Bovine Genotype Research Articles

Detection and molecular characterization of major enteric pathogens in calves in central Ethiopia

BackgroundCalf diarrhea is a major cause of morbidity and mortality in the livestock sector worldwide and it can be caused by multiple infectious agents. In Ethiopia, cattle are the most economically important species within the livestock sector, but at the same time the young animals suffer from high rates of morbidity and mortality due to calf diarrhea. However, studies including both screening and molecular characterization of bovine enteric pathogens are lacking. Therefore, we aimed to both detect and molecularly characterize four of the major enteric pathogens in calf diarrhea, Enterotoxigenic Escherichia coli (E. coli K99 +), Cryptosporidium spp., rotavirus A (RVA), and bovine coronavirus (BCoV) in calves from central Ethiopia. Diarrheic and non-diarrheic calves were included in the study and fecal samples were analyzed with antigen-ELISA and quantitative real-time PCR (qPCR). Positive samples were further characterized by genotyping PCRs.ResultsAll four pathogens were detected in both diarrheic and non-diarrheic calves using qPCR and further characterization showed the presence of three Cryptosporidium species, C. andersoni, C. bovis and C. ryanae. Furthermore, genotyping of RVA-positive samples found a common bovine genotype G10P[11], as well as a more unusual G-type, G24. To our knowledge this is the first detection of the G24 RVA genotype in Ethiopia as well as in Africa. Lastly, investigation of the spike gene revealed two distinct BCoV strains, one classical BCoV strain and one bovine-like CoV strain.ConclusionsOur results show that Cryptosporidium spp., E. coli K99 + , RVA and BCoV circulate in calves from central Ethiopia. Furthermore, our findings of the rare RVA G-type G24 and a bovine-like CoV demonstrates the importance of genetic characterization.

Molecular Characterisation of Cryptosporidium parvum among Cattle and Cattle Handlers from Tripura (India) and the Associated Risk Factors

Background: Cryptosporidium parvum is major protozoan parasite of both animals and humans with zoonotic significance. There is a paucity of information on its occurrence and associated risk factors in North Eastern states, India. The present study aimed at the molecular characterization of Cryptosporidium from cattle and cattle handlers in West district of Tripura and risk associates analysis. Methods: Faecal samples were randomly collected from cattle and cattle handlers (100 each), of West district, Tripura. The samples were subjected to sheather’s sucrose flotation, modified Zeihl Neelsen (mZN) staining and PCR assay targeting the 18S SSUr-RNA gene for detection of Cryptosporidium. The polemerised chain reaction- Restriction length polymorphism (PCR-RFLP) was done to detect Cryptosporidium spp. and C. parvum genotypes. Association of the epidemiological variables in relation to host and environment were studied for comparative analysis. Result: The incidence of Cryptosporidium was 16 per cent and 7 per cent in cattle and cattle handlers, respectively. The molecular characterisation based on PCR-RFLP analysis revealed 14 C. parvum and two C. andersoni and three C. parvum in cattle handlers. All the 14 C. parvum from cattle and one C. parvum from cattle handlers belonged to bovine genotype (genotype II) and other two C. parvum from cattle handlers belonged to the human genotype (genotype I). Cryptosporidiosis in both cattle and cattle handlers were strongly associated with younger age group and diarrhoeic faecal consistency with significantly (p less than 0.01) higher occurrence. However, significantly (p less than 0.05) higher predominance of monsoon season in occurrence of the disease was observed in cattle and sex predominance was not observed in both cattle and cattle handlers.

Genotypic and Phylogenetic Profile of Cryptosporidium Parvum Strains from HIV Positive Patients in Maiduguri, Nigeria

Background: Cryptosporidium is an etiologic agent of gastro-intestinal disorders and severe, profuse watery diarrhoea in immunocompromised patients, such as people living with HIV/AIDS.
 Aim: This study was carried out to determine the genotypic and phylogenetic characteristics of Cryptosporidium parvum among HIV patients who usually received antiretroviral therapy (ART) in four selected hospitals in Maiduguri Metropolis.
 Study Design: This is a clinical laboratory study of opportunistic pathogens in HIV/AIDS Patients.
 Place and Duration of Study: This was conducted at the Department of Medical Laboratory Science, the University of Maiduguri in collaboration with the Biological Sciences Department, ATBU Bauchi, Nigeria, between March 2021, and February 2022.
 Methods: A total of 400 faecal specimens were collected from confirmed HIV-positive patients and screened for Cryptosporidium-specific antigen by Enzyme Link Immunosorbent Assay (ELISA). Genomic DNA Extraction was done by Quick-DNATM Faecal Microbe Miniprep with PCR amplification and sequencing of 18s SSU rRNA gene using specific reference primers.
 Results: Out of the 70 HIV/AIDS and Cryptosporidium co-infected patients, 20 of the samples contained 18s SSU rRNA genes, with the highest frequency (45.0%) found in patients from the University Teaching Hospital. The results of phylogenetic analyses indicated that there is significant intra-species diversity in the genus Cryptosporidium. The four human C. parvum isolates differ from the bovine and the two avian isolates in three regions of the 18s rRNA gene.
 Conclusion: The human genotype (genotype I) found in this study is exclusively human and in a single non-human primate, in bovine genotype (genotype II) has proved to be anthroponotic and zoonotic to the livestock. The study, therefore, advocates further genotyping of Cryptosporidium from both HIV-infected patients and immunocompetent hosts from various regions together with surveillance of animal and environmental reservoirs is highly recommended.

