Calculation of identity‐by‐descent probabilities of short chromosome segments

For some purposes, identity‐by‐descent (IBD) probabilities for entire chromosome segments are required. Making use of pedigree information, length of the segment and the assumption of no crossing‐over, a generalization of a previously published graph theory oriented algorithm accounting for nonzero IBD of common ancestors is given, which can be viewed as method of path coefficients for entire chromosome segments. Furthermore, rules for setting up a gametic version of a segmental IBD matrix are presented. Results from the generalized graph theory oriented method, the gametic segmental IBD matrix and the segmental IBD matrix for individuals are identical.     

Nutrient digestibility and evaluation of protein and carbohydrate fractionation of citrus by‐products

The protein and carbohydrate fractionation and nutrient digestibility of citrus by‐products were determined. Ruminal, intestinal and total tract CP disappearance values were measured by a modified three‐step (MTSP) method and in vitro CP disappearance method (IVCP). Test feeds were orange pulp (OP), lime pulp (LP), lemon pulp (LEP), grapefruit pulp (GP), sweet lemon pulp (SLP), bitter lemon pulp (BLP), bergamot orange pulp (BP) and tangerine pulp (TP). The rumen undegradable protein (RUP) fractions of the feedstuffs were obtained by ruminal incubation in three cannulated wethers and incubation in protease solution (protease type xiv, Streptomyces griseus). The data were analysed using completely randomized design. There were significant differences between the tested feeds in protein fractions and acid detergent insoluble nitrogen (ADIN; C fraction) was highest in GP (14.56%) (p < 0.001). For carbohydrate fraction, the highest C fraction was also observed in GP (2.67%) and in relation to the other citrus pulps (p < 0.001). Ruminal CP disappearance was highest in OP (71.89%) (p < 0.001). The level of post‐ruminal CP disappearance, measured by MTSP, was highest for BP (34.94%) (p < 0.001). The highest in vitro dry matter digestibility (IVDMD) was found for TP (80.44%) followed by that estimated for BP (78.38%) (p < 0.001). The estimated metabolizable energy (MJ/kg DM) varied from 9.77 for LP to 12.91 for BP. Tangerine pulp had the highest true rumen digestibility (TRD) (p < 0.001). According to the results, it could be concluded that citrus by‐products have high nutritive value and also, the in vitro techniques can be easily used to determine of the nutritive value of citrus by‐products.     

Fermentation characteristics and microorganism composition of total mixed ration silage with local food by‐products in different seasons

Total mixed ration (TMR) silage in different seasons was prepared with apple refuse, orchardgrass hay, orchardgrass silage, corn silage and a commercial compound feed in Tohoku, Japan, and with tofu cake, brewers' grains, tall fescue hay, Sudangrass hay, timothy hay, alfalfa hay and a commercial compound feed in Shikoku, Japan, respectively, and their fermentation quality and microorganism composition were evaluated. In Tohoku, the TMR silage in spring, autumn and winter displayed poor quality, with pH value above 4.7, and the harmful microorganisms such as escherichia, yeasts and molds were detected even after 60 days of ensiling; but the TMR silage in summer was well preserved and the escherichia were too few to count after 7 days of ensiling. In Shikoku, the TMR silage in all seasons was well preserved, with low pH, high lactic acid contents, and escherichia, yeasts and molds were consistently at or below the detectable numbers after 7 days of ensiling. The results showed that the TMR silage could not produce sufficient lactic acid to improve silage quality under low‐temperature conditions. Therefore, it is necessary to develop preparation techniques of promoting the lactic acid fermentation for TMR silage in cold seasons.     

