Detection and analysis of genome-wide copy number variation in the pig genome using an 80 K SNP Beadchip

Copy number variation (CNV) is an important source of genetic variability in human or animal genomes and play key roles in phenotypic diversity and disease susceptibility. In the present study, we performed a genome-wide analysis for CNV detection using SNP genotyping data of 857 Large White pigs. A total of 312 CNV regions (CNVRs) were detected with the PennCNV algorithm, which covered 57.76 Mb of the pig genome and correspond to 2.36% of the genome sequence. The length of the CNVRs on autosomes ranged from 1.77 Kb to 1.76 Mb with an average of 185.11 Kb. Of these, 220 completely or partially overlapped with 1,092 annotated genes, which enriched a wide variety of biological processes. Comparisons with previously reported pig CNVR revealed 92 (29.49%) novel CNVRs. Experimentally, 80% of CNVRs selected randomly were validated by quantitative PCR (qPCR). We also performed an association analysis between some of the CNVRs and reproductive traits, with results demonstrating the potential importance of CNVR61 and CNVR283 associated with litter sizes. Notably, the GPER1 gene located in CNVR61 plays a key role in reproduction. Our study is an important complement to the CNV map in the pig genome and provides valuable information for investigating the association between genomic variation and economic traits.     

Effects of thermo‐resistant non‐starch polysaccharide degrading multi‐enzyme on growth performance,meat quality,relative weights of body organs and blood profile in broiler chickens

This research was conducted to study the performance and carcass parameters of broiler chickens fed diets supplemented with heat‐treated non‐starch polysaccharide degrading enzyme. A total of 432 one‐day old Ross 308 broiler chickens were allocated to five treatments: (i) CON (basal diet), (ii) E1: CON + 0.05% multi‐enzyme, (iii) E2: CON + 0.1% multi‐enzyme, (iv) E3: CON + 0.05% thermo‐resistant multi‐enzyme and (v) E4: CON + 0.1% thermo‐resistant multi‐enzyme, each treatment consisted of six replications and 12 chickens in each replication. The chickens were housed in three floor battery cages during 28‐day experimental period. On days 1–7, gain in body weight (BWG) improved by feeding the diets supplemented with thermo‐resistant multi‐enzyme. On days 7–21 and 1–28, chickens fed the diets containing thermo‐resistant multi‐enzyme showed improved (p < 0.05) BWG and feed conversion ratio (FCR) compared to CON group. Supplementing the diets with multi‐enzyme or thermo‐resistant multi‐enzyme affected the percentage of drip loss on d 1 (p < 0.05). Drip loss percentage on days 3 and 5 and also meat colour were not affected significantly. Supplementing the diets with multi‐enzyme or thermo‐resistant multi‐enzyme did not affect the relative weights of organs but compared to CON group, relative weight of breast muscle increased and abdominal fat decreased (p < 0.05). Among measured blood constituents, chickens fed supplemented diets with thermo‐resistant multi‐enzyme showed higher (p < 0.05) IgG. Counts of red and white blood cells and lymphocyte percentage were not affected. In conclusion, the results demonstrated that supplementing pelleted diets with thermo‐resistant multi‐enzyme improved performance of broiler chickens.     

Changes of leukocyte counts and expression of pro‐ and anti‐inflammatory cytokines in peripheral leukocytes in periparturient dairy cows with retained fetal membranes

In dairy cows, retained fetal membranes (RFM) affect reproductive performance. The aim of this study was to examine the leukocyte counts and the gene expression of tumour necrosis factor α (TNFα), interleukin 1β (IL‐1β), IL‐8, and IL‐10 in polymorphonuclear leukocytes (PMNs) and peripheral blood mononuclear cells (PBMCs) in cows with (n = 5) or without (n = 5) RFM during the peripartum period. The lymphocyte counts in RFM cows were higher than those in control cows throughout the experiment (p < .05). The expression of IL‐8 in PMNs of control cows was higher (p < .05) compared with that of RFM cows postpartum. In cows with RFM, IL‐1β expression was higher (p < .05) in PMNs at 6 weeks postpartum whereas the expression of IL‐1β was lower (p < .05) in PBMCs at 4 weeks postpartum. The expression of IL‐10 in PBMCs of control cows was higher (p < .05) than that of RFM cows at 2 weeks prepartum and 4 weeks postpartum. Taken together, our data indicate that changes of gene expression of pro‐ and anti‐inflammatory cytokines in RFM cows might be associated with the delayed placental separation and development of uterine inflammation in RFM cows.     