Genetic analysis of the pX region of bovine leukemia virus genotype 1 in Holstein Friesian cattle with different stages of infection.

The pX genetic region of bovine leukemia virus (BLV) includes four genes with overlapping reading frames that code for the Tax, Rex, R3, and G4 proteins. These proteins are involved in the regulation of transcriptional and post-transcriptional viral expression, as well as having oncogenic potential. Our goal was to investigate the pathogenicity of the pX region of BLV genotype 1 in terms of lymphocytosis, lymphomas, and proviral DNA load. We screened 724 serological samples from mixed-age Holstein Friesian cattle from six states in Mexico. Peripheral blood leukocytes (PBLs) were isolated from whole blood with anticoagulant, and genomic DNA was extracted from the PBLs using a commercial kit. Then, a set of primers that hybridize in conserved regions of the BLV pX region were used, which allowed for PCR standardization to detect proviral DNA in infected cells. Positive amplicons were sequenced using the Sanger method, resulting in 1156-nucleotide-long final sequences that included the four pX region genes. The experimental group consisted of 30 animals. Twelve of these had lymphocytosis, six had lymphoma, and 12 were apparently healthy cattle without any signs of lymphocytosis or lymphoma. The presence of lymphoma was detected in six bovine tumor tissues using histopathology, and the presence of BLV was detected by in situ hybridization. Phylogenetic analysis demonstrated that the 30 sequences were associated with genotype 1, and the genetic distance between the sequences ranged from 0.2% to 2.09%. We identified two sequences in the G4 gene: one with a three-nucleotide deletion resulting in the loss of a leucine (AGU_7488L, in a cow with lymphocytosis), and one with a nine-nucleotide deletion resulting in the loss of leucine, proline, and leucine (AGU_18A, in a cow without lymphocytosis). Analysis of the PX region indicated that positive selection had occurred in the G4, rex, and R3 genes, and we found no difference in proviral DNA load between the studied groups. We were unable to establish an association between variations in the pX region and the development of lymphocytosis, lymphoma, asymptomatic status, or proviral DNA load in BLV-infected cattle.

FTIR spectroscopy with machine learning: A new approach to animal DNA polymorphism screening

Technological advances in recent decades, especially in molecular genetics, have enabled the detection of genetic DNA markers associated with productive characteristics in animals. However, the prospection of polymorphisms based on DNA sequencing is still expensive for the reality of many food-producing regions around the world, such as Brazil, demanding more accessible prospecting methods. In the present study, the Fourier transform infrared spectroscopy (FTIR) and machine learning algorithms were used to identify single nucleotide polymorphism (SNP) in animal DNA. The fragments of bovine DNA with well-known polymorphisms were used as a model. The DNA fragments were produced and genotyped by PCR-RFLP and classified according to the genotype (homozygous or heterozygous). FTIR spectra of DNA fragments were analyzed by principal component analysis (PCA) and machine learning algorithms. The best results exhibited 75–95% accuracy in the classification of bovine genotypes. Therefore, FTIR spectroscopy and multivariate analysis can be used as an alternative tool for prospecting polymorphisms in animal DNA. The method can contribute with studies to identify genetic markers associated with animal production and indirectly with food production itself, and reduce pressure on available natural resources.

Concordance rate in cattle and sheep between genotypes differing in Illumina GenCall quality score.

Proper quality control of data prior to downstream analyses is fundamental to ensure integrity of results; quality control of genomic data is no exception. While many metrics of quality control of genomic data exist, the objective of the present study was to quantify the genotype and allele concordance rate between called single nucleotide polymorphism (SNP) genotypes differing in GenCall (GC) score; the GC score is a confidence measure assigned to each Illumina genotype call. This objective was achieved using Illumina beadchip genotype data from 771 cattle (12428767 genotypes in total post-editing) and 80 sheep (1557360 SNPs genotypes in total post-editing) each genotyped in duplicate. The called genotype with the lowest associated GC score was compared to the genotype called for the same SNP in the same duplicated animal sample but with a GC score of >0.90 (assumed to represent the true genotype). The mean genotype concordance rate for a GC score of <0.300, 0.300-0.549, and ≥0.550 in the cattle (sheep in parenthesis) was 0.9467 (0.9864), 0.9707 (0.9953), and 0.9994 (0.99997) respectively; the respective allele concordance rate was 0.9730 (0.9930), 0.9849 (0.9976), and 0.9997 (0.99998). Hence, concordance eroded as the GC score of the called genotype reduced, albeit the impact was not dramatic and was not very noticeable until a GC score of <0.55. Moreover, the impact was greater and more consistent in the cattle population than in the sheep population. Furthermore, an impact of GC score on genotype concordance rate existed even for the same SNP GenTrain value; the GenTrain value is a statistical score that depicts the shape of the genotype clusters and the relative distance between the called genotype clusters.

