The objective of this study was to determine the relationship between the traits of average daily gain, backfat, loin muscle depth, feed intake and feed conversion measured in growing gilts and their subsequent feed intake (as estimated by feed delivery) in lactation, and to estimate the effects of lactation feed intake on subsequent maternal productivity and sow longevity. Phenotypic performance measurements and estimated breeding values (EBV) were compared with first and second parity lactation feed delivery in a group of selected nucleus gilts of 3 genetic lines. The effects of lactation feed delivery on weaning to conception interval, total piglets born in the subsequent litter and lifetime productivity measures were investigated. Genetic parameters for the growing period traits of average daily gain, backfat, loin muscle depth, daily feed intake and feed conversion, as well as maternal productivity traits of litter size (number alive at day 2), weaning to conception interval and litter weaning weight were estimated and EBV were computed. Phenotypes of growth rate, feed intake, backfat and loin muscle depth recorded in the growing period were not good predictors of lactation feed delivery. However, one genetic line (YO-A) showed significant correlations between second parity lactation feed delivery and growth rate and loin muscle depth measured in the growing period. EBV calculated for the growing period traits of growth rate, feed intake and feed conversion showed much stronger relationships with lactation feed delivery than the growing period phenotypes, particularly for parity 2. Parity 2 lactation feed delivery showed favorable correlations with EBV for growth rate and feed conversion and an unfavorable correlation with the growing period daily feed intake EBV. Lactation feed delivery in the first and second parity had significant effects on the odds of occurrence of the next litter, next litter total born, stayability to parity 3 or parity 4 and sow longevity. Since lactation feed intake is very important to subsequent productivity and longevity of sows and has a positive (unfavorable) genetic correlation with growth period feed intake, it is recommended that lactation feed intake be measured directly and included in the selection goal. The correlation between lactation feed delivery in parity 1 and parity 2 was low at 0.28 across genetic lines, leading to the conclusion that lactation feed delivery in the first and second parities appear to be different traits under different control mechanisms. It is concluded that a balanced selection program for maternal lines that includes selection for reduced feed intake, feed conversion or residual feed intake measured in the growing period, should also include selection for increased lactation feed intake (probably in combination with changes in sow body weight or backfat during lactation in order to prevent negative consequences for sow longevity or productivity). It is also recommended that lactation feed intake in the first and later parities be evaluated as separate traits.

Title page, table of contents and abstract only. The complete thesis in print form is available from the University of Adelaide Library. / Net feed intake or residual feed intake is the feed intake of an animal after adjustment for its average weight and weight gain while on the feed test. High net feed efficiency (NFE) animals have a low net feed intake, so the aim is to select animals that have high net feed efficiency in order to reduce the 70% expenditure for feed costs. Thus far, very few studies have been undertaken on beef cattle to identify genetic markers for NFE and to understand the molecular genetics of feed intake regulation and energy balance. Therefore, in an attempt to identify genes and metabolic pathways controlling feed efficiency in beef cattle, three different experimental approaches were taken herein: a) linkage and linkage disequilibrium quantitative trait loci (QTL) mapping for net feed intake in Lirnousin x Jersey animals, b) mitochondrial oxidative phosphorylation enzyme assays in high and low NFE cattle, and c) 2-dimensional fluorescent gel electrophoresis (DIGE) proteomics analysis of mitochondrial proteins. For the cattle QTL mapping, the results from a previous trial were utilized. In the trial, a double back-cross design was employed using two extremely divergent Bos taurus breeds [Jersey (J) dairy breed and Limousin (L) beef breed]. These breeds known to differ in many traits including carcass composition, fat colour, body size, and meat tenderness. Three first cross (F1=X) sires were mated to pure Jersey or pure Limousin cows, creating in total 366 XJ and XL backcross progeny (range 120-156 progeny per sire). The amount of feed consumed each day during the 70-100 day test was recorded