, 0.37, 0.31 en 0.31, vir ʼn enkelvariaat AM analise. Die pas van ʼn AMM het direkte oorerflikhede van 0.31, 0.20 en 0.16 vir onderskeidelik BW, WW and ADG1 gegee, terwyl die maternale oorerflikhede onderskeidelik 0.11, 0.15 en 0.21 was. Vir die saamgestelde ras was die direkte oorerflikhede vir BW, WW en ADG1 onderskeidelik 0.58, 0.32 en 0.30 vir die enkelvariaat AM analise. Verdeling (partisie) van die AMM het direkte oorerflikhede vir BW, WW en ADG1 van onderskeidelik 0.55, 0.17 en 0.14 gegee, terwyl die ooreenstemmende maternale effekte onderskeidelik 0.09, 0.15 en 0.15 was. Die genetiese korrelasies tussen die drekte en maternale effekte was positief en tussen 0.20 en 0.89. Met die multivariaat analise en die pas van die AM, is direkte oorerflikhede van 0.45, 0.37, 0.34, 0.39 en 0.31 vir onderskeidelik BW, WW, ADG1, 18MW en ADG2, vir die Tswana ras bereken. Genetiese korrelasies tussen die groei eienskappe het gewissel tussen 0.16 tot 0.97. Direkte (en maternale) oorerflikhede vir BW, WW en ADG1 was onderskeidelik 0.31(0.11), 0.19(0.15) en 0.14(0.17), vir die Tswana ras. Korrelasies tussen die direkte oorerflikhede vir BW, WW en ADG1 het gewissel tussen 0.45 en 0.95, terwyl die maternale effekte tussen 0.12 en 0.99 gewissel het. Die grootte van die oorerflikhede dui op die moontlikheid van genetiese vordering wat deur seleksie in beide rasse gemaak kan word. Seleksie op grond van WW blyk die mees gepaste wyse te wees waarmee genetiese vordering binne die Tswana ras gemaak kan word, sonder enige langtermyn nadelige effekte.

Total weaning weight records of 29,832 Angus and 15,765 Hereford calves born during 1953 through 1983 in Virginia were used to evaluate phenotypic and genetic trends for adjusted weaning weight (AWWT), weaning weight ratio (WWR) and deviation of AWWT from the mean AWWT of the contemporaries (DEVN). Two approaches, namely the regression techniques and maximum likelihood (ML) procedure were taken to estimate the above trends. The estimates of annual phenotypic trend for AWWT in the Angus and Hereford breeds were .96 and .82 kg/yr, respectively. The sire and dam genetic trends obtained from both approaches for the traits of interest were positive and significant; however, the estimates from the regression analyses were slightly higher than those- from the ML procedure. The estimates of one-half of the sire genetic trends obtained from ML procedure for WWR and DEVN were .40 ± .04 ratio units/yr and .72 ± .07 kg/yr in the Angus breed and the corresponding values for the Hereford breed were .25 ± .06 ratio units/yr and .45 ± .12 kg/yr. The estimates of one-half of the darn trends for the corresponding traits were .32 ± .02 ratio units/yr and .55 ± .04 kg/yr for Angus and .21 ± .03 ratio units/yr and .30 ± .07 kg/yr for Herefords. The application of adjustment factors (to eliminate the bias due to non-random mating and culling levels) to estimates of sire genetic trends in the regression analyses produced estimates more similar to the estimates obtained from the ML procedure. The average annual genetic trends over the study period from the ML procedure for AWWT were 1.27 kg/yr for Angus and .75 kg/yr for Herefords.
Ph. D.

Genetic parameters were estimated using 8086 weaning weight records of Mashona cattle from commercial herds in Zimbabwe, through Derivative-free Restricted Maximum Likelihood (DFREML) procedure fitting an individual animal model. All known additive relationships among animals were incorporated and all sires were assumed to have been bred by unknown parents. A simulation study was carried out to estimate the amount of bias in the estimated genetic parameters caused by the failure to account for the true relationships among the breeding animals.
