bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring major gene-marker phase-typing strategies in marker-assisted selection schemes
Authors: Marshall K. , van der Werf J. H. J. , Henshall J. 
Published: May 2019

AbstractMajor gene-marker phase is generally assumed to be family specific. This has the consequence in relation to marker-assisted selection (MAS) that phase information about each family may need to be collected through progeny testing, which could represent a substantial cost. This paper examines the effect of different policies in relation to major gene-marker phase-typing on response to MAS. The different policies considered varied in the criteria by which individuals were selected for phase-typing, the number of individuals phase-typed, and the frequency of establishing phase. Stochastic simulation of a closed breeding nucleus, with either high or low levels of inbreeding and undergoing selection for two traits, was utilized. Total response under MAS was lower than that under genotypic assisted selection (GAS) for all phase-typing policies. For example, additional gains of 70% under GAS, achieved in year 1 and in comparison with non-MAS, corresponded to additional gains of 43% and 15% under MAS for linkage distances of 1 cM and 20 cM, respectively. The different phase-typing policies examined in relation to MAS did not have any effect on total response, although there were small effects on major gene response. For breeding nuclei with either level of inbreeding, higher major gene response was achieved when phase-typed sires were selected on the basis of high ranking for genetic merit rather than connectivity to the other selection candidates. Further, increasing the number of males phase-typed within any year did not increase the rate of major gene response, although phase-typing in more years was favourable for the large linkage distance. An overall conclusion of this study is that additional gain could be achieved under MAS within a closed nucleus when progeny testing to determine major gene-marker phase was limited to from one to a few individuals.
Comparison of calorimetry and the doubly labelled water technique for the measurement of energy expenditure in Equidae
Authors: Fuller Z. , Maltin C. A. , Milne E. , Mollison G.S. , Cox J. E. , McG. Argo C. 
Published: May 2019

AbstractEvaluations of the energy requirements of working animals have been confounded by the constraints of indirect calorimetric techniques (Cal). This study sought to investigate a non-restrictive methodology, the doubly labelled water (DLW;2H218O) technique, for the measurement of energy expenditure in free ranging equids. Six pony geldings were intravenously injected with DLW in two sequential studies that permitted first, isotope equilibration and half-lives to be determined and then second, heat production (HP) to be measured simultaneously by DLW and traditional (Cal) techniques.In study 1, three animals were injected with DLW, three animals were untreated controls. Blood samples were collected every 30 min for 12 h and thereafter at 24 h intervals for 14 days. Isotopes equilibrated throughout the body water pool within 300 (2H) and 240 (18O) min and half-lives were 6.3 ± 0.6 days (2H) and 5.6 ± 0.4 days (18O).In study 2, HP was simultaneously determined by Cal and DLW over a 4-day period. Animals (no. = 6) were assigned to pairs and in successive weeks two ponies were injected with DLW and confined to metabolism chambers 12 h later. Cal HP was 0.51 ± 0.02 MJ/kg M0.75per day compared with 0.48 ± 0.29 MJ/kg M0.75per day estimated by DLW. Maintenance metabolizable energy intake was 0.53 ± 0.01 MJ/kg M0.75per day (Cal) and 0.50 ± 0.01 MJ/kg M0.75per day (DLW). Validation of the DLW technique may empower essential, systematic appraisal of energy requirements in unrestrained working horses.
Calculation of multiple-trait sire reliability for traits included in a dairy cattle fertility index
Authors: Banos G. , Brotherstone S. , Thompson R. , Woolliams J. A. , Wall E. , Coffey M. P. 
Published: May 2019

