The selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals by increasing accuracy of prediction and reducing generation interval, especially for difficult to measure traits, such as feed efficiency. Feed efficiency is the most important trait in animal production due to its impacts on cost of production and environmental factors. Many metrics measure the feed efficiency, such as ratio of gain to feed (FER), the ratio of feed to gain (FCR) and residual feed intake (RFI). Nevertheless, in ovine, no study with the aim of understand the genetic variants or the accuracy of genomic estimated breeding value (GEBV) for feed efficiency traits was published yet. Moreover, before to apply the genomic information, it is necessary to understand and characterized the population structure, for instance, by linkage disequilibrium (LD). Both genome-wide association studies (GWAS) and genomic selection (GS) leverage LD between marker and causal mutation. Based on the above considerations, the aim of this study was to map LD in ovine, characterized by Brazilian Santa Inês sheep; to search genetic variants for feed efficiency traits (FER, FCR and RFI) through GWAS; and to verify the accuracy of GEBV for RFI. In total, 396 samples (animals) of Longissimus dorsi muscle were collect. A high-density panel of SNP (Illumina High-Density Ovine SNP BeadChip®) comprising 54,241 SNPs was used to obtain the genotyping data. The phenotype data was comprised of 387 animals. The average LD between adjacent markers for two LD metrics, r² and |D\'|, were 0.166 and 0.617, respectively. The degree of LD estimated was lower than reported in other species and it was characterized by short haplotype blocks. Consequently, for genomic analyses, high-density panels of marker are recommended. Many markers were associated to feed efficiency traits in GWAS, mainly to RFI trait. Few candidate genes were reported in this study, highlighting NRF-1 (nuclear respiratory factor 1), which controls mitochondrial biosynthesis, the most important process responsible by a great fraction of the produced energy. Finally, we verified the accuracy of GEBV for RFI using few Bayesian regression models, and we found low accuracy, ranging from 0.033 (BayesB with π=0.9912) to 0.036 (BayesA), which might be explained by the low relationship among animals and small training population. / A seleção com base nos valores genéticos genômicos preditos pode aumentar substancialmente a taxa de ganho genético em animais por meio do aumento da acurácia de predição e redução do intervalo de gerações, especialmente para características de difícil e/ou onerosa mensuração, como eficiência alimentar. A eficiência alimentar é uma das características mais importantes na produção animal devido principalmente aos seus impactos econômicos e ambientais. Muitas métricas representam a eficiência alimentar, por exemplo: a relação do ganho de peso e consumo alimentar (EA), a proporção do consumo alimentar e ganho de peso (CA) e o consumo alimentar residual (CAR). Em ovinos, nenhum estudo com o objetivo de buscar variantes genéticas ou verificar a acurácia do valor genético genômico estimado para eficiência alimentar foi publicado. Adicionalmente, antes de aplicar a informação genômica, é necessário compreender e caracterizar a estrutura da população, como por meio do desequilíbrio de ligação (LD). O estudo de associação genômica (GWAS) e seleção genômica (GS) consideram o LD entre marcador e a mutação causal. Com base nas considerações acima, o objetivo deste estudo foi mapear o LD em ovinos, caracterizado pela raça ovina Santa Inês; localizar variantes genéticas para as características de eficiência alimentar (EA, CA e CAR) utilizando a abordagem GWAS; e verificar a acurácia da estimação dos valores genéticos genômico para o CAR. No total, foram coletadas 396 amostras (animais) do músculo Longissimus dorsi, para posterior genotipagem utilizando o painel de alta densidade (Illumina High-Density Ovine SNP BeadChip®), compreendendo 54.241 SNPs. O banco fenotípico é composto por 387 animais. O LD médio entre marcadores adjacentes para duas métricas de LD, r² e |D\'|, foram 0,166 e 0,617, respectivamente. O grau de LD estimado foi menor que o relatado em outras espécies e foi caracterizado por blocos de haplótipos curtos. Consequentemente, para as análises genômicas são recomendados painéis de marcadores de alta densidade. No GWAS, foram encontrados muitos marcadores associados aos fenótipos, em especial, à característica CAR. Alguns genes candidatos foram relatados neste estudo, destacando-se o NRF-1 (fator respiratório nuclear 1), que controla a biossíntese mitocondrial, o processo mais importante responsável por grande parte da produção de energia. Finalmente, verificamos a acurácia do valor genético genômico estimado para o CAR usando modelos de regressão Bayesiana, e encontramos baixos valores para acurácia (0,033 a 0,036) o que pode ser explicado pelo baixo grau de relacionamento entre os indivíduos e tamanho reduzido da população de treinamento.