Use of quantitative real‐time PCR to assess the in vitro survival of specific DNA gene sequences of rumen microbes under simulated abomasal conditions

The use of specific DNA sequences (DS) as a microbial marker in post‐rumen digesta requires their persistence and integrity throughout gastric digestion. The aim of this study was to evaluate in vitro the survival of microbial DS during gastric digestion and the factors involved. Gastric pH had a highly significant effect on the integrity of DS. pH 4.2 allows for a significant growth of microbes in the medium, but at pH 1.2, almost all of the DS were hydrolysed. In the presence of carboxymethylcellulose, the effect of pH was reduced, pepsin activity was inhibited and gene survival increased considerably. In the simulated abomasal conditions (pH = 2.3, 2 g/l of carboxymethylcellulose, and 40‐min retention time), almost all of the bacterial genes and around 78% of the protozoa gene sequences retained their molecular integrity throughout gastric digestion, although factors such as acidity and viscera retention time might compromise the utilisation of DS as a microbial marker.     

Effect of Maternal Age on the Ratio of Cleavage and Mitochondrial DNA Copy Number in Early Developmental Stage Bovine Embryos

Age-associated deterioration in both the quality and quantity of mitochondria occurs in older women. The main aim of this study was to examine the effect of age on mitochondrial DNA copy number (mtDNA number) in early developmental stage bovine embryos as well as the dynamics of mtDNA number during early embryo development. Real-time PCR was used to determine mtDNA number. In vitro-produced embryos 48 h after insemination derived from Japanese black cows, ranging in age from 25 to 209 months were categorized based on their cleavage status. There was an overall negative relationship between the age of the cow and cleavage status, to the extent that the ratio of embryos cleaved over the 4-cell stage was greater in younger cows. The mtDNA number did not differ among the cleaved status of embryos. In the next experiment, oocytes collected from each donor cow were divided into 2 groups containing 10 oocytes each, in order to compare the mtDNA number of mature oocytes and early developmental stage embryos within individuals. Upon comparing the mtDNA number between oocytes at the M2 stage and early developmental stage 48 h post insemination, mtDNA number was found to decrease in most cows, but was found to increase in some cows. In conclusion, age affects the cleaving ability of oocytes, and very old cows (> 180 months) tend to have lower mtDNA numbers in their oocytes. The change in mtDNA number during early development varied among individual cows, although overall, it showed a tendency to decrease.     

Practical capability of a DNA pool‐based genome‐wide association study using BovineSNP50 array in a cattle population

Genome‐wide association mapping for complex traits in cattle populations is a powerful, but expensive, selection tool. The DNA pooling technique can potentially reduce the cost of genome‐wide association studies. However, in DNA pooling design, the additional variance generated by pooling‐specific errors must be taken into account. Therefore, this study aimed to investigate factors such as: (i) the accuracy of allele frequency estimation; (ii) the magnitude of errors in pooling construction and in the array; and (iii) the effect of the number of replicate arrays on P‐values estimated by a genome‐wide association study. Results showed that the Illumina correction method is the most effective method to correct the allele frequency estimation; pooling errors, especially array variance, should be taken into account in DNA pooling design; and the risk of a type I error can be reduced by using at least two replicate arrays. These results indicate the practical capability and cost‐effectiveness of pool‐based genome‐wide association studies using the BovineSNP50 array in a cattle population.     

Comparative evaluation of DNA integrity using sperm chromatin structure assay and Sperm‐Ovis‐Halomax during in vitro capacitation of cryopreserved ram spermatozoa

This study aimed to compare the ability of sperm chromatin structure assay (SCSA^®) and Sperm‐Ovis‐Halomax^® to detect DNA fragmentation in frozen‐thawed ram spermatozoa incubated under capacitating conditions in synthetic oviductal fluid (SOF) supplemented with oestrous sheep serum (SOF‐ESS) at multiple time points (0–240 min). Incubation in SOF‐ESS had no significant effects on SCSA^® parameters while the percentage of spermatozoa with fragmented DNA measured by Sperm‐Ovis‐Halomax^® increased after 180 min of incubation. In addition, no correlation or agreement was found between the techniques, suggesting that SCSA^® and Sperm‐Ovis‐Halomax^® may quantify different types of DNA damage in ram spermatozoa under these experimental conditions.     

