Search

Objective: Recently, indigenous Korean grass Sasa quelpaertensis Nakai (SQ) has garnered much interest as a roughage source for livestock to mitigate its adverse effects on habitat diversity. Thus, the objective of the present study was to evaluate the ruminal fermentation, palatability, and nutrient digestibility of SQ for Korean native beef cattle (Hanwoo) using in vitro rumen fermentation, in situ rumen degradability, and in vivo feeding trials.Methods: Using in vitro tests with rumen fluid as the inoculum for 48 h, ruminal fermentation of SQ was evaluated and compared with that of other roughage sources commonly used in Korea (i.e., rice straw, Timothy hay, and Italian ryegrass [IRG]). Additionally, an in situ trial 96 h was performed using three cannulated Hanwoo steers. Further, an in vivo trial was performed using eight Hanwoo steers to compare the palatability of SQ with rice straw in total mixed ration (TMR) and forage-concentrate separate feeding conditions. Finally, an in vivo digestibility trial of SQ fed as TMR of two particle sizes was performed with four Hanwoo steers.Results: In vitro and in situ trials revealed that SQ was comparable or superior to rice straw in terms of the ruminal fermentation characteristics of pH, gas production, total volatile fatty acid content, and effective ruminal dry matter digestibility (DMD), although its fermentability was lower than that of Timothy hay and IRG. In the palatability test, steers showed a greater preference for SQ when given as TMR. The total tract DMD of SQ fed as TMR was 75.9%±1.37%, and it did not differ by particle size.Conclusion: The feed value of SQ as a roughage source for Hanwoo steers is comparable or superior to that of rice straw, particularly when provided as TMR.

Objective: This study aimed to validate and evaluate the dry matter (DM) intake prediction model of the Korean feeding standards for dairy cattle (KFSD).Methods: The KFSD DM intake (DMI) model was developed using a database containing the data from the Journal of Dairy Science from 2006 to 2011 (1,065 observations 287 studies). The development (458 observations from 103 studies) and evaluation databases (168 observations from 74 studies) were constructed from the database. The body weight (kg; BW), metabolic BW (BW0.75, MBW), 4% fat-corrected milk (FCM), forage as a percentage of dietary DM, and the dietary content of nutrients (% DM) were chosen as possible explanatory variables. A random coefficient model with the study as a random variable and a linear model without the random effect was used to select model variables and estimate parameters, respectively, during the model development. The best-fit equation was compared to published equations, and sensitivity analysis of the prediction equation was conducted. The KFSD model was also evaluated using in vivo feeding trial data.Results: The KFSD DMI equation is 4.103 (±2.994)+0.112 (±0.022)×MBW+0.284 (±0.020) ×FCM–0.119 (±0.028)×neutral detergent fiber (NDF), explaining 47% of the variation in the evaluation dataset with no mean nor slope bias (p>0.05). The root mean square prediction error was 2.70 kg/d, best among the tested equations. The sensitivity analysis showed that the model is the most sensitive to FCM, followed by MBW and NDF. With the in vivo data, the KFSD equation showed slightly higher precision (R2 = 0.39) than the NRC equation (R2 = 0.37), with a mean bias of 1.19 kg and no slope bias (p>0.05).Conclusion: The KFSD DMI model is suitable for predicting the DMI of lactating dairy cows in practical situations in Korea.

A total of three Gram-positive, and oxidase and catalase-negative facultative anaerobic non-motile bacteria were isolated from the rumen fluid of cows and goats and these strains were designated CNU_G2