利用微卫星标记鉴定德州驴亲子关系

试验旨在建立一套适用于德州驴亲子关系的鉴定体系。选取13个微卫星基因座作为标记,采集了53头德州驴血液样本,其中子代驴驹16头,候选父本13头,候选母本24头,用酚-仿法抽提血液基因组进行PCR扩增和基因扫描,并利用Peak Scanner Software v1.0软件读取基因型分型结果。对微卫星基因座的遗传多样性进行分析,利用似然法（Cervus 3.0软件）和排除法对个体间的亲子关系进行了鉴定。结果显示,13个微卫星基因座的平均等位基因数、平均观测杂合度（Ho）、平均期望杂合度（He）和平均多态信息含量（PIC）分别为6.846、0.689、0.671和0.625。期望杂合度与观测杂合度之差在0.002~0.088之间,差值较小。13个微卫星基因座的累计排除概率（EP）达到0.990以上。微卫星基因座具有高度多态性和较高的排除概率,适用于遗传分析和个体鉴定。利用Cervus 3.0软件基于似然法分析得到了16头子代驴驹的最似亲本,结合排除法对这16头驴驹及其最似亲本进行基因型比对,最终在53头德州驴中确定了11个亲子对。本试验建立了以13个微卫星位点作为核心标记,将似然法和排除法相结合作为主要分析方法的德州驴亲子关系鉴定体系,为育种工作提供参考资料。     

Effect of treating alfalfa silage with pistachio by‐products extract on Saanen dairy goats performance and microbial nitrogen synthesis

A lactation experiment was conducted to determine the influence of addition of pistachio by‐products extract (PBE) to alfalfa silage (AS) on performance, rumen fermentation, milk yield and composition, and microbial nitrogen synthesis. Eight multiparous dairy goats (1.8 ± 0.25 kg of milk yield) were used in a replicated 4 × 4 Latin square design with a 2 × 2 factorial arrangement of treatments to compare two types of AS (supplemented with or without PBE) with two levels of dietary crude protein (14% vs. 16% CP). Dietary treatments were (i) AS with 14% CP of DM diet without PBE (14%CP?PBE), (ii) AS with 14% CP of DM diet with PBE (14%CP + PBE), (iii) AS with 16% CP of DM diet without PBE (16%CP?PBE) and (iv) AS with 16% CP of DM diet with PBE (16%CP + PBE). PBE was sprayed on fresh alfalfa at a ratio of 500 ml/kg alfalfa DM to get the final concentration of 1% tannin as tannic acid equivalent on DM basis. Intake of CP was greater (p < 0.01) in goats fed 16% CP diets than those fed 14% CP diets, regardless of PBE supplementation. Supplementation of PBE tended to decrease (p = 0.09) rumen NH₃‐N concentration regardless of the level of CP in the diet. Supplementation of PBE tended (p = 0.09) to decrease total purine derivatives regardless of the level of CP in the diet with no significant change in microbial nitrogen supply. Efficiency of microbial nitrogen synthesis (EMNS) had a tendency (p = 0.07) to decrease in PBE supplemented diets. There was also a tendency (p = 0.10) for more EMNS in 14% CP fed goats than those fed 16% CP diets. Therefore, AS supplemented with PBE may lead to less concentration of ruminal NH₃‐N because of decreased degradation of CP by rumen micro‐organisms in response to pistachio by‐products tannins.     

ORIGINAL ARTICLE: Effect of rendering on protein and fat quality of animal by‐products

This work studies the effect of rendering on quality of meat and bone meals (MBM) processed in two Spanish rendering plants according to the standard procedure recommended by 96/499/EC Directive for MBM category III. Twelve samples of raw animal by‐products and their corresponding meals were analysed for chemical composition, amino acids (AA) content, FDNB‐reactive lysine content, pepsin digestibility, protein dispersibility index (PDI) and fatty acids (FA) content. There was a high variation in MBM composition between and within plants, mainly in the ash and fat content. Rendering caused a decrease in the total (p < 0.05) and the essential (p < 0.01) AA content (in crude protein basis) in both plants, because of a decrease in lysine (p < 0.001), methionine (p < 0.05), threonine (p < 0.01), leucine (p < 0.01), valine (p < 0.01) and phenylalanine (p < 0.01). Besides, there was a reduction in the cystine (p < 0.001), serine (p < 0.01) and aspartic acid (p < 0.01) content. The FDNB‐reactive lysine to total lysine ratio and pepsin digestibility only decreased (p < 0.001) in the plant with more severe treatment conditions, whereas the PDI increased (p < 0.05) by the process in both plants. The saturated to unsaturated FA ratio increase on average from 0.73 to 0.88 after rendering, because of the decrease in both linoleic and linolenic acids content and the increase in palmitic and stearic acids content. The results indicate that rendering has negative effects on protein and fat quality of MBM. Variability between and within plants is attributed to differences in raw material, processing conditions and fat removing efficiency. Therefore, a continuous monitoring is recommended to assure the quality of each batch before use.     