Kinetics of Plasma Cell‐Free DNA and Creatine Kinase in a Canine Model of Tissue Injury

Background

Cell‐free DNA (cfDNA) comprises short, double‐stranded circulating DNA sequences released from damaged cells. In people, cfDNA concentrations correlate well with disease severity and tissue damage. No reports are available regarding cfDNA kinetics in dogs.

Objectives/Hypothesis

Cell‐free DNA will have a short biological half‐life and would be able to stratify mild, moderate, and severe tissue injury. Our study aims were to determine the kinetics and biological half‐life of cfDNA and to contrast them with those of creatine kinase (CK).

Animals

Three groups of 10 dogs undergoing open ovariohysterectomy, surgery for cranial cruciate ligament rupture (CCLR), or hemilaminectomy.

Methods

Plasma for cfDNA and CK analysis was collected at admission, at induction of anesthesia, postsurgery (time 0) and at 6, 12, 24, 36, 48, 60, and 72 hours after surgery.

Results

The biological half‐life of plasma cfDNA and CK were 5.64 hours (95% confidence interval [CI 95], 4.36–7.98 hours) and 28.7 hours (CI95, 25.3–33.3 hours), respectively. In the hemilaminectomy group, cfDNA concentrations differed significantly from admission at 6–12 hours after surgery. Creatine kinase activity differed among the surgical groups and reached a peak 6 hours after surgery. In the ovariohysterectomy and CCLR groups, plasma CK activity 72 hours after surgery did not differ from admission activity of the ovariohysterectomy group. In contrast, in the hemilaminectomy group, plasma CK activity after 72 hours did not return to the ovariohysterectomy group admission activity.

Conclusions and Clinical Importance

Plasma CK activity has a longer biological half‐life than previously thought. In contrast to plasma CK activity, cfDNA has a short half‐life and could be a useful marker for peracute severe tissue injury.     

Polymorphisms in the bovine hemoglobin‐beta gene provide evidence for gene‐flow between wild species of Bos (Bibos) and domestic cattle in Southeast Asia

The electrophoretic variation in bovine hemoglobin‐beta (HBB) is one of the most investigated genetic markers. The presence of a unique HBB variant, HBB^X, in Southeast Asian cattle has been reputed as a sign of gene‐flow from wild bovine species. In this study, we analyzed the DNA sequences of HBB genes in domestic and wild bovine species to verify this belief. Isoelectric focusing of HBB chain revealed that the HBB^X in domestic cattle had dimorphism and was separated into HBB^X1 and HBB^X2. The HBB^X1 had the same DNA sequence of the common HBB variant in gayal (Bos gaurus frontalis), while some of the HBB^X2 were identical with that of Cambodian banteng (Bos javanicus birmanicus). As a result, we confirmed that the bovine HBB variants can be a good indicator of introgression between wild and domestic cattle. The HBB^X1 was always predominant to HBB^X2 in the continental populations, suggesting that the gaur had contributed to the gene pool of domestic cattle in this region much more than the banteng. On the other hand, the mitochondrial DNA analysis could not detect gene‐flow from wild species. Autosomal markers that can trace the phylogeny between alleles are suitable for the assessment of bovine interspecific introgression.     

The use of lingual venous blood to determine the acid‐base and blood‐gas status of dogs under anesthesia