The hand-held laser methane detector (LMD) technique has been suggested as an alternative method for measuring methane (CH4) emissions from enteric fermentation of ruminants in the field. This study aimed to establish a standard procedure for using LMD to assess CH4 production in cattle and evaluate the efficacy of the protocol to detect differences in CH4 emissions from cattle fed with diets of different forage-to-concentrate (FC) ratios. Experiment 1 was conducted with four Hanwoo steers (584 ± 57.4 kg body weight [BW]) individually housed in metabolic cages. The LMD was installed on a tripod aimed at the animal's nostril, and the CH4 concentration in the exhaled gas was measured for 6 min every hour for 2 consecutive days. For the data processing, the CH4 concentration peaks were identified by the automatic multi-scale peak detection algorithm. The peaks were then separated into those from respiration and eructation by fitting combinations of two of the four distribution functions (normal, log-normal, gamma, and Weibull) using the mixdist R package. In addition, the most appropriate time and number of consecutive measurements to represent the daily average CH4 concentration were determined. In experiment 2, 30 Hanwoo growing steers (343 ± 24.6 kg BW), blocked by BW, were randomly divided into three groups. Three different diets were provided to each group: high FC ratio (35:65) with low-energy concentrate (HFC-LEC), high FC ratio with high-energy concentrate (HFC-HEC), and low FC ratio (25:75) with high-energy concentrate (LFC-HEC). After 10 d of feeding the diets, the CH4 concentrations for all steers were measured and analyzed in duplicate according to the protocol established in experiment 1. In experiment 1, the mean correlation coefficient between the CH4 concentration from respiration and eructation was highest when a combination of two normal distributions was assumed (r = 0.79). The most appropriate measurement times were as follows: 2 h and 1 h before, and 1 h and 2 h after morning feeding. Compared with LFC-HEC, HFC-LEC showed 49% and 57% higher CH4 concentrations in exhaled gas from respiration and eructation (P0.01). In conclusion, the LMD method can be applied to evaluate differences in CH4 emissions in cattle using the protocol established in this study.The hand-held laser methane detector (LMD) technique has been suggested as a potential method for measuring methane (CH4) emissions from enteric fermentation of ruminants in the field. This study aimed to establish a standard procedure for using LMD to assess CH4 production in cattle and evaluate the efficacy of the protocol to detect differences in CH4 emissions from cattle fed with diets of different forage-to-concentrate (FC) ratios which is known to affect CH4 emissions. Experiment 1 was conducted to establish a protocol for measuring and analyzing the CH4 emissions from cattle using LMD. In experiment 2, 30 Hanwoo growing steers were divided into three groups and fed with a diet of high FC ratio (35:65) with low-energy concentrate (HFC-LEC), high FC ratio (35:65) with high-energy concentrate (HFC-HEC), or low FC ratio (25:75) with high-energy concentrate (LFC-HEC). The CH4 concentrations for all steers were measured in duplicate according to the protocol established in experiment 1. HFC-LEC showed 49% and 57% higher CH4 concentrations in exhaled gas from respiration and eructation, respectively (P0.01), than LFC-HEC. In conclusion, the LMD method can be applied to evaluate differences in CH4 emissions in cattle using the protocol established in this study.

Genome-wide association studies (GWAS) have accelerated the identification of functional trait loci in cattle and identified single nucleotide polymorphisms (SNPs) in candidate genes associated with fertility and production traits in high milk yield dairy cattle. The fertility of Hanwoo (Korean native beef cattle) has declined after the adaptation of a selection program for high quantity and quality meat. However, there are few GWAS studies of fertility in beef cattle. We performed a genome-wide association study of 40 Korean native beef cattle heifers with imputed 770 K genotype and identified 12 significant SNPs within seven regions on three chromosomes (BTA 8, BTA 16 and BTA 24) associated with services per conception (SPC). Five SNPs were located in the

Understanding the utilization of feed energy is essential for precision feeding in beef cattle production. We aimed to assess whether predicting the metabolizable energy (ME) to digestible energy (DE) ratio (MDR), rather than a prediction of ME with DE, is feasible and to develop a model equation to predict MDR in beef cattle. We constructed a literature database based on published data. A meta-analysis was conducted with 306 means from 69 studies containing both dietary DE and ME concentrations measured by calorimetry to test whether exclusion of the y-intercept is adequate in the linear relationship between DE and ME. A random coefficient model with study as the random variable was used to develop equations to predict MDR in growing and finishing beef cattle. Routinely measured or calculated variables in the field (body weight, age, daily gain, intake, and dietary nutrient components) were chosen as explanatory variables. The developed equations were evaluated with other published equations. The no-intercept linear equation was found to represent the relationship between DE and ME more appropriately than the equation with a y-intercept. The y-intercept (−0.025 ± 0.0525) was not different from 0 (P = 0.638), and Akaike and Bayesian information criteria of the no-intercept model were smaller than those with the y-intercept. Within our growing and finishing cattle data, the animal’s physiological stage was not a significant variable affecting MDR after accounting for the study effect (P = 0.213). The mean (±SE) of MDR was 0.849 (±0.0063). The best equation for predicting MDR (n = 106 from 28 studies) was 0.9410 ( ± 0.02160) +0.0042 ( ± 0.00186) × DMI (kg) – 0.0017 ( ± 0.00024) × NDF(% DM) – 0.0022 ( ± 0.00084) × CP(% DM). We also presented a model with a positive coefficient for the ether extract (n = 80 from 22 studies). When using these equations, the observed ME was predicted with high precision (R2 = 0.92). The model accuracy was also high, as shown by the high concordance correlation coefficient (>0.95) and small root mean square error of prediction (RMSEP), 93%), without mean or slope bias (P > 0.05). We concluded that dietary ME in beef cattle could be accurately estimated from dietary DE and its conversion factor, MDR, predicted by the dry matter intake and concentration of several dietary nutrients, using the 2 equations developed in this study.