electronically for each animal. Feed intake data were processed by calculating the least-square means for each animal over the test period. The data for net feed intake were analysed using a QTL half-sib interval-mapping model. The interval linkage analysis of whole genome detected six suggestive QTL (BTA 1, 6, 8, 9, 16, and 20) segregating for NFE. Of these 6 QTL, 4 NFE QTL (BTA 1, 6,16, and 20) were homeologous to QTL for NFE observed in fullsib F2 families of mouse selection lines (Fenton 2004). After the NFE data were reanalysed for outliers, a QTL on BTA 11 was re-ranked and placed in the top 4 NFE QTL in terms of size of effect and statistical support, whereas the OTL on BTA 6 and BTA 16 had less support. Since the QTL on BTA 9 was not independent of growth, only 4 QTL (BTA 1, 8, 11 and 20) were targeted for further study herein. These NFE QTL were cross-validated in Angus NFE selection line animals in collaboration with Department of Primary Industries (DPI), Victoria by microsatellite linkage mapping. Two of the QTL on BTA 8 and 20 were confirmed and three other minor QTL on BTA 1, 11, and 20 were detected in the Angus animals. Based on this background information, a comparative genome mapping study was undertaken to identify candidate genes. Using the human and bovine genome Ensembl databases, 205 NFE candidate genes underlying the 4 major QTL regions (BTA 1, 8, 11, and 20) were identified and 61 were sequenced in the mapping F1 Limousin x Jersey mapping sires. In these 61 genes, 308 SNPs were discovered, of which 27 were potentially functional SNPs changing the amino acids. 84 SNPs were selected for genotyping and used for fine mapping the 4 QTL and for SNP association studies with NFE. From the positions of the analyses, the 4 NFE QTL were refined and 27 candidate SNPs in 20 genes showed strong association with NFE in the Limousin x Jersey animals. A ParAllele whole genome scan with a bovine 10K SNP chip was also performed on a subset of the Angus NFE selection line animals by DPI Victoria. 100 ParAllele SNPs had significant association with NFE in the Angus selection line animals. These ParAllele SNPs were tested in the Limousin x Jersey animals and 16 ParAllele SNPs were significantly associated with NFE. Four of these SNPs were located in the NFE QTL on BTA 1, 11 and 20. Based on the candidate genes underlying the 4 NFE QTL, 8 potential metabolic pathways contributing to NFE were identified. These metabolic pathways included mitochondrial oxidative phosphorylation and glucose turnover. Therefore, to determine if these specific pathways are indeed involved in net feed efficiency, oxidative phosphorylation enzyme assays and mitochondrial protein profiling were conducted on progeny from the Angus Trangie NFE selection line animals. Liver and skeletal muscle samples were obtained from extreme high and low NFE animals with an average phenotypic difference of 3 kg net feed intake per day. Using these liver and muscle samples, mitochondria were prepared and assessed. The mitochondrial preparations were assayed for enzyme activity of 3 complexes (Complex I, II and IV) involved in oxidative phosphorylation. The enzyme activities were measured spectrophotometrically and analysed by regression analysis. The activity of the liver mitochondrial Complex I was found to be significantly decreased in the high NFE animals compared to the low NFE animals (p<O.0001). The Complex II and IV activities were increased in the high NFE cattle, but the differences were not statistically significant. Using the mitochondrial preparations, 2-D polyacrylamide gel electrophoresis differential gel electrophoresis (2-D PAGE DIGE) was used to generate a mitochondrial protein profile for the high and low NFE Angus cattle. An ontological analysis based on the differentially expressed proteins (>1.5 fold difference) in the high vs. low NFE cattle unambiguously identified a total of 27 proteins in 6 physiologically different groups. The mitochondria proteomics results also confirmed the involvement of oxidative phosphorylation in net feed intake regulation. Eleven oxidative phosphorylation complex subunit proteins were found to be differentially expressed between the high and low NFE animals. Other differentially expressed proteins included six stress-related proteins, seven energy production and glucose turnover proteins, two protein turnover and nitrogen balance enzymes, and two proteins involved in mitochondrial DNA and protein biosynthesis. Four of the differentially expressed proteins were found in the NFE QTL regions. The results of these experiments provide a better understanding of the relationship between variation in feed efficiency and cellular energy production mechanisms in beef cattle. The proteomics and mitochondrial enzyme assay results suggest that energy metabolism and homeostasis may not be an efficient process in low NFE cattle. Lastly, a set of candidate SNPs are now available for the further validation as markers for selection of NFE in cattle breeding programs. / http://proxy.library.adelaide.edu.au/login?url= http://library.adelaide.edu.au/cgi-bin/Pwebrecon.cgi?BBID=1349183 / Thesis (Ph.D.) -- University of Adelaide, School of Agriculture, Food and Wine, 2008