O consumo alimentar residual (CAR) é uma medida de eficiência alimentar independente do crescimento e do peso à maturidade. O melhoramento genético para CAR pode reduzir o custo de alimentação de bovinos, porém uma melhor compreensão dos processos biológicos relacionados ao CAR é necessária. Além disso, associações entre CAR e qualidade de carcaça têm sido pouco investigadas em raças zebuínas. Desta forma, o objetivo com este estudo foi avaliar o metabolismo protéico, a composição corporal, as características de carcaça e a qualidade de carne em bovinos zebuínos com alto e baixo CAR. Adicionalmente, foi testada a hipótese da existência de interações entre CAR e peso vivo ao abate para características de carcaça e composição corporal. Setenta e dois novilhos da raça Nelore (16 a 21 meses de idade, 334±19 kg de peso vivo inicial [PV]) foram mantidos em confinamento e alimentados ad libitum (74,5% NDT; 14,3%PB) por 70 dias. O consumo de matéria seca (CMS) e o ganho médio de peso (GMD) diários foram medidos individualmente. Os 12 novilhos com maior CAR e os 12 com menor CAR foram classificados como grupos de alto e baixo CAR, respectivamente (fase de seleção) e foram alimentados até quando alcançassem pesos vivo ao abate de 460, 490, 520 e 550 kg (fase de terminação). Antes do abate, foi realizada colheita total de urina para a determinação da excreção diária de 3-metil-histidina e da taxa fracional de degradação miofibrilar. A composição química corporal foi estimada pelo método de diluição isotópica utilizando óxido de deutério. A maciez objetiva da carne e a atividade de proteases cálcio-dependentes foram determinadas no músculo Longissimus. Na fase de seleção, novilhos com baixo CAR tiveram menores CMS, conversão alimentar, CAR e ganho de gordura sobre a garupa que novilhos com alto CAR, mas nenhuma diferença foi observada no GMD, no PV final, na gordura subcutânea e na área do Longissimus. Na fase de terminação, nenhuma interação foi observada entre CAR e PV ao abate. Não houve diferenças entre animais mais e menos eficientes quanto ao peso e rendimento de carcaça, gordura renal, pélvica e inguinal, vísceras, área de Longissimus, gordura subcutânea, marmorização, aparas e porção comestível. Novilhos com baixo CAR apresentaram menos gordura sobre o trato gastrintestinal (TGI) que novilhos com alto CAR. Não foram observadas diferenças quanto ao índice de fragmentação miofibrilar, força de cisalhamento e atividade do sistema calpaína. As taxas fracionais de degradação, síntese e acréscimo protéico foram similares entre os grupos de CAR. Novilhos Nelore com baixo CAR depositaram menos gordura subcutânea na carcaça em pesos vivos entre 340 e 460 kg. Em pesos mais elevados (460-550 kg), as características de carcaça e a composição corporal não foram influenciadas pelo CAR, mas indivíduos menos eficientes apresentaram maior massa de gordura visceral. A seleção de bovinos zebuínos para baixo CAR pode diminuir a ingestão de alimentos e melhorar sua eficiência alimentar, sem comprometer a qualidade da carne. / Residual feed intake (RFI) is a feed efficiency trait that is independent of growth rate and mature weight. Genetic improvement in RFI may reduce the costs of feeding cattle, however a better understanding of biological processes underlying variation in RFI is necessary. Moreover, associations between RFI and carcass quality have been poorly investigated in Zebu breeds. Therefore, this study aimed to evaluate protein metabolism, body composition, carcass traits and meat quality in high- and low-RFI Zebu cattle. In addition, the hypothesis that there are interactions between RFI and harvest body weight for carcass traits and body composition was investigated. Seventy-two Nellore steers (16 to 21 month-old, 334±19 kg initial body weight [BW]) were fed a finishing ration (74.5% TDN, 14.3%CP) on an ad libitum basis, for 70 days. Daily dry matter intake (DMI) and body weight gain (ADG) were measured individually. The 12 lowest and the 12 highest RFI steers were classed as low- and high-RFI groups, respectively (selection phase), and were fed until reaching slaughter BW of 460, 490, 520 and 550 kg (finishing phase). Before slaughter, total urine was collected for determination of daily 3-methylhistidine excretion and myofibrillar protein breakdown rates. Body chemical composition was estimated by the isotope dilution method using deuterium oxide. Objective tenderness and Ca+2-dependent protease activities were measured on Longissimus muscle. In the selection phase, low-RFI steers had lower DMI, feed:gain, RFI, and ultrasound rump fat thickness gain than high-RFI cattle, but no differences were observed for ADG, final BW, ultrasound fat thickness and Longissimus area. In the finishing phase, no interactions were observed between RFI and slaughter BW. No differences between more and less efficient cattle were observed for hot carcass weight, dressing percentage, kidney, pelvic and inguinal fat, visceral mass, Longissimus area, backfat thickness, marbling score, trimmings and retail product yield. Low-RFI steers presented less fat on the gastrointestinal tract (GIT) than high-RFI cattle. No differences were observed for myofibrillar fragmentation index, Warner-Bratzler shear force and calpain system activities. Fractional rates of protein degradation, synthesis and accretion were similar between high- and low-RFI cattle. Low-RFI Nellore steers may store less subcutaneous carcass fat at body weights ranging from 340 and 460 kg. At higher body weights (460-550 kg), carcass traits and body composition are not affected by RFI, but least efficient cattle present greater visceral fat mass. Breeding zebu cattle for improved RFI may decrease feed intake and improve feed efficiency without compromising meat quality.