Exogenous enzymes have been used to improve nutrient utilization in several species of livestock, particularly swine and poultry. In addition, improved immunological and metabolic traits have been reported in nonruminants. The objective of this study was to determine the effects of β-mannanase supplementation on milk yield and composition, and immunological and metabolic responses in lactating Holstein dairy cows. Two weeks after calving, 20 Holstein cows (10 multiparous and 10 primiparous) were blocked by parity and assigned to 1 of 2 diets for 182 d. All cows were housed in the same environment and fed the same basal diet. The basal diet of the treatment group was supplemented with β-mannanase (CTCBio Inc., Seoul, South Korea) at 0.1% of concentrate dry matter. No differences were detected between the control and enzyme supplement groups in milk yield parameters or milk composition. Supplementation of β-mannanase enzyme reduced blood haptoglobin levels in supplemented multiparous cows compared with controls. Furthermore, nonesterified fatty acid concentration levels tended to be lower in cows fed β-mannanase, regardless of parity. Neither immunoglobulin G nor milk somatic cell count was affected by β-mannanase supplementation, regardless of parity. The number of insemination services tended to be lower in cows fed diets supplemented with β-mannanase. Results from this study suggest that supplementation of β-mannanase exogenous enzyme could help to reduce instances of systemic inflammation and decrease fat mobilization in lactating Holstein cows. Multiparous cows are considered susceptible to acute infections and inflammation; thus, the enzyme had a greater effect in multiparous cows.

We aimed to assess whether predicting the metabolizable energy (ME) to digestible energy (DE) ratio (MDR), rather than a prediction of ME with DE, is feasible and to develop a model equation to predict MDR in beef cattle. For this, we constructed a literature database based on published data. A meta-analysis was conducted with 306 means from 69 studies containing both dietary DE and ME concentrations measured by calorimetry to test whether the exclusion of the y-intercept is adequate in the linear relationship between DE and ME. A random coefficient model with study as the random variable was used to develop equations to predict MDR in growing and finishing beef cattle. The developed equations were evaluated with other published equations. The no-intercept linear equation represented the relationship between DE and ME more appropriately than the equation with a y-intercept. Within our growing and finishing cattle data, the animal’s physiological stage was not a significant variable affecting MDR after accounting for the study effect (P = 0.213). The mean (± SE) of MDR was 0.849 (± 0.0063). Two linear equations with the dry matter intake and content of several dietary nutrients were developed to predict MDR. When using these equations, the observed ME was predicted with high precision (R2 = 0.92). The model accuracy was also high, as shown by the high concordance correlation coefficient (> 0.95) and small root mean square error of prediction (RMSEP), less than 5% of the observed mean. Moreover, a significant portion of the RMSEP was due to random bias (> 93%), without mean or slope bias (P > 0.05). We concluded that dietary ME in beef cattle could be accurately estimated from dietary DE and its conversion factor, MDR, using the two equations developed in this study.

OBJECTIVE DNA methylation plays a major role in regulating the expression of genes related to traits of economic interest (e.g., weight gain) in livestock animals. This study characterized and investigated the functional inferences of genome-wide DNA methylome in the loin (longissimus dorsi) muscle (LDM) of swine. METHODS A total of 8.99 Gb methylated DNA immunoprecipitation sequence data were obtained from LDM samples of eight Duroc pigs (four pairs of littermates). The reference pig genome was annotated with 78.5% of the raw reads. A total of 33,506 putative methylated regions (PMR) were identified from methylated regions that overlapped at least two samples. RESULTS Of these, only 3.1% were commonly observed in all eight samples. DNA methylation patterns between two littermates were as diverse as between unrelated individuals (p = 0.47), indicating that maternal genetic effects have little influence on the variation in DNA methylation of porcine LDM. The highest density of PMR was observed on chromosome 10. A major proportion (47.7%) of PMR was present in the repeat regions, followed by introns (21.5%). The highest conservation of PMR was found in CpG islands (12.1%). These results show an important role for DNA methylation in species- and tissue-specific regulation of gene expression. PMR were also significantly related to muscular cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism. CONCLUSION This study indicated the biased distribution and functional role of DNA methylation in gene expression of porcine LDM. DNA methylation was related to cell development, cell-cell communication, cellular integrity and transport, and nutrient metabolism (e.g., insulin signaling pathways). Nutritional and environmental management may have a significant impact on the variation in DNA methylation of porcine LDM.

The objective of this study was to compare the effects of two isoforms of methionine (Met) supplementation, L-Met or D-Met, on transcriptome expression in broiler chickens under acute heat stress. A total of 240 one-day-old chicks were randomly assigned to one of four treatments in a 2 × 2 factorial arrangement: thermo-neutral vs. acute heat-stress and L-Met vs. D-Met supplementation. On day 14, the heat-stressed group was exposed to 32°C for 6 h, while the others remained at 25ºC. Six chicks per treatment were randomly selected and harvested to isolate total RNA from the blood, ileum, and liver tissues. Two RNA samples from each tissue of the same treatment group were randomly selected and pooled with equal amount. A total of 1.87 billion of raw reads were obtained from 36 samples (four treatments × three tissues × three composited replicates) using the Illumina HiSeq 4000 platform. The reads, mapped to the reference genome build (Gallus_gallus-5.0), were used to identify differentially expressed genes (DEG, false-discovery rate < 0.05) using DESeq2. Functional enrichment of DEG was tested using DAVID. A total of 38, 71, and 16 genes were differentially expressed in response to the interaction between heat stress and Met isoforms in the blood, ileum, and liver, respectively. These DEGs were functionally enriched for regulation of cholesterol homeostasis, gluconeogenesis, and bile acid synthesis. Unlike the L-Met group, IL4I1, SERPIN1, and CSRP2, related to immune response, neuroprotection, cell proliferation, and dedifferentiation, were all increased by heat stress in the D-Met group. The expression of PCK1, CYP7A1, SORCS1, related to abnormally increased blood glucose by heat stress, were also changed in the D-Met. Compared to D-Met, L-Met supplementation appeared to reduce abnormal cellular and physiological responses by heat stress in broilers.