Master of Science / Department of Animal Sciences and Industry / Robert D. Goodband / A study was conducted on a commercial sow farm to determine the effects of parity and stage of gestation on growth and feed efficiency of gestating sows. These data were also used to model changes in composition of maternal weight gain and products of conceptus throughout gestation. Feed intake and BW were measured daily from d 5 to 112 of gestation for 712 females. From d 5 to 39 of gestation, ADFI was lowest for parity 3+ sows compared to the other periods of gestation. Parity 2 sows, although provided the same feed allowance, had greater ADFI during the first period than parity 3+ sows. Average daily gain was lowest and G:F was the poorest from d 5 to 39 for each parity group compared with d 40 to 109 of gestation. Parity 1 and 2 sow ADG increased following d 39 of gestation but decreased from d 75 to 109. Parity 3+ sow ADG increased in each subsequent period of gestation. Parity 1 sows had the greatest ADG and G:F in comparison to parity 2 and 3+ sows in each period of gestation. Energy available for maternal growth was estimated after accounting for the energy needed to meet the sow’s maintenance requirement and the energy required for the growth of the conceptus. Following d 39 of gestation, energy available for maternal growth decreased at the expense of maintenance and conceptus requirements in each subsequent period of gestation for each parity group. After accounting for the weight of the conceptus, maternal ADG decreased from d 39 to 74, and increased d 74 to 109 of gestation, regardless of parity. Maternal G:F was greatest for parity 1 sows in most gestation periods. In conclusion, parity and stage of gestation impact sow feed efficiency and maternal growth with parity 1 sows having the greatest weight gain and best feed efficiency.

Single nucleotide polymorphism (SNP) methodology is being used as a means to determine genetic merit in beef cattle by interrogating animal genomes and associating the findings with performance traits. The ability to predict future trait performance is highly attractive to beef cattle producers as they can make important management and financial decisions earlier and with more certainty. To fully realize the potential of SNP testing technology the methodology must be vetted to assure producer confidence. The purpose of this project is to assess three sources of information for beef cattle trait assessment. These information sources are: SNP testing, Expected Progeny Differences (EPDs) and direct animal measures. To conduct this study, young beef bulls (n=181) consigned to the SIU Beef Evaluation Station were utilized in an 84-day period to obtain direct measures. The SIU Beef Evaluation Station uses the Calan-Broadbent confinement feeding system which allows researchers to monitor individual animal feed intake and weight gain. Feed efficiency traits are important to the cattle industry since feed is generally among the largest input cost to producers. The evaluation of bulls also assesses reproductive and carcass traits which are also important to the producer’s financial success.Individual animal performance information was sent to the bull’s respective breed association for determination of EPD’s. Blood samples were submitted to a commercial company for SNP testing (Igentiy Gold and Igenity Beef Profile, Neogen, Lincoln, NE). Data was analyzed using pairwise comparisons by source of information. Pearson correlations were used to determine the direction and the strength for sources of information to vary together. Data was determined to be correlated when the correlation coefficient was 0.3 < r < - 0.3. No correlation was observed between RFISIU :RFINEO (r = 0.042), RFINEO:F/GSIU (r = - 0.09), RFISIU:ADGNEO (r = 0.091), RFISIU:ADGSIU (r = - 0.039), RFINEO:ADGNEO (r = 0.236), BWNEO:BWSIU (r = 0.115), FRAMESIU:BWSIU (r = 0.111), FRAMESIU:BWEPD (r = 0.159), FRAMESIU:ADGSIU (r = 0.148), FRAMESIU:ADGNEO (r = -0.005), BWSIU:BWEPD (r = 0.256), and BWNEO:BWEPD (r = 0.226). Correlations were observed between RFISIU:F/GSIU (r = 0.455), ADGSIU :ADGNEO (r = 0.353), and FRAMESIU:BWNEO (r = 0.326).This study determined that beef bulls should continue to be performance tested due to discrepancies between sources of information for key animal performance traits. Assessment of SNPs used in the commercial test should continue.