Das allgemeine Ziel der vorliegenden Doktorarbeit war es, den Zusammenhang von Fressverhalten, Futteraufnahme, Milchproduktion und Stoffwechselkrankheiten bei Milchkühen in der Frühlaktation zu untersuchen. Dafür wurden Daten von 70 laktierenden Deutschen Holstein-Friesischen Milchkühen (1. -7. Laktation) gesammelt. Das Fressverhalten wurde mittels eines elektronischen Fütterungssystems überwacht, welches die elektronische Kennung jeder einzelnen Kuh beinhaltete. Während der ersten Studie dieser Arbeit basierte die Analyse des Fressverhaltens der Milchkühe auf jedem Einzelbesuch; dabei war ein Besuch als die Zeit definiert, in der eine einzelne Kuh mit ihrem Kopf im Trog verweilte, unabhängig davon, wie die Kuh diese Zeit verbrachte. Während der zweiten und dritten Studie wurden die Besuche in Mahlzeiten unterteilt, die auf einem Mahlzeitenkriterium basieren, welches wie folgt berechnet wurde: Eine Mischung aus zwei normalen Verteilungen wurde an die Verteilungen der Intervallängen zwischen den Besuchen, die mittels des natürlichen Logarithmuses umgerechnet wurden waren, angepasst. Innerhalb dieser Studien wurde der Einfluss der Laktation, des Laktationsstatus und des Milchleistungsniveaus auf das Fressverhalten und die Futteraufnahme untersucht. Die letzte Studie bestimmte die Auswirkungen von Stoffwechselkrankheiten auf das Fressverhalten, die Futteraufnahme und die Milchproduktion. Die Ergebnisse deuten darauf hin, dass die Mahlzeit die wichtigere Einheit als der Einzelbesuch ist, um das Fressverhalten zu beschreiben. Laktationsnummer, Laktationsstatus und Milchleistungsniveau waren entscheidend für die Charakteristika des Fressverhaltens und die Futteraufnahme. Die höher Korrelation zwischen Fressverhalten, z.B. Dauer und Umfang einer Mahlzeit, verweisen darauf, dass das Messen der Fresszeit für das Berechnen der Futteraufnahme genutzt werden kann. Stoffwechselkrankheiten hatten einen entscheidenen Einfluss auf das Fressverhalten, die Futteraufnahme und die Milchproduktion. Die Beobachtung der Charakteristika des Fressverhaltens könnte bei der Früherkennung des bei Kühen bestehenden erhöhten Risikos an Stoffwechselstörungen hilfreich sein. / The overall objective of this PhD thesis was to investigate the relationships between feeding behaviour, feed intake, milk production, and metabolic-related production diseases of dairy cows during early lactation. Data from 70 lactating German Holstein Friesian dairy cows (parity 1 to 7) were collected. The feeding behaviour monitoring was conducted by using an electronic feeding system, which was equipped with an electronic identification of each individual cow. In the first study of this dissertation, the feeding behaviour of dairy cows was analysed based on the individual visits, with a visit being defined as the time spent by an individual cow with her head in one of the troughs regardless of how the cow spent that time. In the second and third studies, the visits were clustered in meals based on a “meal criterion”, which was calculated by fitting a mixture of two normal distributions to the distributions of the natural logarithm (LN)-transformed lengths of the interval between visits. In these studies, the effects of parity, stage of lactation, and milk yield level on feeding behaviour and feed intake were investigated. The final study determined the effects of metabolic-related production diseases on feeding behaviour, feed intake, and milk production. The results suggested that the meal is the more relevant unit than the individual visit for describing feeding behaviour. Parity, stage of lactation, and milk yield level had significant effects on feeding behaviour characteristics and feed intake. The high correlation between feeding behaviour such as meal duration and feed intake (meal size) suggests that measuring the time spent eating could be used to estimate the feed intake. Metabolic-related production diseases had significant effects on feeding behaviour, feed intake, and milk production. The monitoring of feeding behaviour characteristics might be helpful to detect the cows’ risk for metabolic-related production diseases at an early stage.

Esse trabalho foi desenvolvido para avaliar a relação entre diferentes medidas de eficiência utilizadas na bovinocultura de corte e as características de desempenho, carcaça e termografia infravermelho (TIV) em bovinos Nelore confinados. Foram utilizados 111 bovinos Nelore, machos não-castrados contemporâneos, com idade aproximada de 16±2 meses, peso corporal médio de 420±55 kg. Os animais foram confinados por 91 dias, sendo 21 dias de adaptação às instalações e à dieta. A dieta foi a mesma para todos os animais e composta por 73% de concentrado e 27% de volumoso. O consumo de matéria seca (CMS) foi avaliado diariamente, enquanto o peso vivo, medidas de ultrassom para avaliação de características de carcaça e imagens de TIV foram realizadas a cada 28 dias até o dia 70. A partir dos dados de CMS foram calculados o consumo alimentar residual (CAR), ganho de peso residual (GPR), consumo e ganho residual (CGR). Após a obtenção dos dados foram realizadas análises de associação (correlação e regressão) visando à identificação de possíveis relações entre as diferentes características com as medidas de eficiência. Não houve correlação entre o GMD com o CAR (r=0,001), e com o CGR (r= 0,114), enquanto o GPR apresentou correlação com o GMD (r= 0,588). O CMS foi correlacionado com o CAR (r= 0,612) e com o CGR (r= -0,532) e não houve correlação com o GPR (r= -0,002). Não houve correlação entre as medidas de eficiência com as características de peso vivo inicial (PVI) e peso vivo final (PV70). Dentre as características de carcaça avaliadas ao abate, apenas o GPR apresentou correlação com a gordura renal pélvica e inguinal (GRPIkg), trato gastrintestinal (TGIkg) e peso de corpo vazio (PCVZkg) na ordem de (r= 0,240), (r= 0,226) e (r= 0,210), respectivamente. Entre as medidas de carcaça avaliadas por ultrassom, apenas a espessura de gordura subcutânea (EGS) final apresentou correlação com o CAR (r= 0,348), GPR (r= -0,188) e CGR (r= -0,340), enquanto a espessura de gordura da picanha (EGP) final apresentou correlação apenas com o CAR (r= 0,233) e CGR (r= -0,200). Houveram correlações entre o ganho de EGS e o CAR (r= 0,371) e CGR (r= 0,345), porém o ganho de EGP se correlacionou apenas com o CAR (r= 0,202). Não foram observadas correlações