Three studies were conducted to test the hypothesis that dietary spray-dried plasma (SDP) might improve pregnancy rate by ameliorating inflammation, using mice in an experimental model that produces a low pregnancy rate. Mated female mice (C57BL/6 strain) were purchased and shipped from a vendor (Bar Harbor, ME) to the university facility (Urbana, IL) on the day the vaginal plug was found (gestation day [GD] 1), arriving at the laboratory on GD 3 after 2 d transport by air and ground. Mice (Exp. 1: n = 250, 16.0 ± 1.2 g BW; Exp. 2: n = 202, 16.2 ± 1.2 g BW; Exp. 3: n = 156, 16.4 ± 1.1 g BW) were housed in individual cages and randomly assigned to dietary treatments (Exp. 1: 0 [CON] and 8% SDP in the diet, ≥ 90 mice/diet; Exp. 2: 0, 1, 2, 4, and 8% SDP in the diet, ≥ 40 mice/diet; Exp. 3: 0, 1, and 8% SDP in the diet, 48 mice/diet) fed from arrival. In Exp. 1 and 2, pregnancy of each mouse was determined on GD 17 based on BW, shape of abdomen, and inspection postmortem, and maternal growth performance from GD 3 to 17 was measured. On GD 19, pregnant mice in Exp. 2 were euthanized to measure number of fetuses and fetal and placental weights. Pregnancy rates in CON were low in both Exp. 1 (11%) and Exp. 2 (7%). The SDP consistently and markedly increased (P < 0.05) pregnancy rates in both Exp. 1 (49%) and Exp. 2 (35-43%) compared with the CON. In Exp. 3, 12 randomly selected mice were euthanized immediately after they arrived as an initial group. From GD 4 to 7, randomly selected mice were also euthanized each day (12 mice/diet). After euthanasia, the abdominal cavity was opened to check pregnancy by uterine inspection and to collect blood and uterus samples for immune measurements. The SDP increased (P < 0.05; 40 vs. 15%) pregnancy rate compared with the CON. Concentrations of indicators of inflammation and stress (uterine TNF-α and IFN-γ, and serum TNF-α, C-reactive protein, and cortisol) were greatest (P < 0.05) and an anti-inflammatory cytokine (TGF-β1) was lowest (P < 0.05) soon after arrival, on GD 3 or 4. The SDP decreased (P < 0.05) the uterine concentrations of TNF-α and IFN-γ, and serum TNF-α, C-reactive protein, and cortisol, compared with the CON, but increased (P < 0.05) the uterine concentration of TGF-β1. In conclusion, dietary SDP improves the low pregnancy rates in this model, apparently by attenuating inflammation.

The objectives of this study were 1) to evaluate the effects of vaccination against foot-and- mouth disease (FMD) on growth performance, nutrient digestibility, hematological parameters, and behavior in a ruminant animal and 2) to investigate a possible strategy for reducing its adverse effect. A total of 12 Korean native goats (Capra hircus coreanae; 19.8 ± 2.9 kg) were used in a crossover design with 3 experimental periods and 3 treatments, randomized and balanced for counteracting possible carry-over effects. The treatments were 1) control, 2) co-injection with a commercially available dipyrone (CADI), and 3) supplementation with γ-amino butyric acid (GABA) at 10 g/kg in concentrate mix. Each period lasted 4 wk, and the vaccination against FMD was performed at 2 wk after the start of each period. The goats were individually housed in a metabolic cage and fed ad libitum with a diet consisting of bermuda grass and commercial concentrate mix (6:4, wt/wt). Dry matter intake, ADG, nutrients digestibility, hematological parameters, and behavioral activities of the goats were measured before and after vaccination. Although DMI was not decreased (P > 0.05), ADG was decreased by the vaccination to the goats (P < 0.01). The total number of leukocytes was increased while that of erythrocytes was decreased by the FMD vaccination (P < 0.01). The vaccination shortened standing time while extended lying time and the time spent in drinking (P < 0.05). The treatment by CADI reduced the adverse effect of vaccination on ADG and goat behavior compared with control and GABA treatment (P < 0.05). We concluded that the FMD vaccination decreased ADG of the goats without depression of diet intake, and CADI may attenuate the adverse effect of the FMD vaccination.