AbstractThe advent of genetic evaluations for fertility traits in the UK offers valuable information to farmers that can be used to control fertility problems and safeguard against involuntary culling. In addition to estimated genetic merit, proof reliabilities are required to make correct use of this genetic information. Exact reliabilities, based on the inverse of the coefficient matrix, cannot be estimated for large data sets because of computational restrictions. A method to calculate approximate reliabilities was implemented based on a six-trait sire model. Traits considered were interval between first and second calving, interval between first calving and first service, non-return rate 56 days post first service, number of inseminations per conception, daily milk yield at test nearest day 110 and body condition score. Sire reliabilities were calculated in four steps. Firstly, the number of effective daughters was calculated for each bull, separately for each trait, based on total number of daughters and daughter distribution across herd-year-seasons. Secondly, multiple-trait reliabilities were calculated, based on bull daughter contribution, applying selection index theory on independent daughter groups. Thirdly, (great-) grand-daughter contribution was added to the reliability of each bull, using daughter-based reliability of sons and maternal grandsons. An adjustment was made to account for the probability of bull and son or grandson having daughters in the same herd-year-season. Without the adjustment, reliabilities were inflated by proportionately 0·15 to 0·25. Finally, parent (sire and maternal grandsire) contribution was added to the reliability of each bull. The procedure was first tested on a data subset of 28 061 cow records from 285 bulls. Approximate reliabilities were compared with exact estimates based on the inverse of the coefficient matrix. Mean absolute differences ranged from 0·014 to 0·020 for the six traits and correlation between exact and approximate estimates neared unity. In a full-scale application, sire reliability for the fertility traits increased by proportionately 0·47 to 0·79 over single-trait estimates and the number of bulls with a reliability of 0·60 or more increased by 42 to 115%.
The relationship between the body shape of living pigs and their carcass morphology and composition
Authors: Doeschl A. B. , Green D. M. , Whittemore C. T. , Schofield C. P. , Fisher A. V. , Knap P. W. 
Published: May 2019

AbstractThe conformation, tissue composition, and chemical composition of three types of pigs, given food ad libitum and slaughtered over a nominal live weight range of 35 to 115 kg, was assessed in relation to data provided on the live animals by a visual image analysis (VIA) system. The pig types were named as ‘3⁄4 Landrace’, ‘1⁄2 Pietrain’, and ‘1⁄4 Meishan’ types, representing ‘attenuated’, ‘blocky’, and ‘flabby’ types. Three analyses of the shape, conformation and composition data were performed. First, the relationship between conformation and age/size was assessed using linear regression of logarithmically transformed VIA and carcass data. In relation to age, ‘1⁄2 Pietrain’ pigs were found by both VIA and carcass measurements to have the widest shoulders. Both analyses also found this type to have the widest ham, trunk, and shoulders in relation to body length across most of the body length range studied, although the greatest rate of increase in ham width in relation to body length was found in the ‘1/4 Meishan’ type pigs. Second, the relationship between composition and VIA shape was examined using linear regression of transformed and standardized data. Significant relationships were found between fat, lipid, muscle, and protein weight and VIA shape, although relationships were weaker for protein and muscle weight. For fat and lipid, the VIA shape measures from the trunk region proved the most informative, whereas the VIA ham measures proved the most informative for muscle and protein. Third, detrended measures of composition/conformation and shape were used to remove the effect of animal size from the data. Removal of the variation due to growth generally led to substantial decreases in the adjusted R2statistics and in the R2-like statistics for prediction. Although in the models without detrending, relative fat and lipid weight had been found most strongly correlated with VIA shape, relative muscle was found most strongly correlated with shape in the detrended data. This was considered to result from the low between-animal variation in the data set combined with greater across-weight variation in fat and lipid weights than muscle and protein weights in the data without trend removal. Future trials with greater between-animal variation imposed would allow more precise determination of the relationship between conformation and shape.
The effects of dietary oil inclusion and oil source on apparent digestibility, faecal volatile fatty acid concentration and manure ammonia emission
Authors: Leek A. B. G. , Beattie V. E. , J. V. O’Doherty  
Published: May 2019