entre as medidas de eficiência e TIV, porém, esses resultados podem ter sido influenciados pelos fatores ambientais. A AOL não apresentou correlação com nenhuma das medidas de eficiência avaliadas. Dessa forma conclui-se que, o CAR é a medida que mais se aplica n seleção de animais de menor CMS, sem prejuízos as características de desempenho. Adicionalmente, o CAR e CGR selecionam animais mais eficientes em termos de menor consumo, enquanto que o GPR seleciona animais de maior GMD. / The aim of the present study was to evaluate the relationship between different efficiency indexes used in beef cattle and performance, carcass traits and thermography in Nellore cattle at the feedlot system. A total of 111 Nellore male, with around 16±2 months age and 420±55 kg of body weight, were used. The animals were confined for 91 days, with 21 days for adaptation to the facilities and diet. The diet was the same for all animals, and composed by 73% of concentrate and 27% of roughage. Dry matter intake (DMI) was evaluated daily, and performance, ultrasound measurements and infrared thermography images were performed every 28 days until day 70. From the DMI measurements, residual feed intake (RFI), residual weight gain (RWG), residual intake and body weight gain (RIG) were calculated. From the data obtained, association analysis (correlation and regression) were performed to identify the possibilities relationships between the different characteristics with the efficiency measures. The ADG showed no correlation with RFI (r= 0.001) and RIG (r= 0.114); however, the RWG was correlated with ADG (r= 0.588). DMI was correlated with RFI (r= 0.612) and RIG (r= -0.532) and there was no correlation with RWG (r= -0.002) There was no correlation between efficiency measures with initial body weight (IBW) and final body weight (BW70). For carcass traits, evaluated at slaughter, only the RWG showed correlation with pelvic renal and inguinal fat (PRIFkg), gastrintestinal tract (GITkg) and empty body weight (EBWkg) in order of the (r= 0.240), (r= 0.226) and (r= 0.210), respectively. For carcass measurements evaluated by ultrasound, the final backfat thickness (BFT) showed correlation with RFI (r= 0.348), RWG (r= -0.188) and RIG (r= -0.340), while final subcutaneous fat thickness on the Biceps femoris muscle (BFTP8) showed a correlation with RFI (r= 0.233) and RIG (r= -0.220). In addition, BFT gain has been also correlated with RFI (r= 0.371) and RIG (r= 0.345); however, the BFTP8 gain only showed correlation with the RFI (r=0.202). There was no correlation between efficiency measures and the infrared thermography (IRT). The rib eye area (REA) showed no correlation with any the efficiency measures evaluated. In conclusion, the RFI is the measure that most applies in the selection of animals of smaller DMI, without damage to the performance traits. In addition, the RFI and RIG can promoter the selection of more efficient animals by lower consumer, whereas the RWG selected great ADG animals.

A seleção de bovinos de corte para eficiência alimentar (EA) é bastante vantajosa não só do ponto de vista produtivo e econômico como também por ajudar a diminuir o impacto ambiental da produção pecuária. Por ser uma característica multifatorial e de mensuração onerosa, objetivou-se com esse trabalho, a partir da expressão gênica global hepática de animais com alta eficiência alimentar (AEA) e baixa eficiência alimentar (BEA), identificar novos genes, funções biológicas e genes reguladores associados a esse fenótipo. Para isso, 98 bovinos Nelore foram avaliados quanto ao desempenho em confinamento, medidas de EA, ultrassonografia de carcaça, bioquímica sérica, biometria, rendimento de carcaça, maciez de carne e avaliação de líquido ruminal. Além disso, 8 animais de AEA e 8 animais de BEA, selecionados pela medida de consumo e ganho residual ao final do confinamento, tiveram dados de perfil transcriptômico hepático analisados por 3 abordagens: expressão gênica diferencial, co-expressão e co-expressão diferencial. Foi observado que os grupos de AEA e BEA apresentaram desempenho igual quanto ao peso inicial e final, ganho de peso, rendimento de carcaça e área de olho de lombo. Por outro lado, os animais de BEA tiveram maior consumo de alimentos e maior deposição de gordura subcutânea e visceral. Além disso, os animais de BEA apresentaram níveis elevados de colesterol e de GGT e a análise de perfil transcriptômico mostrou estar relacionada à resposta imunológica, inflamação e metabolismo de lipídeos. Baseado nesses resultados e em pesquisas em humanos criou-se a hipótese de que os animais de BEA são mais susceptíveis a infecção bacteriana no fígado em resposta à mudança da dieta a pasto para a dieta de confinamento. / The selection of beef cattle to feed efficiency (FE) traits is very important not only from the productive and economic perspective but also for helping to reduce the environmental impact of livestock production. Being a multifactorial and expensive to measurement trait, the aim of this work was to analyze the liver global gene expression profile of animals with high feed efficiency (HFE) and low feed efficiency (LFE), to identify new genes, biological functions and regulatory genes associated to this phenotype. For this purpose, 98 Nellore cattle were evaluated regarding feedlot performance, FE measures, carcass ultrasound, serum biochemistry, biometric measures, carcass evaluation, meat tenderness and evaluation of ruminal fluid. In addition, 8 animals of HFE and 8 animals of LFE, selected by the measure of residual intake and body weight gain at the end of feeding trial, had liver transcriptomic profile data analyzed by three approaches: differential gene expression, co-expression and differential co-expression. It was observed that HFE and LFE groups showed equal performance for initial and final weight, weight gain, carcass yield and rib eye area. On the other hand, the animals of LFE had higher feed intake and increased deposition of subcutaneous and visceral fat. In addition, animals of LFE showed higher levels of cholesterol and GGT and transcriptomic profile analysis showed to be related to immune response, inflammation and lipid metabolism. Based on these results and research in humans we created the hypothesis that the LFE animals are more susceptible to bacterial infection in the liver in response to the change of pasture diet to feedlot diet.