The interrelationship between muscle and adipose tissues plays a major role in determining the quality of carcass traits. The objective of this study was to compare metabolic differences between muscle and intramuscular adipose (IMA) tissues in thelongissimus dorsi(LD) of Hanwoo (Bos taurus coreanae) using the RNA-seq technology and a systems biology approach. The LD sections between the 6th and 7th ribs were removed from nine (each of three cows, steers, and bulls) Hanwoo beef cattle (carcass weight of430.2±40.66 kg) immediately after slaughter. The total mRNA from muscle, IMA, and subcutaneous adipose and omental adipose tissues were isolated and sequenced. The reads that passed quality control were mapped onto the bovine reference genome (build bosTau6), and differentially expressed genes across tissues were identified. The KEGG pathway enrichment tests revealed the opposite direction of metabolic regulation between muscle and IMA. Metabolic gene network analysis clearly indicated that oxidative metabolism was upregulated in muscle and downregulated in IMA. Interestingly, pathways for regulating cell adhesion, structure, and integrity and chemokine signaling pathway were upregulated in IMA and downregulated in muscle. It is thus inferred that IMA may play an important role in the regulation of development and structure of the LD tissues and muscle/adipose communication.

Finding ways to reduce roughage feeding without negatively affecting rumen health has been of interest in ruminant nutrition. The present study aimed to investigate the effects of quality and content of roughage on growth performance, ruminal fermentation, and blood metabolite levels in growing steers. Twenty-four Hanwoo steers (224 ± 24.7 kg) participated in this 24-week trial. The animals were fed TMR. Two types of concentrate mixes [high spec (HS) and low spec (LS)] were prepared to formulate iso-nitrous and iso-caloric TMR. The treatments were arranged as a 2 x 2 factorial with treatments consisting of 32% timothy and 68% HS (THS), 24% timothy with 76% LS (TLS), 24% ryegrass with 76% HS (RHS), and 17% ryegrass with 83% LS (RLS). Individual feed intakes were recorded using an automated system. Rumen fluid and blood before morning feeding were sampled and BW was measured every four weeks. Rumen fluid was collected using a stomach tube for five consecutive days at different sampling times each day (0800, 1100, 1300, 1500, and 1700). Mean DMI (7.33 kg) and ADG (1,033 g) did not differ among treatments. However, interactions between forage type and concentrate mix were observed in rumen and blood parameters (P < 0.05). Total VFA concentration was higher (P < 0.05) in TLS-fed steers than in the others. When timothy was provided, lower inclusion of roughage decreased propionate, increased butyrate, and increased acetate:propionate ratio. The opposite trends were observed when ryegrass was the source of roughage. In addition, the concentrations of plasma total protein, alanine transaminase, Ca, inorganic P, total cholesterol, triglycerides, and creatine were affected by treatments (P < 0.05). We concluded that rumen fermentation and body metabolism of the growing steers were affected by the quality and inclusion level of roughage in the diet, even though growth performance was unaffected. Key Words

© 2017 American Dairy Science Association Exogenous fibrolytic enzymes have been shown to be a promising way to improve feed conversion efficiency (FCE). β-Mannanase is an important enzyme digesting the polysaccharide β-mannan in hemicellulose. Supplementation of diets with β-mannanase to improve FCE has been more extensively studied in nonruminants than in ruminants. The objective of this study was to investigate the effects of β-mannanase supplementation on nutrient digestibility, FCE, and nitrogen utilization in lactating Holstein dairy cows. Twelve post-peak-lactation multiparous Holstein cows producing 45.5 ± 6.6 kg/d of milk at 116 ± 19.0 d in milk were randomly allotted to 1 of 3 treatments in a 3 × 3 Latin square design with 3 periods of 18 d (15 d for adaptation plus 3 d for sample collection). All cows were fed the same basal diet and the 3 treatments differed only by the β-mannanase dose: 0% dry matter (DM; control), 0.1% of DM (low supplement, LS), and 0.2% of DM (high supplement, HS) supplemented to the basal diet. Supplementation of β-mannanase enzyme at the LS dose reduced dry matter intake (DMI) but did not affect milk yield or milk composition. Cows receiving LS produced 90 g more milk per kg of DMI compared with control cows. Somatic cell count (SCC) in milk was lower for cows fed the LS diet compared with cows fed control diets. Cows fed LS diet had lower DM, organic matter and crude protein digestibility compared with cows fed control diets. Starch, neutral detergent fiber, and acid detergent fiber digestibility were not affected by LS. Milk yield, DMI, SCC, and nutrient digestibility did not change for HS. Despite the reduced crude protein digestibility, reduced N intake led to similar fecal N excretions in LS cows and control cows (234 vs. 235 g/cow per day). Urinary N excretions remained similar between enzyme-fed and control cows (~190 g/cow per day), although the percentage of N intake partitioned to urinary N tended to be greater in LS than in control cows (31 vs. 27%). Cows fed LS significantly improved the percentage of apparently absorbed N partitioned to milk protein N (42 vs. 38%). When supplemented at 0.1% of dietary DM, β-mannanase can improve FCE and lower the SCC of dairy cows without affecting milk yield, milk composition, or total manure N excretions of dairy cows.