Genetic differences between the weaning weights of Mashona cattle in commercial herds and in small holder herds were estimated using performance records of progeny from 2 reference bulls, 3 bulls from commercial herds, 14 bulls from Makoholi Research Station and 20 bulls from small holder farms. The findings from this study were used as a basis for simulating different strategies of improving the weaning weights of Mashona cattle through the creation of nucleus herds. Estimates ($ pm$s.e) of direct heritability (h$ sb{ rm A} sp2$), maternal heritability (h$ sb{ rm M} sp2$) and the correlation between direct and maternal genetic effects (r$ sb{ rm AM}$) were 0.243 $ pm$ 0.046, 0.392 $ pm$ 0.031 and $-$0.282 $ pm$ 0.081, respectively. When a permanent environmental effect of the dam (c$ sp2$) was fitted, the estimates of h$ sb{ rm A} sp2$, h$ sb{ rm M} sp2$, r$ sb{ rm AM}$ and c$ sp2$ were 0.281 $ pm$ 0.026, 0.113 $ pm$ 0.022, $-$0.269 $ pm$ 0.106 and 0.228 $ pm$ 0.023, respectively. No significant trends were observed in direct breeding values but there was a decline in maternal breeding values. The simulation study indicated that the bias in h$ sb{ rm A} sp2$ and h$ sb{ rm M} sp2$ resulting from the lack of sire pedigrees was trivial if the correlation between direct and maternal genetic effects was high and a large proportion of dams had known pedigrees.
The progeny test showed that both the mean breeding values of the reference sires and the bulls from commercial farms were significantly higher than the mean breeding values of small holder bulls for birth weight (by 1.6 and 1.7 kg, respectively) and weaning weight (by 10.4 and 11.0 kg, respectively). The strategies that selected breeding animals on their maternal genetic values resulted in the highest responses for weaning weight.
It was concluded that maternal genetic values of Mashona cattle should be improved to allow this breed to compete favourably as a maternal breed in commercial agriculture.

The main revenue source for beef cattle farmers is the price they are awarded for carcasses based on carcass value (i.e., carcass weight, conformation and fat score) which is influenced by genetic and environmental factors (e.g., herd management). In order to improve profitability, accurate means of evaluating and improving both sets of factors influencing carcass trait performance are necessary. This would entail optimal management of genetic resources and herd practices. Furthermore, access to a large international germplasm pool would facilitate faster genetic gain. The objective of this thesis was to generate tools for the enhancement of carcass trait genetic and herd management evaluations both at a national and international level. The data used in the thesis originated from the Irish and UK national cattle databases and consisted of 336,944 Irish and 147,876 UK cattle of multiple beef and dairy breeds from 9,572 Irish and 3,385 UK commercial herds. Livestock mature at different rates depending on a number of factors including the genetic background; therefore, the optimum age at which to slaughter the progeny of different sires may differ. Chapter 2 examined sire level genetic profiles for three carcass traits (carcass weight, conformation and fat score) in cattle using data from the Republic of Ireland. Variance components for each trait across age at slaughter were estimated using sire random regression models. Heritability estimates of carcass traits across ages at slaughter varied depending on gender (heifers, steers, young bulls) and the trait in question, and ranged from 0.08 (± 0.02) to 0.34 (± 0.02) for carcass weight, from 0.24 (± 0.02) to 0.42 (± 0.02) for conformation score and from 0.16 (± 0.03) to 0.40 (± 0.02) for fat score. Genetic correlations between traits across ages at slaughter were all significantly less than unity, indicating that different genetic mechanisms control these traits across life. The results from chapter 2 show that genetic variability in the progeny growth trajectory of sires exists and that this variability in the growth profiles of sires for carcass traits may be exploited in breeding programmes. As carcass traits are a function of both the genetics of the animal and the environment in which the animal is reared, chapter 3 aimed to quantify the contribution of the herd environment to the same three beef carcass traits, with particular emphasis on generating finishing herd-specific profiles for carcass traits across