A alimentação é um dos custos mais relevantes da produção de bovinos de corte e melhorar a eficiência na utilização de nutrientes é essencial para a viabilidade da produção, dado o atual cenário de crescente demanda por proteína animal e mercado altamente competitivo. Nesse contexto, a proteômica surge como uma importante ferramenta na busca por alternativas que aumentem a eficiência alimentar (EA) de bovinos de corte. Assim, o objetivo deste trabalho é caracterizar o proteoma hepático de bovinos Nelore classificados quanto à EA. Noventa e oito animais foram avaliados em projeto anterior e seis indivíduos de baixa (BEA) e alta eficiência (AEA) tiveram amostras de fígado coletadas no abate, congeladas em Nitrogênio líquido e armazenadas em freezer à -80 ºC. Após a extração e precipitação das proteínas, as amostras foram processadas por duas abordagens distintas: digeridas com tripsina em solução e analisadas em cromatógrafo líquido de alta eficiência acoplado ao espectrômetro de massas (LC-MS/MS); e previamente separadas em gel para posterior digestão e análise (GeLC-MS/MS). Os dados adquiridos por LC-MS/MS foram analisados com o programa MaxQuant contra os bancos de Bos taurus e Bos indicus do Uniprot para identificação das proteínas, e os resultados analisados com o programa Perseus. Os dados obtidos por GeLC-MS/MS foram analisados com os programas Mascot Distiller e X! Tandem e validados no Scaffold Q+ contra o banco Bos taurus do Uniprot e os resultados analisados com os programas Scaffold Q+ e Perseus. Para abordagem LC-MS/MS, 376 proteínas foram quantificadas e submetidas à análise de abundância diferencial e construção de redes de co-expressão pelo WGCNA, identificando 42 proteínas diferencialmente abundantes (PDAs, p < 0,05) e três módulos significativamente associados à EA. Pela abordagem GeLC-MS/MS foram quantificadas 102 proteínas, das quais cinco foram PDAs (p-valor < 0,05). Três PDAs foram comuns às duas abordagens proteômicas. As proteínas associadas negativamente à EA foram principalmente relacionadas à síntese lipídica, degradação de ácidos graxos, enzimas do sistema do citocromo P450 e processos oxidativos. Por outro lado, as proteínas positivamente relacionadas à EA, foram principalmente envolvidas em processamento e enovelamento de proteínas, além de proteínas atuantes na manutenção da integridade e restauração do citoesqueleto celular. Em ambos os grupos também foram identificadas proteínas que atuam no sistema imunológico e resposta inflamatória. Estes resultados comprovam experimentos anteriores do grupo e demonstram a existência de diferença entre os proteomas do fígado de animais eficientes e ineficientes. / Feeding is one of the most relevant cost of beef cattle production and improving nutrient utilization efficiency is essential for the viability of production, given the current scenario of increasing demand for animal protein and highly competitive market. In this context, proteomics appears as an important tool in the search for alternatives that increase the feed efficiency (FE) of beef cattle. Thus, the aim of this work is to characterize the hepatic proteome of beef cattle selected for divergent FE. Ninety-eight animals were evaluated in a previous project, and six individuals with low feed efficiency (LFE) and six with high feed efficiency (HFE) had liver samples collected at slaughter, frozen in liquid Nitrogen and stored in a freezer at -80 °C. After protein extraction and precipitation, the samples were processed by two different approaches: digested with trypsin in solution and analyzed in a high efficiency liquid chromatograph coupled to the mass spectrometer (LC-MS/MS); and previously separated in gel for further digestion and analysis (GeLC-MS/MS). Data acquired by LC-MS/MS were analyzed with MaxQuant software against the Bos taurus and Bos indicus Uniprot databases for proteins identification and the results analyzed with Perseus software. The data obtained by GeLC-MS/MS were analyzed with the softwares Mascot Distiller and X! Tandem and validated in the Scaffold Q+, against Bos taurus Uniprot database and results analyzed with the softwares Scaffold Q+ and Perseus. For the LC-MS/MS approach, 376 proteins were quantified and submitted to differential abundance analysis and co-expression networks by WGCNA, identifying 42 differentially abundant proteins (DAPs, p < 0.05) and three modules significantly associated with FE. For the GeLC-MS/MS approach, 102 proteins were quantified, of which five were DAPs (p-value < 0.05). Three DAPs were common to both proteomics approaches. Proteins negatively associated with FE were mainly related to lipid synthesis, degradation of fatty acids, cytochrome P450 system enzymes and oxidative processes. On the other hand, proteins positively related to FE were mainly involved in protein processing and folding, maintenance of the integrity and restoration of the cellular cytoskeleton. In both groups were also identified proteins that play a role on the immune system and inflammatory response. These results prove previous experiments of the group and demonstrate the existence of difference between liver proteomes of efficient and inefficient animals.