The sequence of cattle genome provided a valuable opportunity to systematically link genetic and metabolic traits of cattle. The objectives of this study were 1) to reconstruct genome-scale cattle-specific metabolic pathways based on the most recent and updated cattle genome build and 2) to identify duplicated metabolic genes in the cattle genome for better understanding of metabolic adaptations in cattle. A bioinformatic pipeline of an organism for amalgamating genomic annotations from multiple sources was updated. Using this, an amalgamated cattle genome database based on UMD_3.1, was created. The amalgamated cattle genome database is composed of a total of 33,292 genes: 19,123 consensus genes between NCBI and Ensembl databases, 8,410 and 5,493 genes only found in NCBI or Ensembl, respectively, and 266 genes from NCBI scaffolds. A metabolic reconstruction of the cattle genome and cattle pathway genome database (PGDB) was also developed using Pathway Tools, followed by an intensive manual curation. The manual curation filled or revised 68 pathway holes, deleted 36 metabolic pathways, and added 23 metabolic pathways. Consequently, the curated cattle PGDB contains 304 metabolic pathways, 2,460 reactions including 2,371 enzymatic reactions, and 4,012 enzymes. Furthermore, this study identified eight duplicated genes in 12 metabolic pathways in the cattle genome compared to human and mouse. Some of these duplicated genes are related with specific hormone biosynthesis and detoxifications. The updated genome-scale metabolic reconstruction is a useful tool for understanding biology and metabolic characteristics in cattle. There has been significant improvements in the quality of cattle genome annotations and the MetaCyc database. The duplicated metabolic genes in the cattle genome compared to human and mouse implies evolutionary changes in the cattle genome and provides a useful information for further research on understanding metabolic adaptations of cattle.

Department of Animal Science and Biotechnology, Chungnam National University, Daejeon 305-764, KoreaABSTRACT Chicken is an important livestock as a valuable biomedical model as well as food for human, and there is a strong rationale for improving our understanding on metabolism and physiology of this organism. The first draft of chicken genome assem-bly was released in 2004, which enables elaboration on the linkage between genetic and metabolic traits of chicken. The objectives of this study were thus to reconstruct metabolic pathway of the chicken genome and to construct a chicken specific pathway genome database (PGDB). We developed a comprehensive genome database for chicken by integrating all the known annotations for chicken genes and proteins using a pipeline written in Perl. Based on the comprehensive genome annotations, metabolic pathways of the chicken genome were reconstructed using the PathoLogic algorithm in Pathway Tools software. We identified a total of 212 me-tabolic pathways, 2,709 enzymes, 71 transporters, 1,698 enzymatic reactions, 8 transport reactions, and 1,360 compounds in the current chicken genome build, Gallus_gallus-2.1. Comparative metabolic analysis with the human, mouse and cattle genomes re-vealed that core metabolic pathways are highly conserved in the chicken genome. It was indicated the quality of assembly and anno-tations of the chicken genome need to be improved and more researches are required for improving our understanding on function of genes and metabolic pathways of avian species. We conclude that the chicken PGDB is useful for studies on avian and chicken metabolism and provides a platform for comparative genomic and metabolic analysis of animal biology and biomedicine.(Key words : metabolic reconstruction, chicken genome, pathway genome database, bioinformatics)To whom correspondence should be addressed : swseo@cnu.kr'(Gallus gallus)()*+,!-./012 345 6+78!- 9, :*)'(; ?34%@ABCD EFGHIJK L8M>NO+P % QRS=TUB, %B%d+Z[e% f, 0gHhf, ;ijkA #lm 6Q` a=nopqc% , BQ 34rst!-uF. B;ejv+Bwx yzB{>|}~V{>K B}€=TU%&‚=:ƒue„ †34, {}|+‡ˆ†E+BUW, :ƒ‰>NO+{}|Š?\](genome-scale model)=TJ‹ Œ-uF(Schilling et al., 1999). {}|Š?\]J‹(.Ž{}$B[: , >=Že‘ pqc{}$’ “’B‚##”•J‹, U‹–X—=˜F. {}|Š?\]J‹=™U;š4›œ ž‰8Ÿu9 , +bc idp. ¢% £e¤A ¢% =z—F¥% |B{}|;š4[ r‰¦F(Seo and Lewin, 2009). §Ž, Pathway Tools v¨©a8e}|;š4•[ ue«{¬u,­¬®Š7e« , PathoLogic ¯¤d°= ¬u± {}|B†E²MetaCyc(Caspi et al., 2006)+z—m;š4•P