用微卫星标记技术对动物进行亲子鉴定

亲子鉴定的传统方法主要有四种：标准抗血清法、多价抗血清法、电泳区分蛋白型法、DNA指纹法。以微卫星为基础的多态性记是近来发展最快的一类新型DNA分子标记技术，由于其杂合度高，多态性好等优点，在物种多样性研究、亲缘关系进行研究以及育种学领域得到广泛应用。近来特别是在法医学领域中用于个体识别和亲子鉴定，被认为是准确性最好的一种检测技术。主要介绍应用微卫星标记技术对动物进行亲子鉴定的基本原理与方法以及研究进展，以促进该项技术的推广应用。     

Genome‐wide re‐sequencing and transcriptome analysis reveal candidate genes associated with the pendulous comb phenotype in domestic chickens

To determine the causative variations associated with two chicken comb phenotypes, pendulous comb (PC) or upright comb (UC), two pooled genomic DNA samples from PC and UC chickens were re‐sequenced by Next‐Generation Sequencer, and genome‐wide Single nucleotide polymorphisms (SNPs) were detected. Using three selective sweep approaches, F_ST, θπ, and Tajima's D, with top 5% window values serving as the threshold, a total of 84 positively selective genes (PSGs) were identified. There were no SNPs in exons of the PSGs with significant differences in allele frequencies between the two comb phenotype groups. Then, 515 differentially expressed genes (DEGs) between the PC and UC were identified by RNA‐seq. Three genes including CD36 (CD36 molecule), ADAMTSL3 (ADAMTS‐like 3), and AOX1 (aldehyde oxidases 1) are overlapped between PSGs and DEGs. After genotyping seven candidate SNPs in the regulatory regions of the three overlapping genes in 120 chickens from two other breeds, two variants (rs14607046 and rs731818051) in the regulatory regions of AOX1 and ADAMTSL3 were found to have significant differences in allele frequency between the PC and UC, suggesting that the two variants may be causative mutations for PC. Overall, our study shed light on the genetic basis underlying the PC phenotype in chickens.     

Use of monosodium glutamate by‐product in cow diet on performance of lactating dairy cows

Eight multiparous lactating Holstein cows were randomly assigned in a 4 × 4 replicated Latin square design to receive four dietary treatments. The dietary treatments were monosodium glutamate by‐product (MSGB) replacement for soybean meal in concentrate at four levels: MSGB replacement at 0, 20, 40 and 60%, respectively. Pangola hay was given on an ad libitum basis. It was found that total dry matter intake, concentrate intake, pangola hay intake and all apparent digestibilities were not different among treatments. Ammonia nitrogen concentration in the rumen at 4 h post‐feeding was significantly different, in which the 0% treatment had the highest (P < 0.05) while the 20% treatment had the lowest. Milk fat percentage was the highest (P < 0.05) in the 0% treatment. MSGB replacement at 40% and 60% were shown to be the lowest (P < 0.05) feed cost for milk production, and profitability of milk production was the highest (P < 0.05) for the 60% treatment. Based on this experiment, it could be concluded that MSGB replacement for soybean meal at 20‐60% in the feed for dairy cows presented no negative effects on their performances. In addition, it could decrease feed cost 2.9‐17.3% and increase milk production profit up to 33.3% in the 60% treatment.     