different ages at slaughter. The data analysed in chapter 3 was from animals slaughtered in UK abattoirs. Genetic and finishing-herd-year of slaughter parameters were generated using random regression analysis. Across slaughter age and gender, the proportion of phenotypic variance accounted for by finishing-herd-year of slaughter variance was between 30.83%-71.48% for carcass weight, 21.38%-26.29% for conformation score and between 10.88%-44.04% for fat score. These parameters indicate that the finishing herd environment is an at least equally important contributor to carcass trait variability as the genetic background of animals, and amenable to improvement with appropriate management practices. The final study of the thesis was to investigate the feasibility of across-country carcass trait genetic evaluations. Examination of the level of genetic connectedness between Ireland and the UK found 225 distinct bulls common to both countries. These common bulls were related to 80,707 Irish and 23,162 UK animals with carcass records in each population. Genetic correlations for carcass traits between Ireland and the UK were almost unity, ranging from 0.92 (± 0.31) for fat score to 0.96 (± 0.17) for carcass weight, indicating that the carcass traits recorded in both countries are genetically essentially equivalent. These strong genetic correlations between carcass traits in both countries enabled the direct pooling of carcass data for the purpose of across-country genetic evaluations (breeding value estimation). An increased rate of genetic gain for carcass traits per generation was predicted from across-country selection compared to within country selection ranging from 2% (conformation score in Ireland) to 33.77% (conformation score in the UK). This improved gain was primarily due to greater intensity of selection and somewhat more accurate estimated breeding values when carcass records and pedigree information from both countries were combined. The results presented in this thesis demonstrate that routinely collected abattoir data in Ireland and the UK can be exploited to produce additional selection and on-farm management tools. The results also show that access to across-country carcass trait genetic evaluations would allow UK and Irish beef farmers to make more informed decisions on the selection of seed stock needed to increase genetic gain and profits. Outcomes of this thesis pave the way to improvements in national carcass traits genetic evaluations in Ireland and the UK based on appropriate age at slaughter and also demonstrate the feasibility of across-country carcass trait genetic evaluations between Ireland and the UK. The scope for further areas of research includes the identification of specific management practices for optimal herd performance for carcass traits. Additionally, across-country carcass trait genetic evaluations based on random regression models across different ages at slaughter would also be of benefit to beef producers in Ireland and the UK. Finally, the viability of across-country genetic evaluations for additional carcass traits, such as carcass cut weights should be explored.

Orientador: Henrique Nunes de Oliveira
Banca: Raysildo Barbosa Lobo
Banca: Maria Eugenia Zerlotti Mercadante
Banca: Marcílio Dias Silveira da Mota
Banca: Luiz Artur Loyola Chardulo
Resumo: Foram utilizados dados de 116406 bovinos da raça Nelore, participantes do Programa de Melhoramento Genético da Raça Nelore (PMGRN), nascidos entre 1995 e 2005, com o objetivo de estimar parâmetros genéticos para os pesos padronizados aos 120(P120), 210(P210), 365(P365), 450(P450) e 730(P730) dias de idade e para os ganhos em peso do nascimento aos 120(GP120), dos 120 aos 210 (GP210), dos 210 aos 365(GP365), dos 365 aos 450(GP450) e dos 450 aos 730(G730), além de avaliar a tendência genética das características citadas, tanto para efeito direto como materno. Os componentes de variância foram estimados pelo método de máxima verossimilhança restrita utilizando o programa AIREMLF90, sob modelo animal, o qual incluiu como efeitos fixos, os grupos de contemporâneos e idade da vaca ao parto e como aleatórios, efeito genético aditivo direto para todas as características estudadas e efeito genético materno para P120, P210, P365, GP120, GP210 e GP365. As estimativas de herdabilidade direta foram 0,21, 0,22, 0,22, 0,34, 0,28, para cada peso, respectivamente, e 0,19, 0,20, 0,18, 0,18 e 0,20, para os respectivos ganhos em peso. As