Chromosome-level genome assembly of the shuttles hoppfish, Periophthalmus modestus

Background The shuttles hoppfish (mudskipper), Periophthalmus modestus, is one of the mudskippers, which are the largest group of amphibious teleost fishes, which are uniquely adapted to live on mudflats. Because mudskippers can survive on land for extended periods by breathing through their skin and through the lining of the mouth and throat, they were evaluated as a model for the evolutionary sea-land transition of Devonian protoamphibians, ancestors of all present tetrapods. Results A total of 39.6, 80.2, 52.9, and 33.3 Gb of Illumina, Pacific Biosciences, 10X linked, and Hi-C data, respectively, was assembled into 1,419 scaffolds with an N50 length of 33 Mb and BUSCO score of 96.6%. The assembly covered 117% of the estimated genome size (729 Mb) and included 23 pseudo-chromosomes anchored by a Hi-C contact map, which corresponded to the top 23 longest scaffolds above 20 Mb and close to the estimated one. Of the genome, 43.8% were various repetitive elements such as DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. Ab initio and homology-based gene prediction identified 30,505 genes, of which 94% had homology to the 14 Actinopterygii transcriptomes and 89% and 85% to Pfam familes and InterPro domains, respectively. Comparative genomics with 15 Actinopterygii species identified 59,448 gene families of which 12% were only in P. modestus. Conclusions We present the high quality of the first genome assembly and gene annotation of the shuttles hoppfish. It will provide a valuable resource for further studies on sea-land transition, bimodal respiration, nitrogen excretion, osmoregulation, thermoregulation, vision, and mechanoreception.

Nitrogen Intake and Its Partition on Urine, Dung and Products of Dairy and Beef Cattle in Chile

Nitrogen that is excreted through the urine and dung of cattle is an important source of nitrous oxide and ammonia emissions. In Chile, several studies have evaluated nitrogen (N) intake and its partitioning into urine and dung from beef and dairy cattle, however, there are no studies collating all data into one central database, which would allow an estimation of N excretion and its key variables to be developed. The aim of this study was to determine the N partition (milk or meat, urine and dung) and variables influencing the nitrogen use efficiency (NUE) and urinary N excretion of cattle based on a database generated from Chilean studies. The search of studies was carried out using a keyword list in different web-based platforms. Nitrogen excretion into urine and dung was calculated using equations reported in the literature for beef and dairy cattle. Mixed models were used to identify variables influencing the N partitioning. Nitrogen intake and its partitioning into the animal product, urine and dung were higher for dairy compared to beef cattle. For dairy cattle, NUE was influenced by milk yield, the non-fibrous carbohydrates (NFC)/crude protein ratio, acid detergent fiber intake and milk urea N (MUN), while urinary N excretion was influenced by milk yield, MUN and NFC intake. For beef cattle, N intake and its excretion were greater for grazing compared to the confined system, while NUE was greater for confined animals. This database supplies new information on N intake and its partitioning (milk, meat, urine and dung) for dairy and beef cattle, which can be used for the estimation of greenhouse gas emissions from pasture-based livestock in Chile. Additionally, our study supplies new information on nutritional variables determining NUE and urinary N excretion for dairy cattle, which can be used by farmers to reduce N excretion into the environment.

Effect of protein and glucogenic precursor supplementation on forage digestibility, serum metabolites, energy utilization, and rumen parameters in sheep