A mechanistic and dynamic model was developed to represent physiological aspects of particle dynamics in the reticulo-rumen (RR) and to predict rate of passage out of the RR (Kp) of forage particles quantitatively. The model consists of 2 conceptual pools with 3 spatial compartments of particles; the compartment the particle enters is based on functional specific gravity (FSG). The model assumes 2 major pressure gradient-driven flows of particles out of the RR through the reticulo-omasal orifice between 2 consecutive primary reticular contractions. One is associated with the second phase of primary reticular contraction and involves propulsion of particles in the vicinity of the honeycomb structure of the reticulum from the RR. The second flow involves movement of particles in the reticulum without selection by size. Particle outflow rate was assumed to be proportional to liquid outflow rate. The passage coefficient, defined as the ratio of particle to liquid outflow rate, was estimated for each particle group by an equation derived from the probability of passage based on FSG and particle size. Particles retained on a 1.18-mm screen were defined as large particles. When the model was evaluated with 41 observations in an independent database, it explained 66% of the variation in observed Kp of forage particles with a root mean square prediction error of 0.009. With 16 observations that also included measurements of liquid passage rate, the model explained 81 and 86% of the variation in observed Kp liquid and Kp forage, respectively. An analysis of model predictions using a database with 455 observations indicated that the assumptions underlying the model seemed to be appropriate to describe the dynamics of forage particle flow out of the RR. Sensitivity analysis showed that probability of a particle being in the pool likely to escape is most critical in the passage of large forage particles, whereas the probability of being in the reticulum as well as in the likely to escape pool is important in the passage of small forage and concentrate particles. The FSG of a particle is more important in determining the fate of a particle than its size although they are correlated, especially for forage particles. We conclude that this model can be used to understand the factors that affect the dynamics of particle flow out of the RR and predict Kp of particles out of the RR in dairy cattle.

Current ration formulation systems used to formulate diets on farms and to evaluate experimental data estimate metabolizable energy (ME)-allowable and metabolizable protein (MP)-allowable milk production from the intake above animal requirements for maintenance, pregnancy, and growth. The changes in body reserves, measured via the body condition score (BCS), are not accounted for in predicting ME and MP balances. This paper presents 2 empirical models developed to adjust predicted diet-allowable milk production based on changes in BCS. Empirical reserves model 1 was based on the reserves model described by the 2001 National Research Council (NRC) Nutrient Requirements of Dairy Cattle, whereas empirical reserves model 2 was developed based on published data of body weight and composition changes in lactating dairy cows. A database containing 134 individually fed lactating dairy cows from 3 trials was used to evaluate these adjustments in milk prediction based on predicted first-limiting ME or MP by the 2001 Dairy NRC and Cornell Net Carbohydrate and Protein System models. The analysis of first-limiting ME or MP milk production without adjustments for BCS changes indicated that the predictions of both models were consistent (r(2) of the regression between observed and model-predicted values of 0.90 and 0.85), had mean biases different from zero (12.3 and 5.34%), and had moderate but different roots of mean square errors of prediction (5.42 and 4.77 kg/d) for the 2001 NRC model and the Cornell Net Carbohydrate and Protein System model, respectively. The adjustment of first-limiting ME- or MP-allowable milk to BCS changes improved the precision and accuracy of both models. We further investigated 2 methods of adjustment; the first method used only the first and last BCS values, whereas the second method used the mean of weekly BCS values to adjust ME- and MP-allowable milk production. The adjustment to BCS changes based on first and last BCS values was more accurate than the adjustment to BCS based on the mean of all BCS values, suggesting that adjusting milk production for mean weekly variations in BCS added more variability to model-predicted milk production. We concluded that both models adequately predicted the first-limiting ME- or MP-allowable milk after adjusting for changes in BCS.

Dairy ration formulation to meet protein and amino acid requirements with the National Research Council Nutrient Requirements of Dairy Cattle (NRC, 2001) model depends on accuracy of predicting feed passage rates out of the rumen. The NRC (2001) passage rate (Kp) equations were evaluated for validity and sensitivity to input variables in predicting supplies of rumen degraded protein, rumen undegraded protein, and metabolizable protein. The database used in the development of the 3 Kp equations (for dry forage, wet forage, and concentrate) was used to independently derive the 3 equations using a meta-analysis technique. To extract quantitative relationships between statistically significant input variables and rate of passage, a random coefficients model that used each study effect as a random variable was used. The database was comprised of studies that only used rare earth markers. Outliers were identified by acceptance criteria defined a priori or the difference in fit statistic (DFFITS) value; 319, 63, and 139 treatment means were used to develop the Kp equations for dry forage, wet forage, and concentrate, respectively. We found that the sign of the regression coefficient for concentrate content in diet dry matter in the equation for Kp dry forage was inverted; it should be positive. A sensitivity analysis was conducted with a spreadsheet version of the NRC (2001) model developed for this study, using the Monte Carlo technique. The sensitivity analysis indicated that all Kp predictions were the most sensitive to variation in DM intake, and thus accurate measurement of DM intake is the most important factor in predicting Kp. Predictions for protein supply (rumen degraded protein, rumen undegraded protein, and metabolizable protein) were sensitive to variability in amount of feed crude protein (CP, %DM), digestion rate (Kd) of the B fraction of feed CP (%/h), and the Kp for concentrate (%/h), due to the high proportion of dietary CP in lactating dairy rations coming from concentrates. The sensitivity analysis indicated that accurate determinations of DMI, the Kd of the B fraction of feed CP, and feed CP are the most important variables needed to predict MP supply in lactating dairy cows with the NRC (2001) model. We conclude that the empirical Kp equations in the model are suitable for predicting passage rate in lactating dairy cows. More accurate predictions of Kp will require the development of a more mechanistic model that accounts for more of the biologically important variables (e.g., physical property of particles, liquid flow, and timely variation of intake) affecting passage rate.