herdabilidades maternas foram 0,26, 0,25 e 0,12, para P120, P210 e P365 e 0,23, 0,17, 0,12 para GP120, GP210 e GP365. As correlações direto-maternas foram todas negativas, exceto para P365 (0,06). As tendências genéticas diretas foram todas positivas. As tendências maternas foram quase nulas para todas as características. As estimativas de herdabilidade para os pesos padronizados e para os ganhos em peso indicam que a seleção pode promover mudanças genéticas. As herdabilidades maternas para P120, P210, P365 e GP365 indicam que a seleção nestas características pode contribuir para melhorar a habilidade materna do rebanho. Os ganhos genéticos diretos observados, para todas as características estão aquém dos ganhos potenciais da raça Nelore... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Data of 116406 bovines of the Nellore beef cattle, participants of the Programa de Melhoramento Genético da Raça Nelore (PMGRN), been born between 1995 and 2005 were used with the objective to estimate genetic parameters for the 120-days weight (P120), 210-days weight (P210), 365-days weight (P365), 450-days weight (P450) and 730-days weight (P730) and for the weight gain from birth to 120(GP120), from 120 to 210(GP210), from 210 to 365(GP365), from 365 to 450(GP450) and from 450 to 730 days weight(GP730), besides evaluating the genetic trends of the traits, so much for the direct effect as for the maternal. The variance components were estimated by the restricted maximum likelihood method using the program AIREMLF90. The animal model included fixed effects for contemporary groups and age of the dam at calving, and also included random effects for genetic direct effects for all the studied traits and genetic maternal effect for P120, P210, P365, GP120, GP210 and GP365. The estimative of direct heritability were 0,21, 0,22, 0,22, 0,34, 0,28, for each weight, respectively and 0,19, 0,20, 0,18, 0,18 and 0,20, for the respective weight gains. The maternal heritability were 0,26, 0,25 and 0,12, for P120, P210 and P365 and 0,23, 0,17, 0,12 for GP120, GP210 and GP365. The direct-maternal correlations were all negatives except for P365 (0,06). The direct genetic trends were all positive ones. The maternal trends were almost null for all the traits. The estimative of heritability for the adjusted weights and for the weight gains indicated that the selection could promote genetic changes. The maternal heritability for P120, P210, P365 and GP365 indicated that the selection in these traits could contribute to improve the maternal ability of the herd. The direct genetic gain observed, for all the traits were on this side of the potential gain of the Nellore beef cattle... (Complete abstract click electronic access below)
Doutor

In the present study samples from four native Turkish Cattle Breeds
South Anatolian Red (n= 48), East Anatolian Red (n= 34), Anatolian Black (n= 42) and Turkish Grey (n=46) and elite bulls of Holstein (n=21) were genotyped with respect to two milk production enhancer genes, Prolactin (PRL) and Diacylglycerol acyltransferase (DGAT1), and one disease (Complex Vertebral Malformation) causing gene (SLC35A3). A allele frequency for PRL gene, believed to be positively associated with the milk yield in cattle, ranged between 0.5645 (Anatolian Black) - 0.7558 (South Anatolian Red). K allele frequency which is thought to be related with the milk fat content in cattle varied between 0.7794 (East Anatolian Red) - 0.9250 (Anatolian Black). Complex Vertebral Malformation gene was not observed in any of the examined individuals (n= 164), hence, SLC35A3 locus was monomorphic. Pairwise Fst values based on the two polymorphic loci revealed that breeds are not significantly different from each other with respect to these two genes. Correlations, but weak, between the PRL A allele frequency and milk yield and similarly DGAT1 K allele and milk fat content was observed, Principle Component Analysis generated two compound axis based on the two polymorphic loci. Positions of the breeds on the first axis were correlated with the milk fat content of the breeds, perfectly. Again, positions of the breeds on the second axis were correlated with the milk yield of the breeds. Furthermore, PCA revealed that both A of PRL and K of DGAT1 genes seemed to have contributions in milk yield Results are believed to be useful for the management efforts of Turkish native cattle breeds.

Thesis (MScAgric (Animal Sciences))--University of Stellenbosch, 2010.