A alimentação é um dos custos mais relevantes da produção de bovinos de corte e melhorar a eficiência na utilização de nutrientes é essencial para a viabilidade da produção, dado o atual cenário de crescente demanda por proteína animal e mercado altamente competitivo. Nesse contexto, a proteômica surge como uma importante ferramenta na busca por alternativas que aumentem a eficiência alimentar (EA) de bovinos de corte. Assim, o objetivo deste trabalho é caracterizar o proteoma hepático de bovinos Nelore classificados quanto à EA. Noventa e oito animais foram avaliados em projeto anterior e seis indivíduos de baixa (BEA) e alta eficiência (AEA) tiveram amostras de fígado coletadas no abate, congeladas em Nitrogênio líquido e armazenadas em freezer à -80 ºC. Após a extração e precipitação das proteínas, as amostras foram processadas por duas abordagens distintas: digeridas com tripsina em solução e analisadas em cromatógrafo líquido de alta eficiência acoplado ao espectrômetro de massas (LC-MS/MS); e previamente separadas em gel para posterior digestão e análise (GeLC-MS/MS). Os dados adquiridos por LC-MS/MS foram analisados com o programa MaxQuant contra os bancos de Bos taurus e Bos indicus do Uniprot para identificação das proteínas, e os resultados analisados com o programa Perseus. Os dados obtidos por GeLC-MS/MS foram analisados com os programas Mascot Distiller e X! Tandem e validados no Scaffold Q+ contra o banco Bos taurus do Uniprot e os resultados analisados com os programas Scaffold Q+ e Perseus. Para abordagem LC-MS/MS, 376 proteínas foram quantificadas e submetidas à análise de abundância diferencial e construção de redes de co-expressão pelo WGCNA, identificando 42 proteínas diferencialmente abundantes (PDAs, p < 0,05) e três módulos significativamente associados à EA. Pela abordagem GeLC-MS/MS foram quantificadas 102 proteínas, das quais cinco foram PDAs (p-valor < 0,05). Três PDAs foram comuns às duas abordagens proteômicas. As proteínas associadas negativamente à EA foram principalmente relacionadas à síntese lipídica, degradação de ácidos graxos, enzimas do sistema do citocromo P450 e processos oxidativos. Por outro lado, as proteínas positivamente relacionadas à EA, foram principalmente envolvidas em processamento e enovelamento de proteínas, além de proteínas atuantes na manutenção da integridade e restauração do citoesqueleto celular. Em ambos os grupos também foram identificadas proteínas que atuam no sistema imunológico e resposta inflamatória. Estes resultados comprovam experimentos anteriores do grupo e demonstram a existência de diferença entre os proteomas do fígado de animais eficientes e ineficientes. / Feeding is one of the most relevant cost of beef cattle production and improving nutrient utilization efficiency is essential for the viability of production, given the current scenario of increasing demand for animal protein and highly competitive market. In this context, proteomics appears as an important tool in the search for alternatives that increase the feed efficiency (FE) of beef cattle. Thus, the aim of this work is to characterize the hepatic proteome of beef cattle selected for divergent FE. Ninety-eight animals were evaluated in a previous project, and six individuals with low feed efficiency (LFE) and six with high feed efficiency (HFE) had liver samples collected at slaughter, frozen in liquid Nitrogen and stored in a freezer at -80 °C. After protein extraction and precipitation, the samples were processed by two different approaches: digested with trypsin in solution and analyzed in a high efficiency liquid chromatograph coupled to the mass spectrometer (LC-MS/MS); and previously separated in gel for further digestion and analysis (GeLC-MS/MS). Data acquired by LC-MS/MS were analyzed with MaxQuant software against the Bos taurus and Bos indicus Uniprot databases for proteins identification and the results analyzed with Perseus software. The data obtained by GeLC-MS/MS were analyzed with the softwares Mascot Distiller and X! Tandem and validated in the Scaffold Q+, against Bos taurus Uniprot database and results analyzed with the softwares Scaffold Q+ and Perseus. For the LC-MS/MS approach, 376 proteins were quantified and submitted to differential abundance analysis and co-expression networks by WGCNA, identifying 42 differentially abundant proteins (DAPs, p < 0.05) and three modules significantly associated with FE. For the GeLC-MS/MS approach, 102 proteins were quantified, of which five were DAPs (p-value < 0.05). Three DAPs were common to both proteomics approaches. Proteins negatively associated with FE were mainly related to lipid synthesis, degradation of fatty acids, cytochrome P450 system enzymes and oxidative processes. On the other hand, proteins positively related to FE were mainly involved in protein processing and folding, maintenance of the integrity and restoration of the cellular cytoskeleton. In both groups were also identified proteins that play a role on the immune system and inflammatory response. These results prove previous experiments of the group and demonstrate the existence of difference between liver proteomes of efficient and inefficient animals.

Esse trabalho foi desenvolvido para avaliar a relação entre diferentes medidas de eficiência utilizadas na bovinocultura de corte e as características de desempenho, carcaça e termografia infravermelho (TIV) em bovinos Nelore confinados. Foram utilizados 111 bovinos Nelore, machos não-castrados contemporâneos, com idade aproximada de 16±2 meses, peso corporal médio de 420±55 kg. Os animais foram confinados por 91 dias, sendo 21 dias de adaptação às instalações e à dieta. A dieta foi a mesma para todos os animais e composta por 73% de concentrado e 27% de volumoso. O consumo de matéria seca (CMS) foi avaliado diariamente, enquanto o peso vivo, medidas de ultrassom para avaliação de características de carcaça e imagens de TIV foram realizadas a cada 28 dias até o dia 70. A partir dos dados de CMS foram calculados o consumo alimentar residual (CAR), ganho de peso residual (GPR), consumo e ganho residual (CGR). Após a obtenção dos dados foram realizadas análises de associação (correlação e regressão) visando à identificação de possíveis relações entre as diferentes características com as medidas de eficiência. Não houve correlação entre o GMD com o CAR (r=0,001), e com o CGR (r= 0,114), enquanto o GPR apresentou correlação com o GMD (r= 0,588). O CMS foi