Marbling from intramuscular fat is an important trait of meat quality and has an economic benefit for the beef industry. Quantitative trait loci (QTL) fine mapping was performed to identify the marbling trait in 266 Hanwoo steers using a 10K single nucleotide polymorphism panel with the combined linkage and linkage disequilibrium method. As a result, we found nine putative QTL regions for marbling: three on BTA6, two on BTA17, two on BTA22, and two on BTA29. We detected candidate genes for marbling within 1 cM of either side of the putative QTL regions. Additionally, to understand the functions of these candidate genes at the molecular level, we conducted a functional categorization using gene ontology and pathway analyses for those genes involved in lipid metabolism or fat deposition. In these putative QTL regions, we found 95 candidate genes for marbling. Using these candidate genes, we found five genes that had a direct interaction with the candidate genes. We also found SCARB1 as a putative candidate gene for marbling that involves fat deposition related to cholesterol transport.

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production. Fil: Bovine Genome Sequencing and Analysis Consortium. Bovine Genome Sequencing And Analysis Consortium; Estados Unidos Fil: Amadio, Ariel Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Santa Fe. Estación Experimental Agropecuaria Rafaela; Argentina Fil: Poli, Mario Andres. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Genética; Argentina

A mechanistic and dynamic model was developed to represent the physiological aspects of liquid dynamics in the rumen and to quantitatively predict liquid flow out of the reticulorumen (RR). The model is composed of 2 inflows (water consumption and salivary secretion), one outflow (liquid flow through the reticulo-omasal orifice (ROO), and one in-and-out flow (liquid flux through the rumen wall). We assumed that liquid flow through the ROO was coordinated with the primary reticular contraction, which is characterized by its frequency, duration, and amplitude during eating, ruminating, and resting. A database was developed to predict each component of the model. A random coefficients model was used with studies as a random variable to identify significant variables. Parameters were estimated using the same procedure only if a random study effect was significant. The input variables for the model were dry matter intake, body weight, dietary dry matter, concentrate content in the diet, time spent eating, and time spent ruminating. Total water consumption (kg/d) was estimated as 4.893 x dry matter intake (kg/d), and 20% of the water consumed by drinking was assumed to bypass the RR. The salivary secretion rate was estimated to be 210 g/min during chewing. During ruminating, however, the salivation rate was assumed to be adjusted for the proportion of liquid in the rumen. Resting salivation was exponentially related to dry matter intake. Liquid efflux through the rumen wall was assumed to be the mean value in the database (4.6 kg/h). The liquid outflow rate (kg/h) was assumed to be a product of the frequency of the ROO opening, its duration per opening, and the amount of liquid passed per opening. Simulations of our model suggest that the ROO may open longer for each contraction cycle than had been previously reported (about 3 s) and that it is affected by dry matter intake, body weight, and total digesta in the rumen. When compared with 28 observations in 7 experiments, the model accounted for 40, 70, and 90% of the variation, with root mean square prediction errors of 9.25 kg, 1.84 kg/h, and 0.013 h(-1) for liquid content in the rumen, liquid outflow rate, and fractional rate of liquid passage, respectively. A sensitivity analysis showed that dry matter intake, followed by body weight and time spent eating, were the most important input variables for predicting the dynamics of liquid flow from the rumen. We conclude that this model can be used to understand the factors that affect the dynamics of liquid flow out of the rumen and to predict the fractional rate of liquid passage from the RR in dairy cattle.

Production efficiency decreases when diets are not properly balanced for protein. Sensitivity analyses of the protein fractionation schemes used by the National Research Council Nutrient Requirement of Dairy Cattle (NRC) and the Cornell Net Carbohydrate and Protein System (CNCPS) were conducted to assess the influence of the uncertainty in feed inputs and the assumptions underlying the CNCPS scheme on metabolizable protein and amino acid predictions. Monte Carlo techniques were used. Two lactating dairy cow diets with low and high protein content were developed for the analysis. A feed database provided by a commercial laboratory and published sources were used to obtain the distributions and correlations of the input variables. Spreadsheet versions of the models were used. Both models behaved similarly when variation in protein fractionation was taken into account. The maximal impact of variation on metabolizable protein from rumen-undegradable protein (RUP) was 2.5 (CNCPS) and 3.0 (NRC) kg/d of allowable milk for the low protein diet, and 3.5 (CNCPS) and 3.9 (NRC) kg/d of allowable milk for the high protein diet. The RUP flows were sensitive to ruminal degradation rates of the B protein fraction in NRC and of the B2 protein fraction in the CNCPS for protein supplements, energy concentrates, and forages. Absorbed Met and Lys flows were also sensitive to intestinal digestibility of RUP, and the CNCPS model was sensitive to acid detergent insoluble crude protein and its assumption of complete unavailability. Neither the intestinal digestibility of the RUP nor the protein degradation rates are routinely measured. Approaches need to be developed to account for their variability. Research is needed to provide better methods for measuring pool sizes and ruminal digestion rates for protein fractionation systems.