Beef cattle producers continuously search for nutritional management options that provide flexibility to production scenarios. Due to its positive effects on maternal productivity, early weaning is one such alternative strategy that has received considerable interest. To better understand the effects of early weaning on calf productivity, an extensive literature review and three experiments were conducted to evaluate the effects of early weaning on finishing feed efficiency, marbling development and retail product quality of beef steers. In experiment I, which included 90 Angus-sired steers from four calving seasons, early weaning followed by a short ad libitum concentrate-feeding and pasture-backgrounding phase reduced finishing residual feed intake (RFI) by 7 % (P < 0.0001) and increased carcass marbling score (MS) by 10 % (P < 0.01) when compared to conventionally weaned (CW) contemporaries. Similar effects were observed in experiment II, which included 28 Angus and Simmental-sired steers, as early weaning reduced RFI (P < 0.01) and increased carcass MS (P < 0.01). Lung mass of early weaned (EW) steers was greater than their CW contemporaries (P < 0.05), and was inversely related to RFI (R2 = 0.17; P < 0.05). Finishing treatments in this experiment included a high corn ration and an alternative low corn ration that iso-calorically replaced 50 % of the DM from corn with dried corn gluten feed. Iso-caloric replacement of corn reduced lung mass (P < 0.01), and when combined with the observed increase of EW steers suggests that lung development is affected by dietary energy type at various stages of growth. In experiment III, objective analyses of ribeye steaks obtained from steers included in experiment two revealed that early weaning increased cross-sectional muscle fiber area by 28 % (P < 0.001) and tended to increase (P = 0.08) Warner-Bratzler shear force by 36 %. Nonetheless, these effects were not great enough to alter un-trained consumer perception of texture (P ≥ 0.65), juiciness (P ≥ 0.55), flavor (P ≥ 0.25) or overall acceptability (P ≥ 0.34). Collectively, these results indicate that early weaning enhances finishing feed efficiency and carcass marbling without affecting un-trained consumer sensory perception. / Ph. D.

Master of Science / Animal Sciences and Industry / Jennifer M. Bormann / Feed is the single most expensive cost related to beef cattle production. Currently a 70 d performance test is recommended for accurate calculation of efficiency. Previous research has suggested intake tests can be limited to 35 d. Objectives of this study were to estimate genetic parameters for growth and intake traits, compare two alternative indices for feed efficiency, and quantify the genetic response to selection for feed efficiency combining an intake test with two types of gain data. On–test average daily feed intake (ADFI), on-test average daily gain (ADG), and postweaning gain (PWG) records on 5,606 growing steers and heifers were obtained from the U.S. Meat Animal Research Center in Clay Center, NE. On-test ADFI and ADG data were collected from a minimum of 62 to 148 d testing days. Independent quadratic regressions were fitted for body weight on time, and on-test ADG was predicted from the resulting equations. PWG was calculated by subtracting adjusted 205-d weights from 365-d weights and dividing by 160. Genetic correlations were estimated using multiple trait animal mixed models with ADG, ADFI, and PWG for both sexes as dependent variables. The genetic correlations between ADG and PWG for both steers (0.81) and heifers (0.65) were strong. This indicates PWG is a strong proxy for ADG on-test and long test periods may not be necessary. Indices combining EBVs for ADFI and ADG and for ADFI and PWG were evaluated. For each index, the weighting of gain was arbitrarily set to 1.0 and the weighting for ADFI was the negative of the average of the intra-contemporary group ratio of mean gain divided by mean ADFI. Values were combined with EBV to compute two index values per animal. Pearson correlations for steers (0.96) and heifers (0.45) indicated a strong relationship for steers between the indices. Because more animals can be measured for intake, using PWG increases genetic progress of selection for feed efficiency by 15-17% per year. These findings support using PWG data in combination with ADFI to determine efficient animals, lessen costs, and increase annual feed efficiency genetic change.