ObjectiveTo assess the suitability of lingual venous blood (LBG) as an alternative to arterial blood (ABG) samples in determining acid–base balance and blood–gas status in dogs anesthetized for elective procedures and with medetomidine and isoflurane administration under experimental conditions.Study designProspective, randomized clinical and experimental study.AnimalsClinical population of 18 ASA I/II dogs for elective surgery and five healthy Beagles (3 females and 2 males) for the experimental study.MethodsBlood sampling was simultaneously performed at dorsal pedal arterial and lingual venous sites, generating paired data. Two paired samples were collected from each dog in the clinical part and four from each dog in the experimental part (two during isoflurane anesthesia and two during isoflurane plus medetomidine). A modified Bland and Altman method was used to examine data from the clinical part and the experimental data were subjected to a paired sign's test following transformation where appropriate.ResultsThe pH of LBG overestimated ABG, with limits of agreement of (?0.01, 0.02). The partial pressure of carbon dioxide (PCO₂) of LBG overestimated ABG by 0.6 mmHg [0.1 kPa], with limits of agreement of (?3.5, 4.6) mmHg [?0.5, 0.6 kPa]. The partial pressure of oxygen (PO₂) of LBG underestimated ABG by 86.3 mmHg [?11.5 kPa], with limits of agreement of (?199.8, 27.3) mmHg [?26.6, 3.6 kPa]. During medetomidine administration values for PO₂ (p = 0.03) and lactate (p = 0.03) were lower for LBG when compared with ABG. The LBG value of PO₂ was lower (p = 0.03) during medetomidine and isoflurane administration versus isoflurane alone.Conclusions and clinical relevanceThe pH and PCO₂ of LBG samples provide clinically acceptable substitutes of ABG samples in the dog population studied. The wider limits of agreement for PO₂ render it less reliable as a substitute for ABG. The difference in PO₂ identified between LBG and ABG during medetomidine administration may not preclude the use of LBG as substitutes for ABG samples.     

Punctal stenosis in 6 dogs following the long‐term use of topical neomycin‐polymyxin B‐dexamethasone

Six dogs were diagnosed with punctal stenosis following the long‐term use of topical neomycin‐polymyxin B‐dexamethasone (NPD). All patients were initially presented for ophthalmic diseases requiring ongoing anti‐inflammatory therapy. Five of the 6 dogs had previously or concurrently been treated with topical anti‐inflammatory medications other than NPD. One patient exclusively received topical NPD prior to the diagnosis of punctal stenosis. The onset of punctal stenosis following therapy with NPD was variable among patients, ranging from 4 months to over 1 year. Diagnosis of punctal stenosis was made based upon the presence of epiphora and visualization of fibrotic tissue over the nasolacrimal puncta.     

Methyl donors dietary supplementation to gestating sows diet improves the growth rate of offspring and is associating with changes in expression and DNA methylation of insulin‐like growth factor‐1 gene

The study aimed to investigate the effects of maternal dietary methyl donors on the performance of sows and their offspring, and the associated hepatic insulin‐like growth factor‐1 (IGF‐1) expression of the offspring. A total of 24 multiparous sows were randomly fed the control (CON) or the CON diet supplemented with methyl donors (MD) at 3 g/kg betaine, 15 mg/kg folic acid, 400 mg/kg choline and 150 μg/kg VB₁₂, from mating until delivery. After farrowing, sows were fed a common lactation diet through a 28‐days lactation period and six litters per treatment were selected to be fed until at approximately 110 kg BW. Maternal MD supplementation resulted in greater birthweight (p < 0.05) and increased the piglet weights (p < 0.01) and litter weights (p < 0.05) at the age of day 28, compared with that in CON group. The offspring pigs in the MD group had greater ADG (p < 0.05) and tended to lower F:G ratio (p = 0.07) compared with that of CON group from day 28 to 180 of age. The offspring pigs from MD group had greater serum IGF‐1 concentrations and expressions of hepatic IGF‐1 gene and muscular IGF‐1 receptor (IGF‐1r) protein at birth (p < 0.05), and greater hepatic IGF‐1 protein (p = 0.03) and muscular IGF‐1r gene expressions (p < 0.05) at slaughter, than that from the CON group. Moreover, the methylation at the promoter of IGF‐1 gene in the liver of newborn piglets and finishing pigs was greater in the MD group than that of the CON group (p < 0.05). In conclusion, maternal MD supplementation throughout gestation could enhance the birthweight and postnatal growth rate of offspring, associated with an increased expression of the IGF‐1 gene and IGF‐1r, as well as the altered DNA methylation of IGF‐1 gene promotor.     