ENGLISH ABSTRACT: The aim of this study was to evaluate the Simbra breed of cattle for certain non-genetic as well as genetic parameters influencing live weight traits in the breed. Live weight traits included birth weight (BW), weaning weight at 200 days of age (WW), yearling weight at 400 days of age (YW) and 600 day weight. The Simmental and Simbra Breeders’ Society of Southern Africa availed 148751 records for analysis from the year 1987 till 2009. Due to deficiencies of various kinds in the data and the restrictions imposed for the purposes of the analysis, 56.44% of the records were discarded for BW, 76.55% for WW, 91.54% for YW and 96.32% for 600-day weight. Non-genetic parameters affecting BW, WW, YW and 600-day weight were analysed using the General Linear Models procedure of the Statistical Analysis System (SAS, 2004) software. During this procedure sex of calf, breed composition of calf, breeder of calf, month of birth, year of birth and dam age were fitted in the models. BW, WW, YW and Mature Cow Weight (MCW) were fitted as covariates where possible. It was determined that the fixed effects of sex, dam age, breeder, year and month had a significant (P < 0.05) effect of BW and WW while dam age was not significant (P > 0.05) for YW or 600-day weight. Breed was found non significant for YW. Breeder of the calf accounted for the most variation in BW, WW, YW as well as 600-day weight with a contribution of 17.55%, 25.77%, 18.35% and 10.71% respectively. Tukey’s multiple range tests were performed for testing differences between least square means. Results indicated male calves to be significantly heavier than females for all four traits measured. Breed composition differences were found significant until WW. Calves with higher Brahman percentage weighted more at birth while calves with higher Simmental percentage weighed more at weaning. Middle-aged dams were found to account for heavier calves at both BW and WW while very young dams and very old dams produced lighter calves for the two live weight traits. A number of years showed a significant difference from each other for all the traits measured as well as month of birth. (Co) variance components and the resulting genetic parameters were estimated using single-traits and three-traits analysis by means of Restricted Maximum Likelihood procedures (Gilmour et al., 2002). Appropriate models were selected by means of Log likelihood ratios tests and implemented to estimate genetic parameters for each of the traits studied. Direct additive heritabilities for BW, WW, YW and 600-day weight in the Simbra were respectively 0.56 ± 0.08, 0.67 ± 0.09, 0.70 ± 0.11 and 0.10 ± 0.03 when the most suitable animal model was fitted in single-trait analyses for each trait. Single traits analysis also included maternal additive as well as the correlation between direct additive and maternal additive for BW, WW and YW. Maternal additive heritability estimates of 0.24 ± 0.07, 0.33 ± 0.06 and 0.38 ± 0.07 was obtained for BW, WW and YW. Correlation estimates between direct additive and maternal additive were -0.75 ± 0.07, -0.93 ± 0.07 and -0.85 ± 0.08 for BW, WW and YW respectively. Furthermore, dam permanent environment was included as an additional random effect that increased the log likelihood value significantly. A value of 0.04 ± 0.05 was obtained for dam permanent environment estimate for WW. When a three traits analysis was done for the same traits, but using a significantly smaller data set, direct additive heritabilities of 0.24 ± 0.07 for BW, 0.33 ± 0.06 for WW and 0.38 ± 0.07 for YW were obtained. Genetic and environmental correlation estimates of 0.18 ± 0.16 and 0.09 ± 0.06 between BW and WW; 0.27 ± 0.16 and 0.07 ± 0.06 between BW and YW; as well as 0.52 ± 0.10 and 0.45 ± 0.05 between WW and YW were obtained during the three-trait analysis. The magnitude of the heritabilities obtained in this study indicates that the opportunity exists to make genetic progress through proper selection objectives.