Gooseneck Barnacles are a delicacy in Spain and Portugal and a species harvested for subsistence or commercial fishing across their global range. They are ubiquitous on the Oregon coastline and grow in dense aggregation in the intertidal zone. Reproductive biology of the species makes them particularly susceptible to overfishing, and in the interest of sustainability, aquaculture was explored as one option to supply a commercial product without impacting local ecological communities. A novel aquaculture system was developed and tested that caters to the unique feeding behavior of Pollicipes polymerus. Modified feeds of bio-enhanced rotifers and a blend of up-cycled commercial fish byproduct were administered to barnacles of three different size classes. Growth and propagule potential were tracked in the culture tanks. In addition, a separate experiment was performed to investigate various biometrics associated with feed efficiencies and nutritive content to assess the overall sustainability of this aquaculture system.

A seleção de animais para consumo alimentar residual (RFI) está intrinsecamente associada com a diminuição do consumo matéria seca e é independente do ganho de peso corporal, selecionando animais de eficiência produtiva e econômica, além também de diminuir a emissão de gases de efeito estufa provinda do gado. Neste estudo, amostras de soro de 16 animais selecionados divergentemente para eficiência de alimentação foram coletadas antes do confinamento (dia -21) e avaliadas em uma abordagem metabolômica global, com o objetivo de usar análise diferencial, análise de co-expressão e enriquecimento funcional, identificando marcadores para eficiência de alimentação antes do confinamento. Um analito foi diferencialmente presente entre os animais de baixo e alto RFI. A análise WGCNA identificou 22 e 25 módulos no modo positivo e negativo, respectivamente e, 1 módulo de cada modo foi fortemente associado a RFI (r = 0,53, p-valor &lt;0,05 e r = 0,52, p-valor &lt;0,1 nos modos negativo e positivo, respectivamente). A análise de enriquecimento funcional predize 13 processos biológicos associados à eficiência alimentar, incluindo alterações no metabolismo de vitaminas lipossolúveis, inflamação, estresse oxidativo, metabolismo de aminoácidos e metabolismo de ácidos graxos. Esse trabalho evidencia a possibilidade de se identificar um biomarcador para eficiência alimentar e também sugerem que as diferenças nas respostas ao estresse oxidativo e nos processos inflamatórios já influenciam na variação da eficiência alimentar previamente ao confinamento. / Animal selection for residual feed intake (RFI) is intrinsically associated with decreased consumption of dry matter independent of body weight gain, selecting yielding increased production and economic efficiency but also decreasing the greenhouse gas emission of livestock. In this study, serum samples of 16 animals selected for divergent feed efficiency were collected prior to feedlot (day -21) and evaluated in an untargeted metabolomics approach, with the goal of using differential analysis, co-expression analysis and functional enrichment to identifier markers for feed efficiency prior to the feedlot. One feature was differentially accumulated between low and high RFI. WGCNA analysis identified 22 and 25 modules in positive and negative mode, respectively, of 1 module of each mode was strongly associated with RFI (r= 0.53, p-value &lt;0.05 and r=0.52, p-value &lt; 0.1 to negative and positive mode, respectively). Pathway enrichment analysis yielded 13 biological processes associated with feed efficiency including alterations in vitamins liposoluble metabolism, inflammation, oxidative stress, amino acid metabolism and fatty acid metabolism. Our findings suggest the possibility to identify a biomarker for feed efficiency and also discuss that differences in oxidative stress responses and inflammatory processes could explain the feed efficiency variation prior to feedlot.