correlacionado com o CAR (r= 0,612) e com o CGR (r= -0,532) e não houve correlação com o GPR (r= -0,002). Não houve correlação entre as medidas de eficiência com as características de peso vivo inicial (PVI) e peso vivo final (PV70). Dentre as características de carcaça avaliadas ao abate, apenas o GPR apresentou correlação com a gordura renal pélvica e inguinal (GRPIkg), trato gastrintestinal (TGIkg) e peso de corpo vazio (PCVZkg) na ordem de (r= 0,240), (r= 0,226) e (r= 0,210), respectivamente. Entre as medidas de carcaça avaliadas por ultrassom, apenas a espessura de gordura subcutânea (EGS) final apresentou correlação com o CAR (r= 0,348), GPR (r= -0,188) e CGR (r= -0,340), enquanto a espessura de gordura da picanha (EGP) final apresentou correlação apenas com o CAR (r= 0,233) e CGR (r= -0,200). Houveram correlações entre o ganho de EGS e o CAR (r= 0,371) e CGR (r= 0,345), porém o ganho de EGP se correlacionou apenas com o CAR (r= 0,202). Não foram observadas correlações entre as medidas de eficiência e TIV, porém, esses resultados podem ter sido influenciados pelos fatores ambientais. A AOL não apresentou correlação com nenhuma das medidas de eficiência avaliadas. Dessa forma conclui-se que, o CAR é a medida que mais se aplica n seleção de animais de menor CMS, sem prejuízos as características de desempenho. Adicionalmente, o CAR e CGR selecionam animais mais eficientes em termos de menor consumo, enquanto que o GPR seleciona animais de maior GMD. / The aim of the present study was to evaluate the relationship between different efficiency indexes used in beef cattle and performance, carcass traits and thermography in Nellore cattle at the feedlot system. A total of 111 Nellore male, with around 16±2 months age and 420±55 kg of body weight, were used. The animals were confined for 91 days, with 21 days for adaptation to the facilities and diet. The diet was the same for all animals, and composed by 73% of concentrate and 27% of roughage. Dry matter intake (DMI) was evaluated daily, and performance, ultrasound measurements and infrared thermography images were performed every 28 days until day 70. From the DMI measurements, residual feed intake (RFI), residual weight gain (RWG), residual intake and body weight gain (RIG) were calculated. From the data obtained, association analysis (correlation and regression) were performed to identify the possibilities relationships between the different characteristics with the efficiency measures. The ADG showed no correlation with RFI (r= 0.001) and RIG (r= 0.114); however, the RWG was correlated with ADG (r= 0.588). DMI was correlated with RFI (r= 0.612) and RIG (r= -0.532) and there was no correlation with RWG (r= -0.002) There was no correlation between efficiency measures with initial body weight (IBW) and final body weight (BW70). For carcass traits, evaluated at slaughter, only the RWG showed correlation with pelvic renal and inguinal fat (PRIFkg), gastrintestinal tract (GITkg) and empty body weight (EBWkg) in order of the (r= 0.240), (r= 0.226) and (r= 0.210), respectively. For carcass measurements evaluated by ultrasound, the final backfat thickness (BFT) showed correlation with RFI (r= 0.348), RWG (r= -0.188) and RIG (r= -0.340), while final subcutaneous fat thickness on the Biceps femoris muscle (BFTP8) showed a correlation with RFI (r= 0.233) and RIG (r= -0.220). In addition, BFT gain has been also correlated with RFI (r= 0.371) and RIG (r= 0.345); however, the BFTP8 gain only showed correlation with the RFI (r=0.202). There was no correlation between efficiency measures and the infrared thermography (IRT). The rib eye area (REA) showed no correlation with any the efficiency measures evaluated. In conclusion, the RFI is the measure that most applies in the selection of animals of smaller DMI, without damage to the performance traits. In addition, the RFI and RIG can promoter the selection of more efficient animals by lower consumer, whereas the RWG selected great ADG animals.

Thesis (MSc. (Animal Production)) -- University of Limpopo, 2018 / A study was done to determine the effect of Acacia (A.) karroo, A. tortilis or A. nilotica leaf meal inclusion in a diet on methane emission and productivity of yearling male Boer goats fed a basal diet of Avena sativa hay. The first part of the study was conducted to determine and compare nutrient contents and tannin levels of A. karroo, A. tortilis and A. nilotica leaf meals and Avena sativa hay in a completely randomised design. The diets means were compared using Fisher’s least significant difference at the 5 % level of probability. The three Acacia species had higher (P<0.05) crude protein contents compared to Avena sativa hay, ranging from 12.42 to 14.49 %. No tannins were detected in Avena sativa hay. Among Acacia species, A. nilotica leaves had higher (P<0.05) total phenolic and total tannin contents than A. karroo and A. tortilis leaves, the latter being similar (P>0.05). All three Acacia species had similar (P>0.05) contents of condensed tannins, ranging from 1.49 to 1.76 %. However, only A. nilotica leaves had hydrolysable tannins of 128 mg/g. The second part of the study was conducted to determine the effect of A. karroo, A. tortilis or A. nilotica leaf meal inclusion level on diet intake and digestibility, methane emission, productivity and blood profiles of yearling male Boer goats. A total of three experiments were conducted and different goats were used in each experiment. A grand total of thirty six (twelve per experiment) yearling male Boer goats with initial mean live weights of 23 ± 2 kg (experiment 1), 23 ± 2 kg (experiment 2) and 23 ± 2 kg (experiment 3) were used in 21-day experiments. The goats were randomly assigned to four dietary treatments, each containing A. karroo, A. tortilis or A. nilotica leaf meal inclusion levels at 10, 15, 20 and 30 % with Avena sativa hay as a basal diet. Each goat was housed in well-ventilated individual metabolic pen. The diets were replicated three times. The data collected were subjected to analysis of covariance and analysis of variance in a completely randomized design using SAS. Differences were separated at 5 % level of probability. Additionally, regression equations were used to determine the relationships and responses in optimal diet intake and digestibility, methane emission, productivity and blood profiles of yearling male Boer goats to differing inclusion levels of A. karroo, A. tortilis and A. nilotica leaf