AFRIKAANSE OPSOMMING: Die doel van hierdie studie was om die Simbra bees ras te evalueer op grond van sekere niegenetiese so wel as genetiese parameters wat lewende gewig beïnvloed. Gereelde en akkurate opnames van lewende gewig, is ‘n goeie indikasie van groei potensiaal en is ‘n minimim vereiste vir meeste beesras telings genootskappe. Lewende gewigs eienskappe sluit in geboorte gewig (BW), speen gewig gemeet op 200 dae (WW), jaaroue gewig gemeet op 400 dae (YW) en finale gewig gemeet op 600-dag gewig. Die Simmentaler en Simbra genootskap van Suid Afrika het 148751 rekords beskikbaar gestel vir evaluasie vanaf die jaar 1987 tot 2009. Daar was egter groot tekort komings aan die gewewe data en dus is daar 56.44% van die rekords vir BW nie gebruik nie, 76.55% vir WW, 91.54% vir YW en 96.32% vir 600-dag gewig. Nie-genetiese parameters wat die onderskeie lewende gewigte beïnvloed het, is geanaliseer deur Algemene Lineêre Modelle met behulp van die Statistiese Analitiese Sisteem (SAS, 2004) sagteware. Gedurende die analise is geslag van die kalf, ras samestelling, teler van die kalf, maand van geboorte, jaar van geboorte asook moeder ouderdom gepas in die modelle vir die onderskeie gewigte. Geboorte gewig, speen gewig, jaaroue gewig asook volwasse koei gewig is gepas in elk van die modelle as ko-variate. Volgens die resutate is daar vasgestel dat geslag van die kalf, moeder ouderdom, teler, jaar, maand en volwasse koei gewig almal ‘n betekenisvolle (P < 0.05) invloed gehad het op BW en WW. Die moederouderdom was nie betekenisvol (P > 0.05) vir YW of 600-dag gewig nie. Die ras samestelling was ook nie betekenisvol gevind vir YW. Teler van die kalf was verantwoordelik vir die meeste variasie in BW, WW, YW asook 600-dag gewig met ‘n bydrae van 17.55%, 25.77%, 18.35% en 10.71% onderskeidelik. Tukey se veelvuldige vergelykings toets is gebruik om onderskeid te tref tussen “least square means”. Resultate het aangedui dat manlike diere swaarder weeg as vroulike diere tot en met finale gewig. Ras samestelling vir BW en WW was betekenisvol verskillend vir die diere. Kalwers met ‘n hoër Brahmaan persentasie het swaarder BW opgelewer as dié met ‘n hoër Simmentaler persentasie, terwyl kalwers met ‘n hoër Simmentaler persentasie swaarder geweeg het met speen en dus ideal is vir speen kalwer produksie stelsels. Middel-jarige moeders het swaarder kalwers geproduseer met geboorte en speen as baie jong en - ou moeders. Sommige jare waarin van die kalwers gebore is, het ook betekenisvol van mekaar verskil asook die maand waarin die kalf gebore is. Ko) variansie faktore en opeenvolgende genetiese parameters is bepaal met behulp van enkeleienskap analises asook meervuldige-eienskap analises deur middel van die “Restricted Maximum Likelihood” prosedure (Gilmour et al., 2002). Modelle is opgestel vir elk van die gewigte deur die geskikte genetiese terme toe te voeg en te toets met behulp van “Log likelihood tests” om sodoende die onderskeie genetiese parameters te bepaal. Direkte genetiese oorerflikhede bepaal deur enkeleienskap analises vir die Simbra ras was as volg, 0.56 ± 0.08 vir BW, 0.67 ± 0.09 vir WW, 0.70 ± 0.11 vir YW en 0.10 ± 0.03 vir 600-dag gewig. Die direkte maternale genetiese oorerflikhede tydens dieselfde enkel-eienskap analise vir die onderkeie gewigte was 0.24 ± 0.07 vir BW, 0.33 ± 0.06 vir WW en 0.38 ± 0.07 vir YW. Korrelasies tussen direkt genetiese en direk maternale eienskappe was sterk negatief. ‘n Waarde van -0.75 ± 0.07 is bepaal vir BW, -0.93 ± 0.07 vir WW en -0.85 ± 0.08 vir YW. ‘n Adisionele faktor was ook ingelsuit vir WW, naamlik die permanente omgewing van die moeder, wat ‘n waarde opgelewer het van 0.04 ± 0.05. Tydens die veelvuldige-eienskap analise het die oorerflikhede merkwaardig verminder vir die betrokke gewigte en kan ook waargeneem word as die meer korrekte genetiese weergawe. Direkte genetiese oorerflikhede van 0.24 ± 0.07 vir BW, 0.33 ± 0.06 vir WW en 0.38 ± 0.07 vir YW was bepaal. Hierdie matig tot hoë parameters dui op genetiese vordering deur middel van korrekte seleksie prosedures. Genetiese- en omgewing korrelasies is ook bepaal tydens die analise en het positiewe waardes opgelewer. ‘n Genetiese korrelasie waarde van 0.18 ± 0.16 tussen BW en WW is bepaal asook ‘n waarde van 0.27 ± 0.16 tussen BW en YW en ‘n waarde van 0.52 ± 0.10 tussen WW en YW. Hierdie korrelasies dui daarop dat na-speengewigte vermeerder kan word deur te selekteer vir verhoogde WW sonder om BW dramties te vermeerder. Omgewings korrelasie waardes van 0.09 ± 0.06 tussen BW en WW, 0.07 ± 0.06 tussen BW en YW asook ‘n waarde van 0.45 ± 0.05 tussen WW en YW is gevind. Genetiese neigings is bepaal vir die onderskeie gewigte deur die gemiddelde voorspelde teelwaardes aan te teken teenoor elke jaar wat bereken was tydens die enkel-eienskap analises vir die onderskeie gewigte. Groot variasie asook negatiewe tendense vir WW en YW is ondervind van jaar tot jaar en dui daarop dat die seleksie doelwitte vir lewendige gewig nie in plek gestel is nie en is dit nodig om te her evalueer.