The objectives of these studies were (1) evaluate the relationship between temperament, blood parameters, and performance in Brahman calves (n = 300); (2) evaluate the relationship between residual feed intake (RFI) and reproductive development in Brahman bulls (n = 41). Serum was collected at 24 h and d 21 to 24, and analyzed for total protein (TP) immunoglobulin G (IgG), and cortisol (CS). Calves were weighed at 24 h, weighed and evaluated for temperament using exit velocity (EV) at d 21 to 24, and at 28 d intervals thereafter. Beginning 28 d prior to weaning, and at 28 d intervals through 56 d post-weaning calves were evaluated for pen score (PS) used to calculate temperament score (TS = (EV+PS)/2). The average TS from 28 d prior to weaning and weaning was used to generate temperament groups; calves 1 SD below the mean being calm, those 1 SD above the mean being temperamental and all remaining classified as intermediate. Calf TS influenced WW (P = 0.04) and ADG from birth to weaning (P = 0.03). Serum TP at 24 h affected (P < 0.05) WW and ADG from birth to weaning. Serum IgG at 24 h affected (P = 0.03) WW. Brahman bulls (n = 41) were evaluated for RFI, insulin-like growth factor I (IGF-I), temperament, reproductive development, and ultrasound carcass traits. Serum was collected at d 0 and d 70 of the feeding trial and analyzed for IGF-I. Bulls were classified as efficient, intermediate, or inefficient (RFI classification method I) and as efficient or inefficient (RFI classification method II). Bulls were evaluated for temperament at weaning using TS. Temperament influenced (P < 0.05) IGF-I concentrations at d 0. Reproductive development was not affected (P > 0.05) by TS. Residual feed intake classification did not influence (P > 0.05) age at reproductive milestones. Ultrasound carcass traits were not affected by TS or RFI. Serum TP at 24 h was a viable indicator of future growth performance. Temperamental animals had lower growth rates in both studies. Reproductive development was not affected by RFI. BW at reproductive milestones was lower in temperamental bulls.

Objectives of this study were to determine if variation in energy expenditures contributed to differences in feed efficiency between low and high RFI steers. Nine steers with the lowest and highest residual feed intakes (RFI) were selected from 169 Braunvieh-sired crossbred steers that were individually fed a pelleted roughage-based diet for 77 d. Following the RFI measurement period, heat production (HP) measurements were obtained using indirect calorimetry while steers were fed the same roughage diet (RD) and on a high-concentrate diet (CD). Linear regression analyses of log HP or retained energy on ME intake were used to determine energy partitioning. Motion and lying activity were measured concurrently with HP on the RD and CD. During the RFI measurement period, low RFI steers had lower (P < 0.01) RFI (-1.7 vs. 1.6 ± 0.17 kg/d), DMI (7.7 vs. 10.2 ± 0.42 kg/d) and feed:gain ratio (F:G; 7.2 vs. 10.6 ± 0.60), but similar final BW and ADG compared to high RFI steers. However, there were smaller differences in DMI (8.4 vs. 9.7 ± 0.38 kg/d; P < 0.05; 7.56 vs. 8.16 ± 0.31; P = 0.19) and F:G (10.0 vs. 10.9 ± 0.40; P = 0.36; 6.5 vs. 7.5 ± 0.30; P < 0.05) between low and high RFI steers, on the RD and CD, respectively. ME for maintenance (MEm; kg .75 d–1) and the partial efficiencies of ME used for maintenance and gain were similar for low and high RFI steers. Likewise, no differences were found in fasting HP or fed HP. Motion activity was lower (P < 0.05) for low RFI steers compared to high RFI steers during fasting HP. Covariate analysis of HP at the same activity level yielded similar results. At slaughter, weights of lung and trachea (P < 0.05), spleen (P < 0.05) and adrenal gland (P = 0.07) were higher for low RFI cattle. The lack of differences in energy partitioning between divergent RFI steers may have been the result of alterations in feeding behavior or stress imposed by adapting steers to calorimetry chambers.