AbstractAn investigation was conducted to test the hypothesis that dietary oil inclusion increases ammonia nitrogen (NH3-N) emission from the manure, due to a negative effect of either unsaturated or saturated oil on microbial activity in the intestine. Dietary oil was included at 45 g/kg, as either crude palm oil (PO), soya oil (SO) or a 50: 50 SO: PO blend (OB), to a basal barley-soya-wheat diet (control) at the expense of dextrose and maize starch. Diets were formulated to contain 13·2 MJ digestible energy per kg and 11·0 g/kg lysine. Four boars were assigned to each dietary treatment, and were transferred to metabolism crates (mean live weight, 74·0 (± 2·89) kg) following 14 days dietary acclimatization. Urine and faeces were collected separately over a 5-day digestibility/nitrogen (N) balance period and a 2-day manure collection period. Inclusion of dietary oil increased apparent digestibility of oil (P < 0·01) and decreased the apparent digestibility of dry matter (P < 0·01) and gross energy (P < 0·05). Dietary oil did not affect the apparent digestibility of nitrogen, acid-detergent fibre, neutral-detergent fibre or hemicellulose. Apparent digestibility of oil was lower when oil was included as PO compared with SO and OB (P < 0·001). The concentration of faecal volatile fatty acid (VFA) was similar in all treatments, although the acetic: propionic acid ratio was lower when oil was included as PO and OB compared with SO (P < 0·05). N balance, manure N concentration and NH3-N emission was not affected by oil inclusion or oil source. In conclusion, dietary oil inclusion reduced apparent dry matter and energy digestibilities, although no effect on fermentation was indicated by digestibility of fibre or faecal VFA content. Consequently, ammonia emission was not affected by dietary oil included at 45 g/kg.
Relationship between graded doses of three microbial phytases and digestible phosphorus in pigs
Authors: Paditz K. , Kluth H. , Rodehutscord M. 
Published: May 2019

AbstractThe efficacy of three microbial phytases to increase the amount of digestible phosphorus (dP) was studied in pigs. A basal diet was prepared meeting the requirements of 30-kg pigs with the exception of P. Concentrations (in g/kg dry matter) were: P 2·9, phytate P 1·3, calcium (Ca) 6·9, and crude protein 208. Intrinsic phytase activity was below detection limit. Microbial phytase was supplemented from three sources (Aspergillus niger (Asp), Peniophora lycii (Pen), and consensus phytase (Con)) at the following levels (phytase units (FTU) per kg diet): 150, 300, 450, 600 and 900. Diets were pelleted without steam. Forty-eight male castrated crossbred pigs ((Large White X German Landrace) X Pietrain) initially weighing, on average, 28 kg were individually penned. Each of the 16 diets was offered to three pigs in three consecutive periods of 17 days each, resulting in nine replicates per treatment. No animal received the same diet twice. Faeces were spot-sampled for each individual pig twice daily for the last 7 days of each period. TiO2was used as an indigestible marker. An exponential function was fitted to the data, and both marginal and cumulative efficacies of phytases were described on the basis of the resulting functions.No significant period effect was detected for any of the obtained data. On overall average, daily live-weight (LW) gain was 730 g, and 2.57 kg food were needed per kg LW gain. Neither criterion was significantly affected by source or level of supplementary phytase. Digestibility of organic matter and crude protein averaged 0.90 and 0.84, respectively, again without a significant treatment effect. Digestible P concentration in no case exceeded 1.5 g/kg DM, indicating that P supply to pigs was marginal in all treatments. Digestibility of P from the basal diet was 0.22. P digestibility was significantly affected (P = 0.001) both by the source and by the level of supplementary phytase. It responded in a non-linear fashion to increasing phytase supplementation, this course being less clear for Pen than for Asp and Con phytase. In no case was a clear plateau in P digestibility reached within the range studied. For Asp and Con, marginal efficacy decreased from about 2 mg dP per incremental FTU at low supplementary level to roughly 0.6 mg dP per incremental FTU. This clear dose dependent effect was not present for the Pen phytase, where about 0.6 to 0.7 mg dP per incremental FTU were released almost irrespective of the level of supplementation. It is concluded that phytases of different origin rank differently from each other regarding their efficacy, depending on the level of supplementation. Dose-response studies are recommended in cases where different phytases are to be compared.
The effect of management system at lambing and flock genetics on lamb output and labour requirements on lowland sheep farms
Authors: Carson A. F. , Dawson L. E. R. , Irwin D. , Kilpatrick D. J. 
Published: May 2019