Thesis (MScAgric)--University Stellenbosch, 2001.
ENGLISH ABSTRACT: The aim of this study was to estimate genetic parameters as well as to evaluate the influence of some genetic factors on preweaning growth traits in a multi breed beef cattle population. These preweaning growth traits were birth weight (BW), weaning weight (WW) and average daily gain (ADG). Three aspects were addressed in this particular study; namely the Estimation of (co)variance components and genetic parameters, the effect of sire breeds and dam genotypes and the contribution of Charolais and Angus breeding levels on weaning traits in a multibreed beef cattle herd. Variance components and resulting genetic parameters of BW, WW and ADG in the population were estimated by Restricted Maximum Likelihood (REML) procedures. Four different unitrait and multitrait animal models were fitted ranging from a simple model with the animal direct effects as the only random effect to the model allowing for both genetic and permanent maternal environmental effects. The model that included directgenetic and permanent maternal environmental effects generally best described the data analysed. The simple model ignoring maternal effects most likely inflated direct heritability estimates. Direct heritability estimates were 0.11, 0.19, and 0.15 for BW, WW and ADG, respectively, fitting a multitrait model that comprised of both the genetic and maternal environmental effects. Under this comprehensive model, maternal heritabilties were low under both analyses, ranging from 0.02 to 0.10. Permanent maternal environmental effects were more important than maternal additive genetic effects for WW and ADG. Direct and maternal genetic correlations range from 0.42 to 0.44 for BW, -0.22 to -0.25 for WW and -0.17 to -0.23 for ADG, while the corresponding estimates ofunitrait analysis varied from 0.58 to 0.61 for BW, -0.43 to-0.53 for WW and -0.49 to -0.79 for ADG. The effect of Charolais and Hereford sires and dam breed genotypes on BW and WW in calves of Hereford, F I, two and three breed rotational as well as terminal crosses among the Charolais, Hereford, Angus and Bonsmara breeds were investigated. BW and WW of the Charolais sired calves were significantly (PAFRIKAANSE OPSOMMING: Die doel van die studie was om genetiese parameters in 'n meerras vleisbeeskudde te beraam, sowel as om die invloed van sekere genetiese faktore te evalueer. Die voorspeense groei-eienskappe het geboortegewig (BW), speengewig (WW) en gemiddelde daaglikse toename (ADG) ingesluit. Drie aspekte is in dié betrokke studie ondersoek, naamlik; die beraming van (ko )variansiekomponente en genetiese parameters, die invloed van ras van vader en moedergenotipe en die invloed van Charolais en Angus bydrae op speeneienskappe in 'n meerras vleisbeeskudde. Variansiekomponente en afgeleide genetiese parameters vir BW, WW en ADG in die kudde is met behulp van die Beperkte Maksimum Waarskynlikheidsprosedure (REML) beraam. Vier verskillende enkel- en meereienskapmodelle is gepas, wat vanaf 'n eenvoudige model wat slegs die direkte effek as enigste toevallige effek, tot dié model waarin beide die genetiese en permanente mateme omgewingseffekte ingesluit is. Die model wat beide die direkte en permanente mateme effekte ingesluit het, het die data die beste gepas. Die eenvoudige model, wat die mateme effekte nie insluit nie, het in alle waarskynlikheid die direkte oorerflikhede oorberaam. Die direkte oorerflikheidsberamingsas onderskeidlik 0.11, 0.19 en 0.15 vir BW, WW en ADG met dié meereienskapmodel wat beide genetiese en mateme effekte ingesluit het. Met die omvattende model was die mateme oorerflikhede laag en het van 0.02 tot 0.10 gewissel. Die permanente mateme omgewingseffekte was belangriker as die direkte mateme effekte vir WW en ADG. Die genetiese korrelasies tussen direkte en mateme effekte het vir BW tussen 0.42 en 0.44, vir WW tussen -0.22 en -0.25 en vir ADG tussen -0.49 en -0.79 gewissel. Die invloed van Charolais en Hereford bulle en moederrasgenotipes op BW en WW van Hereford, F 1, twee- en drieras rotasie sowel as terminale kruisings tussen die Charolais, Hereford, Angus en Bonsmara is ondersoek. BW en WW van kalwers van Charolais bulle was betekenisvol (P