Supplementation of glucogenic precursors in roughage diets may increase production responses due to improved efficiencies of nutrient utilization. Therefore, the objective of this study was to determine the effect of source of supplemental glucogenic potential (GP) on forage digestibility, serum metabolites, energy utilization, and rumen parameters of growing wethers consuming a roughage diet (8.8% crude protein, 71.4% ash-free neutral detergent fiber). Crossbred wethers (49.1 ± 4.7 kg initial BW; n = 16) were utilized in a 4 × 4 replicated Latin Square design with four periods of 21 d. Supplements were designed to supplement increasing amount of GP: (1) no supplementation (CON; 0 g), (2) 40 g of calcium propionate (CAP; 30 g of GP), (3) 70 g of blood meal + 100 g of feather meal (BF; 40 g of GP), or (4) combination of CAP and BF (COMBO; 70 g of GP). Total fecal and urine collection was conducted from d 13 – 17 to calculate digestibility estimates and urinary losses. An acetate tolerance test was administered on d 17 to determine the effect of GP on acetate clearance. Blood samples were collected on d 19 and were analyzed for serum concentrations of glucose, urea N (SUN), non-esterified fatty acids, and amino acids. Rumen fluid was collected on d 21 to determine supplementation effects on ruminal volatile fatty acid (VFA) and ammonia concentrations. Wethers receiving BF and COMBO supplementation had greatest (P ≤ 0.01) DM and OM total tract digestibility. Supplementation did not affect (P ≥ 0.37) NDF digestibility or digestible energy. Urinary nitrogen excretion was greatest (P = 0.02) for BF and COMBO. Circulating serum essential amino acid concentration was increased (P < 0.01) in BF and COMBO compared to CAP and CON. In addition, BF and COMBO had increased (P < 0.01) SUN concentrations compared to CAP and CON. Acetate half-life was not affected (P = 0.39) by supplementation strategy. However, area under the curve (AUC) for acetate was decreased (P = 0.04) with supplementation of BF and COMBO compared to CON-fed wethers. Ruminal propionate concentration was increased (P ≤ 0.01) for wethers fed CAP and COMBO supplementation, which resulted in decreased (P ≤ 0.01) A:P ratio. Overall, these results indicate that the increased propionate supply by providing propionate salts did not result in a protein sparing impact or increased N retention.

Digestibility and nitrogen and water balance in horses fed rhizoma peanut hay

Rhizoma peanut (RP, Arachis glabrata) hay has the potential to meet horses’ crude protein requirements with less nitrogen excretion than other legumes. This study aimed to evaluate nutrient intake, apparent digestibility, and nitrogen balance of RP ‘Florigraze’ hay compared to alfalfa (ALF, Medicago sativa L. ‘Legendary XHD’) and bermudagrass (BG, Cynodon dactylon L. ‘Coastal’) hays when fed to maintenance horses at 2% BW/d on a dry matter (DM) basis. We hypothesized that nutrient intake would be comparable between the legume hays and lesser for BG, and that RP would result in reduced nitrogen excretion compared to alfalfa. Six mature Quarter Horse geldings (593 ± 40 kg; mean ± SD) were randomly assigned to one of the hays in a replicated 3 x 3 Latin square with 21-d periods. A 14-d adaptation phase was followed by a 3-d total fecal and urine collection. Days 18 to 21 were used for a companion study. Intake of nutrients is reported on a DM basis. Digestible energy (DE) intakes from ALF (29.91 Mcal/d) and RP (29.37 Mcal/d) were greater (P < 0.0001) than BG (20.78 Mcal/d). Crude protein (CP) intake was greater (P < 0.0001) for ALF (2.5 kg/d), followed by RP (1.9 kg/d), and BG (1.5 kg/d). All hays exceeded maintenance requirements for DE, CP, Ca, and P. Apparent digestibility of DM and CP were greatest (P < 0.0001) for ALF (69 and 84%), intermediate for RP (61 and 72%), and least for BG (46 and 64%). Apparent digestibility of neutral detergent fiber did not differ (P = 0.2228) among hays, while digestibility of acid detergent fiber (P = 0.0054) was least for RP but similar for ALF and BG. Water intake (kg/d) for ALF (57) was greater (P=0.0068) than RP (45) and BG (41). Greater (P = 0.0271) water retention (kg/d) was observed for ALF (13.5), followed by RP (10.8) and BG (7.5). There was a difference in nitrogen excretion, with greatest urinary nitrogen excretion for ALF (P < 0.0001) and greatest fecal nitrogen excretion for BG (P = 0.0001). Total nitrogen excretion was greater (P < 0.0001) for ALF (278 g/d), followed by RP (211 g/d), and BG (179 g/d). Nitrogen retention was greater (P = 0.0005) for ALF when represented as g/d (ALF: 129, RP: 86, and BG: 57 g/d), but similar (P = 0.0377) to RP when presented as percent of nitrogen intake (ALF: 32, RP: 29, and BG: 24%). Results indicate that rhizoma peanut hay is a suitable legume for horses by meeting DE and CP requirements and having a significant reduction in nitrogen compared to alfalfa.