Whole‐genome sequencing reveals resistome of highly drug‐resistant retail meat and human Salmonella Dublin

Non‐typhoidal Salmonella (NTS) are a significant source of foodborne illness worldwide, with disease symptoms most often presenting as self‐limiting gastroenteritis; however, occasionally the infection spreads and becomes invasive, frequently requiring anti‐microbial treatment. The cattle‐adapted Dublin serovar of NTS has commonly been associated with invasive illness and anti‐microbial resistance (AMR). Here, the enhanced resolution conferred by whole‐genome sequencing was utilized to elucidate and compare the resistome and genetic relatedness of 14 multidrug‐resistant (MDR) and one pan‐susceptible S. Dublin, isolated primarily in Pennsylvania, from fresh retail meat (one isolate) and humans (14 isolates). Twelve different genetic AMR determinants, including both acquired and chromosomal, were identified. Furthermore, comparative plasmid analysis indicated that AMR was primarily conferred by a putative IncA/C2 plasmid. A single pan‐susceptible S. Dublin isolate, collected from the same timeframe and geographical region as the MDR isolates, did not carry an IncA/C2 replicon sequence within its genome. Moreover, the pan‐susceptible isolate was genetically distinct from its MDR counterparts, as it was separated by ≥267 single nucleotide polymorphisms (SNPs), whereas there was a ≤38 SNP distance between the MDR isolates. Collectively, this data set advances our understanding of the genetic basis of the highly drug‐resistant nature of S. Dublin, a serovar with significant public health implications.     

A comparative study of zinc protoporphyrin IX‐forming properties of animal by‐products as sources for improving the color of meat products

The objective of this study was to obtain fundamental data for improving the color of meat products by using animal by‐products. We investigated zinc protoporphyrin IX (ZnPP)‐forming properties of various internal organs from pigs and chickens. ZnPP was formed in the liver, heart and kidney, whereas the porcine spleen and bile, which are involved in the metabolism of heme, did not have ZnPP‐forming properties. The optimum pH values were different among the internal organs and the ZnPP‐forming properties of porcine organs were better than those of chicken organs. The porcine liver showed the greatest ZnPP‐forming properties among all of the internal organs investigated in this study. The optimum pH value for ZnPP formation in the liver was lower than that of skeletal muscle. Oxygen did not inhibit the formation of ZnPP in the liver, unlike in skeletal muscle. Animal by‐products such as the liver have good ability for the formation of ZnPP and might be useful for improving the color of meat products.     

Effects of fermented mushroom (Flammulina velutipes) by‐product diets on growth performance and carcass traits in growing‐fattening Berkshire pigs

This study was conducted to investigate effects of fermented mushroom (Flammulina velutipes) by‐product diets on the growth performance and carcass traits in growing‐fattening Berkshire pigs. The fermented diets mainly contained 40.0% mushroom by‐product, 20.0% formula feed, 26.0% rice bran and supplemental 0.1% probiotics. The mixed ingredients were fermented for 5 days at room temperature. Berkshire pigs (n = 225) were divided into five groups and three replications. The basal diets (C) were substituted by 10% (T1), 30% (T2), 50% (T3) and 70% (T4) fermented mushroom by‐product diets. Crude protein concentration and total calorie in fermented diets were significantly increased (P < 0.05) at the end of fermentation days compared with initial fermentation day. Body weight gain, feed efficiency and carcass weight were significantly lower (P < 0.05) in the T2, T3 and T4 groups than in the control group. Carcass grade was significantly better (P < 0.05) in the pigs fed fermented diets than in the pigs fed control diet and the ratio of high grade (1 plus 2 grades) was higher in the fermented diet groups compared with the control group. Therefore, although a diet of fermented mushroom by‐product decreased growth performance and feed efficiency, it improved the carcass grade in Berkshire pigs.     

Exogenous protease supplementation of poultry by‐product meal‐based diets for broilers: Effects on growth,carcass characteristics and nutrient digestibility