AbstractA study was carried out on six lowland farms in Northern Ireland over 2 years to examine the effect on labour input and lamb output of adopting an outdoor (grass-based) lambing system in comparison to an indoor lambing system. Each farm had four crossbred ewe genotypes – Bluefaced Leicester ✕ Scottish Blackface (BLXB), Texel ✕ Scottish Blackface (TXB), Suffolk ✕ Cheviot (SXCH) and Texel ✕ Cheviot (TXCH) ewes. The ewes were divided into three groups balanced for live weight and condition score and mated with Texel, Suffolk or Beltex rams. Half of the ewes lambed indoors and the other half were turned out to grass three to 6 weeks before lambing and lambed outdoors. BLXB ewes were the most prolific of the four ewe genotypes producing 1·99 lambs per ewe lambed compared with 1·75 for TXB, 1·76 for SXCH and 1·64 for TXCH (P < 0.001). A greater proportion of SXCH ewes lambed without assistance (0·82) compared with BLXB (0.70), TXB (0.71) and TXCH (0.74) ewes (P < 0.01) and subsequently less time was spent lambing SXCH ewes (P < 0.01). This advantage of the SXCH was more marked in the outdoor than in the indoor system (P < 0.01) in terms of lamb output, each of the four ewe genotypes performed similarly in the indoor and outdoor lambing systems. Lambs born in the outdoor system weighed 0.2 kg more at birth compared with those born indoors (P < 0.05). Lamb mortality and lamb output were similar in both systems. Less time was spent catching and moving ewes in the outdoor system compared with the indoor system (P < 0.01). Beltex-sired lambs weighed less at birth (4.9 kg) compared with Texel- (5.1 kg) (P < 0.10) and Suffolk-(5.3 kg) (P < 0.001) sired lambs and had lower live-weight gains from birth to 6 weeks and from birth to weaning (P < 0.001) and lower output of weaned lamb (P < 0.05). The results of this study demonstrate that, compared with indoor lambing systems, similar levels of performance can be achieved through adopting outdoor, grass-based systems. The lack of a significant interaction between ewe or ram genotype and lambing system indicates that all of the genotypes are suitable for incorporating into an outdoor lambing system.
Genetic associations for pathogen-specific clinical mastitis and patterns of peaks in somatic cell count
Authors: Haas Y. de , Barkema H.W. , Schukken Y.H. , Veerkamp R.F. 
Published: May 2019

AbstractGenetic associations were estimated between pathogen-specific cases of clinical mastitis (CM), lactational average somatic cell score (LACSCS), and patterns of peaks in somatic cell count (SCC) which were based on deviations from the typical lactation curve for SCC. The dataset contained test-day records on SCC in 94 781 lactations of 25 416 cows of different parities. Out of these 94 781 lactations, 41 828 lactations had recordings on occurrence of pathogen-specific CM and on SCC, and 52 953 lactations had recordings on SCC only. A total of 5 324 lactations with cases of CM were recorded. Analysed pathogens wereStaphylococcus aureus, coagulase negative staphylococci,Escherichia coli, Streptococcus dysgalactiae, Streptococcus uberis, and culture-negative samples. Pattern definitions were based on three or five consecutive test-day recordings of SCC. They differentiated between short or longer periods of increased SCC, and also between lactations with and without recovery. Occurrence of pathogen-specific CM and presence of patterns of peaks in SCC were both scored as binary traits. Variance components for sire, maternal grandsire, and permanent animal effects were estimated using AS-REML. The estimated heritability for overall CM was 0·04, and similar heritabilities for pathogen-specific CM were estimated. Heritabilities for the patterns of peaks in SCC ranged from 0·01 to 0·06. Heritabilities for LACSCS were 0·07 to 0·08. Genetic correlations with patterns of peaks in SCC differed for each pathogen. Generally, genetic correlations between pathogen-specific CM and patterns of peaks in SCC were stronger than the correlations with LACSCS. This suggests that genetic selection purely on diminishing presence of peaks in SCC would decrease the incidence of pathogen-specific CM more effectively than selecting purely on lower LACSCS.
Physical and chemical composition of the carcass of three different types of pigs grown from 25 to 115 kg live weight
Authors: Whittemore C.T. , Green D.M. , Wood J.D. , Fisher A.V. , Schofield C.P. 
Published: May 2019