meal. v Experiment 1 involved feeding different levels of A. karroo leaf meal inclusion to yearling male Boer goats fed Avena sativa hay as a basal diet. Results of methane emission before and during the experiment indicated that inclusion of A. karroo leaf meal in the diets of goats reduced (P<0.05) methane emission. Similarly, some of the blood parameters before and after experiment were affected (P<0.05) by inclusion of A. karroo leaf meal. However, A. karroo leaf meal inclusion level had no effect (P>0.05) on diet intake, methane emission, live weight changes and digestibility, except (P<0.05) for digestibility of crude fibre. Feed conversion ratio improved linearly with increased A. karroo leaf meal inclusion level. In the case of experiment 2, results of methane emission before and during the experiment indicated that inclusion of A. tortilis leaf meal in the diets of goats reduced (P<0.05) methane emission. Similarly, some of the blood parameters before and after the experiment were affected (P<0.05) by inclusion of A. tortilis leaf meal. However, variation in A. tortilis leaf meal inclusion level had comparable effect (P>0.05) on methane emission, live weight changes and digestibility, except (P<0.05) for digestibility of crude protein and acid detergent fibre. Diet intake and feed conversion ratio were affected (P<0.05) by A. tortilis leaf meal inclusion level. A positive relationship was observed between A. tortilis leaf meal inclusion level and diet intake. In experiment 3, results of methane emission before and during the experiment indicated that inclusion of A. nilotica leaf meal in the diets of goats reduced (P<0.05) methane emission. Similarly, some of the blood parameters before and the after experiment were affected (P<0.05) by inclusion of A. nilotica leaf meal. Apart from diet fat digestibility and feed conversion ratio, no statistical differences (P>0.05) were observed on diet intake, digestibility and live weight changes of goats fed A. nilotica leaf meal inclusion level. Positive relationships were observed between A. nilotica leaf meal inclusion level, diet fat digestibility and feed conversion ratio in male Boer goats. The high crude protein and low tannin contents in A. karroo, A. tortilis and A. nilotica leaves indicate that these Acacia species can be safe to use as a source of protein in animal nutrition if used sparingly. It was noted that nutrient intake, digestibility, vi feed conversion ratio and blood profiles of Boer goats in the present study were optimised at different inclusion levels for all the three Acacia species. This may imply that inclusion levels of A. karroo, A. tortilis and A. nilotica leaf meals for optimal productivity will depend on the Acacia species used and, also, on particular productivity parameters in question. Although, A. karroo, A. tortilis and A. nilotica leaf meal reduced methane emission, optimal reduction in methane emission was not determined. Further validation is required to determine Acacia inclusion levels for optimal methane production and emission by goats. / NRF (National Research Foundation), AGRISETA (Agricultural Sector and Education Training Authority) and NSFAS (National Students Financial Aid Scheme)

The broad objective of the current study was to determine the response of pigs fed on incremental levels of Acacia tortilis leaf meal-based diet. Eight trees of each of the following five dominant leguminous leaf meals; A. tortilis, A. robusta, A. nilotica, A. nigrescens and A. xanthophloea, were individually hand harvested from the same grazing camp at Makhathini Research Station, Jozini, South Africa. The leaf meals were harvested between April and May 2013 after the rainy season at advance stage of maturity. Following the nutritive evaluation of Acacia species, A. tortilis was selected for the feeding experiment. Thirty finishing male F1 hybrid (Landrace × Large White) pigs with an initial weight of 60.6 (s.d. = 0.94) kg were randomly allotted to six dietary treatments containing 0, 50, 100, 150, 200, 250 g/kg DM inclusion levels of A. tortilis leaf meal. Each treatment diet was offered ad libitum to five pigs in individual pens for 21 days. Average daily feed intake (ADFI), body weight, average daily gain (ADG) and gain: feed ratio was measured every week. Blood was collected at the end of the experimental period for the determination of nutritionally-related blood metabolites and activity of Aspartate aminotransferase (AST), alanine amino transferase (ALT) and alkaline phosphatase (ALP). Following a feed withdrawal period of 12 hours, pigs with a mean body weight of 80 ± 15 kg were slaughtered, eviscerated for the collection of livers, kidneys, lungs and heart from each pig and weighed individually using a digital scale. Acacia tortilis and A. xanthophloea leaf meals had the highest CP and fat content (P < 0.01) among all the Acacia species. The NDF and ADF varied significantly across Acacia species (P < 0.05). Acacia robusta had significantly the highest levels of non-structural carbohydrates, whilst A. tortilis had the lowest. The concentration of proanthocynidins varied across the species. Acacia tortilis had significantly high levels (23 g/kg DM) of phosphorus compared to the other species. Acacia nilotica had the highest (P < 0.001) concentration of iron, but it had the lowest (P < 0.01) level of manganese. There was a quadratic decrease in both ADFI and ADG (P < 0.001) with as A. tortilis leaf meal increased. The gain: feed ratio was linearly reduced (P < 0.001) with incremental levels of A. tortilis leaf meal in the diets. Serum concentrations of Fe, AST and ALP increased quadratically (P < 0.01) as A. tortilis leaf meal increased. There was a linear increase in ALT activity with increased leaf meal inclusion. Hepatosomatic index (HSI: liver weight/ body weight x 100), scaled kidney weight and scaled heart weight increased linearly (P < 0.001) as A. tortilis leaf meal increased. There was, however, a quadratic increase in the relative weight of lungs (P < 0.001) as leaf meal increased. In conclusion, the piecewise regression (brocken-stick) NLIN procedure (SAS, 2008; SASA institute Inc.) showed that A. tortilis leaf meal can be included in finisher pig diet up to 150 g/kg DM of feed without negatively affecting growth performance, nutritionally-related blood metabolites, liver enzymes and internal organs of pigs. / M.Sc.Agric. University of KwaZulu-Natal, Pietermaritzburg 2013.