An experiment was conducted to investigate the effects of three levels (0%, 3% and 6%) of poultry by‐product meal (PBM) with or without protease on broiler growth, carcass characteristics and nutrient digestibility from 1 to 35 days. Two hundred and forty birds (n = 240) were fed equi‐caloric and equi‐nitrogenous (ME 2850 kcal/kg; CP 20%) diets throughout the experiment. The enzyme supplementation increased feed intake (p < .01) and body weight gain (p < .01), but feed:gain remained unaffected (p > .05) from 1 to 21 days. Increasing level of PBM decreased feed intake (p < .05), but body weight gain was improved (p < .05) at 3% PBM level during 1 to 21 days. The feed:gain was improved (p < .05) in birds fed diets containing 3% PBM. The feed:gain was also improved in birds fed diets containing 3% PBM from 1 to 35 days. However, feed intake and body weight gain in birds fed diets containing PBM remained unaffected. An interaction (p < .01) on feed intake between enzyme and PBM was noticed during 1 to 21 days. However, no interaction was recorded for body weight gain and feed:gain. The per cent carcass yield improved (p < .01) in birds fed diets supplemented with enzyme. The per cent breast meat yield was depressed (p < .005) in birds fed diets containing PBM. Apparent metabolizable energy (p < .001), nitrogen retention (p < .01), apparent metabolizable energy corrected for nitrogen (p < .001), and apparent digestibility coefficient for nitrogen (p < .01) improved in birds fed diets containing enzyme; however, a reverse was noticed in those fed diets containing only PBM. In conclusion, inclusion of 3% PBM along with supplementation of exogenous protease improved performance and nutrient digestibility in broilers.     

Allele‐specific PCR typing and sequencing of the mitochondrial D‐loop region in four layer breeds

This study aimed to investigate the ability of single nucleotide polymorphism (SNP) haplotypes in chicken mtDNA for presumption of the origins of chicken meat. We typed five SNPs of the D‐loop region in mtDNA by allele‐specific PCR (AS‐PCR) in 556 hens, that is 233 White Leghorn (WL), 50 Dekalb‐TX35 (D‐TX), 140 Barred Plymouth Rock (BPR) and 133 Rhode Island Red (RIR) kept in the National Institute of Livestock and Grassland Science (NILGS, Tsukuba, Japan). Five haplotypes were observed among those chickens by AS‐PCR. WL, D‐TX, BPR and RIR displayed three, two, one and four SNP haplotypes, respectively. By a combination of the haplotypes by AS‐PCR and the breeds, these chickens were classified into 10 groups. After the D‐loop was sequenced in two chickens from every group (20 individuals), 15 SNP sites (including one insertion) and eight sequence haplotypes were observed. In conclusion, haplotype variation was observed in and among the layer breeds of the NILGS. This study demonstrates that SNP haplotypes in mtDNA should be appropriate for the presumption of the origins of chicken meat.     

The effects of replacement of antibiotics with by‐products of oriental medicinal plants on growth performance and meat qualities in fattening pigs

The effect of by‐products of oriental medicinal plants (OMP; T1) containing 0.03% herb extracts (T2) or 0.1% aminolevulinic acid (T3) on the production performance of swine during the finishing period and on its meat quality were investigated. No significant differences were found in the weight gain, feed intake and feed conversion rate among the tested groups (P > 0.05). But the treated group showed higher (P < 0.05) moisture and ash and lower protein than the control group. The T3 group showed a lower meat cholesterol content (38.42 mg/100 g) compared to the other groups (P < 0.05). The vitamin E content of the muscle in the treated groups was higher compared to the control group. No antibiotic content was detected in all treated and control samples. The values of the volatile basic nitrogen (VBN) and thiobarbituric acid reactive substance (TBARS) of the treated groups were significantly lower (P < 0.01) than the control group. The treated groups had significantly better (P < 0.05) sensory‐test scores for color, flavor, off‐flavor and total acceptability compared to the control group.     

Endogenous endophthalmitis caused by Enterococcus faecalis in a cat

A three‐year‐old male neutered domestic shorthair cat was presented for loss of vision associated with hyperthermia, lethargy and anorexia. Ophthalmic examination revealed a bilateral panuveitis. Cytological examination of aqueous and vitreous humours was performed and revealed a suppurative inflammation associated with numerous cocci. Enterococcus faecalis was identified by bacterial culture from aqueous and vitreous humour. No primary infection site was identified. Active uveitis resolved after systemic antibiotic therapy, but the vision loss was permanent. To the authors’ knowledge, this is the first reported case of endogenous bacterial endophthalmitis secondary to E. faecalis infection in a cat.     