AbstractA total of 74 pigs representing three commercially available crossbred types, Landrace (50%), Pietrain (50%) and Meishan (25%), were given food ad libitum over a 25- to 115-kg growth period and serially slaughtered for physical and chemical analysis in five groups at 32, 42, 63, 82 and 114 kg live weight (W). Results are presented in the order of pig type as above. Pig types grew at similar overall rates of live body gain, but the Meishan type ate more food and had greater back fat depth. The Pietrain type was least fat. Dissected fatty tissue grew substantially faster than the carcass as a whole; allometric exponents being 1·64, 1·34 and 1·52 (P < 0·05) for the Landrace, Pietrain and Meishan types respectively. Dissected lean tissue gains were 0·419, 0·427 and 0·308 kg daily (P < 0·01), and dissected fatty tissue gains were 0·251, 0·158 and 0·218 kg daily (P < 0·05); the Meishan type being slowest for lean gain and the Pietrain type slowest for fatty tissue gain. The Pietrain type had the largest cross-sectional area of the longissimus dorsi muscle, and the Meishan type the smallest. The pelvic limb of the Meishan type lost density (as measured by specific gravity) fastest, and that of the Pietrain slowest as the pigs grew. The Meishan type had a lower proportion of its carcass lean and a higher proportion of its carcass fat in the pelvic limb than did the other two types. For each kg of live-weight gain, 0·037, 0·041 and 0·032 kg (P < 0·05) of chemical protein was deposited in the pelvic limb of the three types respectively. Equivalent values for chemical lipid were 0·041, 0·035 and 0·041 (P < 0·05). The Meishan type retained protein at a relatively slower rate in the pelvic limb than in the body as a whole. The Pietrain type had the greatest ultimate protein mass in the pelvic limb. Estimation of whole body protein content as a linear function of pig live weight gives coefficients of 0·154, 0·178 and 0·168 kg (P < 0·05) for the three types respectively. Equivalent values for whole body lipid content were 0·269, 0·214 and 0·274 (P < 0·05). Best estimates of the daily rates of protein retention in the body of the whole live pig were 0·152, 0·197 and 0·142 kg/day for the Landrace, Pietrain and Meishan types respectively.
Estimation of dietary copper requirements of juvenile tilapia,Oreochromis niloticus5O. aureus
Authors: Shiau S.Y. , Ning Y.C. 
Published: May 2019

AbstractAn 8-week feeding trial was conducted to determine the dietary copper (Cu) requirement of juvenile hybrid tilapia,Oreochromis niloticus5O. aureus. Purified diets with eight levels (0, 1, 2, 3, 4, 8, 12 or 20 mg Cu per kg diet) of supplemental Cu were given to tilapia (mean initial weight 0·79±0·03 g). Each diet was given to three replicate groups of fish. The rearing water contained 0·98 µg Cu per l. Weight gain was highest in fish given diets supplemented with 2 mg Cu per kg diet, followed by the group given 1 mg Cu per kg diet, then the unsupplemented control group, and was lowest in the 20 mg Cu per kg diet group. The differences between each of these four groups were significant (P< 0·05). Food efficiency (FE) of fish showed a similar trend to that of weight gain. Blood haemoglobin (Hb) and haematocrit (Hct) concentrations were lowest in fish given ≥ 12 mg Cu per kg diet, followed by fish given the unsupplemented control diet and highest in fish given 2 mg Cu per kg diet (Hb) and 2 and 3 mg Cu per kg diet (Hct). Plasma ceruloplasmin activity was higher in fish given 1 and 2 mg Cu per kg diet, followed by 3 to 12 mg Cu per kg diet and the control group, and lowest in fish given 20 mg Cu per kg diet. The body Cu content in fish generally increased as the dietary Cu supplementation level increased. Analysis by broken-line regression of weight gain percent and by linear regression of the whole-body Cu retention of fish indicated that the adequate dietary Cu concentration in growing tilapia is about 4 mg Cu per kg diet.