Multi‐level mixed models for evaluating factors affecting the mortality and weaning weight of piglets in large‐scale commercial farms in central China

This study investigated the factors affecting piglet mortality (square root of mortality, SQRM) and average weaning weight (AWW) in commercial farms in central China. Information on sow diets, management and climate from 2478 weaning batches completed in 16 pig farms was collected from 2009 to 2013. Multi‐level mixed models, which included batch level (level 1) and farm level (level 2), were used to analyze the factors associated with SQRM and AWW. The mean values of SQRM and AWW were 2.52% (SD = 0.96) and 7.31 (SD = 0.77), respectively. Lactation sow diets supplemented with oregano essential oils (OEOs) decreased the SQRM (P < 0.05) and increased the AWW of piglets (P < 0.01). The SQRM was lower in period 2 (June to September, hot) than in period 1 (February to May, warm) and period 3 (October to January, cold; P < 0.05 and 0.001, respectively). The AWW was lower in periods 2 and 3 than in period 1 (P < 0.01). In conclusion, supplying OEOs to lactation diets can increase the weaning weight and reduce the mortality of piglets. The sources of variations in SQRM and AWW are of greater concern in the warm season than in the hot season.     

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.     

Assessment of pregnancy‐associated glycoprotein (PAG) concentrations in swamp buffalo samples from fetal and maternal origins by using interspecies antisera

Pregnancy‐associated glycoproteins (PAG) constitute a large family of glycoproteins found in the outer placental epithelial cell layer of the placenta in Eutherian species. In ruminants, they are noted to be structurally closely related among the different species. This study was designed to determine PAG concentrations in maternal and fetal plasma, allantoic and amniotic fluids in buffalo species. Antisera (AS) generated in rabbits against distinct PAG molecules were used in three radioimmunoassay (RIA)‐PAG systems: RIA‐1 (antiserum raised against bovine PAG67kDa; AS#497), RIA‐2 (antiserum raised against caprine PAG55 + 62 kDa; AS#706) or RIA‐3 (antiserum raised against buffalo PAG; AS#859). Samples were collected at a slaughterhouse (n = 67). PAG concentrations determined by RIA‐2 gave significantly higher results in both allantoic and amniotic fluids (12.7 ± 2.1 ng/mL and 24.0 ± 7.3 ng/mL, respectively). Regarding maternal and fetal plasma, PAG concentrations obtained by RIA‐2 (21.8 ± 2.4 ng/mL and 20.2 ± 2.5 ng/mL, respectively) and RIA‐3 (25.0 ± 2.2 ng/mL and 21.9 ± 3.2 ng/mL, respectively) were higher than those obtained by RIA‐1 (15.5 ± 1.4 ng/mL and 16.1 ± 1.8 ng/mL, respectively). The correlation among the three systems was very high. The study clearly reveals the ability of different PAG‐RIA systems to measure PAG concentration in swamp buffalo samples.     

Presence of melatonin‐catabolizing non‐specific enzymes myeloperoxidase and indoleamine 2,3‐dioxygenase in the ram reproductive tract

The melatonin catabolism is very complex and not completely understood. Melatonin can be metabolized by free radical interaction, but also pseudo‐enzymatically or by enzymatic pathways. We have previously detected the existence of melatonin‐synthesizing enzymes and melatonin receptors MT1 and MT2 in the ram reproductive tract; thus, in order to start to elucidate melatonin catabolism in these organs, we have investigated the presence of the melatonin‐catabolizing enzymes indoleamine 2,3‐dioxygenase (IDO, both IDO1 and IDO2 isoforms) and myeloperoxidase (MPO) in testis, epididymis and accessory glands. Gene expression analyses by real‐time PCR showed the presence of MPO, IDO1 and IDO2 in all the organs of the ram reproductive tract and revealed that MPO is the main melatonin‐catabolizing enzyme, which is mainly expressed in the testis and the bulbourethral glands (p < .05). These results were further corroborated by immunohistochemical staining, and by Western blot. Likewise, MPO was also evidenced in epididymal and ejaculated spermatozoa by indirect immunofluorescence and Western blot. In conclusion, melatonin‐catabolizing enzymes MPO, IDO1 and IDO2 are expressed in the ram reproductive tract, and MPO is the most expressed one, mainly in the testis and the bulbourethral glands. The presented results warrant further studies on the function of these enzymes and their melatonin‐metabolizing activity.