Growth performance,carcass quality characteristics and colonic microbiota profiles in finishing pigs fed diets with different inclusion levels of rice distillers’ by‐product

The aim of this study was to evaluate the effects of diets containing rice distillers’ by‐product (RDP) on growth performance, carcass characteristics, meat quality, and gut microbiota of fattening pigs. Twenty‐four crossbred finishing pigs (Duroc × Landrace × Yorkshire), 56.9 ± 3.1 kg initial body weight, were randomly allocated to three groups. For 56 days, pigs were fed one of three diets including RDP0 (control), RDP15 (15% RDP in DM), and RDP30 (30% RDP in DM). With RDP level in diet, average daily gain and backfat thickness linearly increased (p < 0.05), and drip loss tended to increase (p ≤ 0.08). In addition, 16S ribosomal RNA gene amplicon profiling showed that RDP was associated with modulation of colonic microbiota composition, especially at family and genus levels. Relative abundance of Porphyromonadaceae and Erysipelotrichaceae families in colonic digesta increased with inclusion of RDP, while that of Enterobacteriaceae decreased. The proportion of genera unclassified Erysipelotrichaceae, and Butyrivibrio increased as inclusion of RDP. These results indicate that up to 30% inclusion in diet of finishing pigs, RDP can modulate colonic microbiota composition, and induces an improvement of animal growth and fat deposition.     

Effects of supplementary mother liquor,by‐product of monosodium glutamate,on in vitro ruminal fermentation characteristics

Mother liquor (ML) is monosodium glutamate by‐product and contains much crude protein (CP). The objective of this study was to investigate the effect of supplementation of two types of MLs having different chemical compositions on in vitro ruminal fermentation characteristics. ML1 had 74% organic matter (OM) and 70% CP and ML2 had 85% OM and 83% CP on a dry matter (DM) basis. The experiments were conducted using 0.5 gDM rolled barley or ryegrass straw as substrates. Urea and freeze‐dried MLs were added at three levels of nitrogen to be isonitrogenous. The ML1 treatment increased gas production compared with the ML2 treatment in barley substrate condition (p < 0.05). The supplementary ML2 increased gas production compared with the supplementary urea, and the digestibilities of DM and neutral detergent fiber expressed exclusive of residual ash (NDFom) were higher for the supplementary ML2 than for the supplementary ML1 in straw substrate condition (p < 0.05). In both the conditions, ammonia nitrogen concentrations of the ML1 and ML2 treatments were lower than that of the urea treatment (p < 0.05). The results indicated that the supplementary ML1 and ML2 activated in vitro ruminal fermentation particularly in concentrate and roughage substrate conditions respectively.     

Effect of marine by‐product meals on hen egg production parameters,yolk lipid composition and sensory quality

The effect of including 5% marine by‐product meals in feeds of laying hens on egg production, composition and sensory characteristics was tested. Marine by‐product meals were prepared using two methods: (i) cooking (100°C/10 min) followed by drying (60°C/24 hr) or (ii) grinding followed by drying. The raw materials used for meal production were scallop or squid viscera, shrimp heads or whole mackerel. A total of 108 laying hens were allocated to nine diet treatments; one control diet (corn and soya bean based) and eight experimental diets, containing 95% of the control feed and 5% of the experimental meal for three weeks. Daily intake was higher in hens fed the dried mackerel and cooked shrimp meals. All the experimental treatments showed significantly higher concentration of n‐3 HUFA in yolk reserves and phospholipids compared to the control (0.12–0.13 g per 100 g), especially those with scallop or squid prepared by both methods (0.53–0.95 g per 100 g). Scallop, squid and shrimp meal inclusion in the feed produced eggs with more astaxanthin (0.22 mg per 100 g) while this carotenoid was absent in the control and mackerel treatments. Visual evaluation of raw yolk colour increased with the inclusion of marine by‐product meals with higher values in hens fed shrimp heads (13), followed by scallop viscera (11), squid viscera (9), and with similar values for mackerel and control (4). The taste, aroma, texture and colour of cooked eggs from different treatments were not statically different when evaluated by a panel of 60 untrained people. These results suggest that meals from marine by‐products are a better alternative for improving egg yolk composition by increasing n‐3 HUFA when compared to fishmeal as they also increase astaxanthin and yolk pigmentation without affecting egg sensory characteristics.