214 Dietary Supplementation with a Combination of Valine and Isoleucine Annuls the Negative Effects of Very Low Protein Diets on Growth and Gut Development of Young Pigs

Increased feed cost, post-weaning diarrhea, and nitrogen excretion are challenging the modern swine industry. Very low-protein (LP) diets (>4% units reduced protein) may reduce feed cost, diarrhea and nitrogen excretion; however, these diets impair growth performance of pigs despite supplementation of limiting amino acids (i.e., lysine, threonine, methionine and tryptophan). The objective of this study was to investigate the effect of valine, isoleucine and combination of both supplemented to VLP diet on growth, thermal radiation, and gut development in young pigs. Forty three-week-old weaned barrows were weighed (6.75 ± 0.14 kg) and randomly assigned to five groups (8 pigs/group) including: 1) standard diet or positive control (PC), 2) LP diet, 3) LP + valine (LPV), 4) LP + isoleucine (LPI) and 5) LP + both valine and isoleucine (LPVI) for five weeks. Daily feed intake and weekly growth characteristics were measured and weekly thermal images were captured. All pigs were euthanized at week 5 and tissue samples collected. All data were analyzed with univariate GLM followed by Tukey’s post-hoc test (SPSS®). Compared to PC, final body weight, average daily gain, average daily protein intake and gain:feed ratio were reduced in LP group, but feeding pigs with LPVI partially or completely recovered these parameters. Pigs fed with LPVI had higher thermal radiation than those fed with PC, LP, and LPI on days 28 and 35 of study and had a greater the area under the curve for thermal radiation than LP and LPI. Duodenal villus width and crypt depth, and ileal villus height were decreased in LP relative to PC, but LPVI either partially or fully recovered these measurements. In conclusion, supplementing a combination of valine and isoleucine recovered the negative effects of very low-protein diets on growth performance and gut development, but increased the thermal radiation in weaned pigs.

319 Predicting Urinary Nitrogen Excretion from Milk Urea Nitrogen of Fresh Forage or Total Mixed Ration Fed Dairy Cows: A Meta-analysis

Urine nitrogen excretion (g/d; UN) represent a significant environmental impact for both confinement feeding and pastoral based dairy systems. It is difficult to measure UN directly due to animal handling and labor requirements, especially in forage based production systems. The currently available milk urea nitrogen (MUN) equations have been shown to overestimate UN excretion of grazing dairy cows compared with an equation using urinary creatinine and UN concentration, indicating that diet may alter the relationship between MUN and UN. This potential was explored using data retrieved (treatment means: n = 69 and 27 for fresh forage [FF] and total mixed ration [TMR] fed cattle, respectively) from the literature and new data obtained from dairy cows fed FF (n = 15) in metabolism crates was used to test the new equations. The TMR data from literature was further split into a training set (to develop the model; n = 53) and a test set (to validate the model; n = 16). There was an interaction for diet type (P < 0.01) where UN (g/d) = 0.023 × MUN (mg/dL) × live-weight (kg, LW) for TMR fed cattle, (similar to a pre-established equation); however, UN (g/d) = 0.015 × MUN × LW for FF fed cattle. For FF based equations, the New MUN equation and the creatinine equation showed good precision and accuracy (Lin’s CCC = 0.79 and 0.74, respectively) and adequate predictive ability (RMSEP = 29.8 and 35.9, respectively). The new MUN equation for TMR fed cattle showed excellent accuracy and precision (Lin’s CCC = 0.87) with good predictive ability (RMSEP = 24.3) for UN excretion (observed mean = 216.5 g/d). The new equations generated during this meta-analysis provide promising predictive ability of UN excretion, which can be used for management considerations, future research, and policy making.

The Dairy Cow Slurry Composition Used as Organic Fertilizer Is Influenced by the Level and Origin of the Dietary Protein

Less than 30% of dairy cattle’s nitrogen ingested is retained in milk. Therefore, large amounts of nitrogen can be excreted in manure and urine with a potential environmental impact. In addition, some legume forages can be more susceptible to proteolysis during the silage process than grasses, and dairy cows fed these legume silages would excrete a larger quantity of nitrogen in slurry. The objectives of this work were to evaluate the amount of nitrogen excretion in dairy cows fed different protein levels and legume silages with a view to improve the slurry quality as a co-product that can be used as fertilizer. Two double 3 × 3 Latin square trials were carried out in order to study three different protein levels (high, medium, and low) and three different silages (grass, faba bean, and field pea). Dry matter intake, milk production, and composition were not affected by treatments. The excretion of ammonia-N in the urine was almost four times lower in the diet with the lowest protein level. The ammonia-N in the urine was twice as high with the pea silage than faba bean and grass silages. In conclusion, the diet containing 13% of protein meets the protein requirement for lactating cows producing 31 kg daily, with low nitrogen excretion in the urine, and the main pathway for the excretion of surplus nitrogen from legume silages is through urine and the metabolization of pea silage protein goes toward ammonia-N.