Microsatellite markers reveal polymorphisms at the 3′ untranslated region of theSLC11A1gene in Zhongdian Yellow cattle (Bos taurus)

Solute carrier family 11-member A1 (SLC11A1) gene encodes natural macrophage resistance-associated protein which regulates activity of macrophages against intracellular pathogens. The objective of this study was to study the polymorphism in the microsatellites present at 3′ untranslated region (UTR) of the SLC11A1 gene in 113 Zhongdian Yellow cattle (Bos taurus). Using DNA bi-directional sequencing, we detected seven alleles (GT10–16) for the first microsatellite (MS1), five alleles (GT12–16) for MS2, and four alleles (GT4–7) for MS3. MS3 is studied for the first time and revealed four novel variants (alleles GT4–7). Alleles GT12 (45.1%), GT13 (59.3%), and GT5 (85.4%) were the most frequent alleles at MS1, MS2, and MS3, respectively, Genotypes G12/12, G13/13, and G5/5 had the highest frequency 0.239, 0.540, and 0.743 at MS1, MS2, and MS3, respectively. Haplotypic data revealed that GT12/GT13 was the most frequent haplotype observed followed by GT12/14 haplotype. Three nucleotide variations were observed in MS1 and MS2. Comparative analysis of GT12/GT12 and GT13/GT13 genotype with other bovine genotypes showed significant difference (P &gt; 0.05). Our results suggest that the homozygous genotypes GT12/GT12 and GT13/GT13 in Zhongdian Yellow cattle might be related to disease resistance. The findings reported in this study would be helpful in cattle breeding programs.

Detection of bovine viral diarrhea virus genotype 1 in aerosol by a real time RT-PCR assay

BackgroundAs a pestivirus of the Flaviviridae family, bovine viral diarrhea virus (BVDV), has imposed a large burden on animal husbandry worldwide, and such virus can be transmitted mainly through direct contact with other infected animals and probably via aerosols. In the present study, we aimed to develop a real-time RT-PCR method for detection of BVDV-1 in aerosol samples.MethodsA pair of primers specific for highly conserved regions of the BVDV-1 5′-UTR was designed. The standard curve and sensitivity of the developed assay were assessed based on 10-fold serial dilutions of RNA molecular standard. The specificity of the assay was evaluated with other pestiviruses and infectious bovine viruses. The clinical performance was examined by testing 169 aerosol samples.ResultsThe results showed that a good linear relationship existed between the standard curve and the concentration of template. The lowest detection limit was 5.2 RNA molecules per reaction. This assay was specific for detection of BVDV-1, and no amplification was found for other pestiviruses such as classical swine fever virus (CSFV), border disease virus (BDV), and common infectious bovine viruses, including BVDV-2, infectious bovine rhinotracheitis virus (IBRV), bovine parainfluenza virus type 3 (BPIV-3), bovine respiratory syncytial virus (BRSV), bovine ephemeral fever virus (BEFV) and bovine coronavirus (BcoV). The assay was highly reproducible with low variation coefficient values (CVs) for intra-assay and inter-assay. A total of 169 aerosol samples collected from six dairy herds were tested using this method. The results showed that the positive detection rate of BVDV-1 was 17.2% (29/169), which was significantly higher compared with the conventional RT-PCR. Additionally, the positive samples (n = 29) detected by real-time RT-PCR were verified by BVDV RPA-LFD, and a concordance rate of 100% was obtained between them.ConclusionsTaken together, we developed a real-time RT-PCR assay for quantitative analysis of BVDV-1 in aerosol samples, and our finding provided valuable insights into the risk on aerosol transmission of BVDV-1.

Phylogenetic analysis of open reading frame of 11 gene segments of novel human-bovine reassortant RVA G6P[1] strain in Pakistan.

Multiple Rotavirus A (RVA) strains are linked with gastrointestinal infections in children that fall in age bracket of 0 to 60 months. However, the problem is augmented with emergence of unique strains that reassort with RVA strains of animal origin. The study describes the sequence analysis of a rare G6P[1] rotavirus strain isolated from a less than 1 year old child, during rotavirus surveillance in Rawalpindi district, Pakistan in 2010. Extracted RNA from fecal specimen was subjected to high throughput RT-PCR for structural and nonstructural gene segments. The complete rotavirus genome of one isolate RVA/Human-wt/PAK/PAK99/2010/G6P[1] was sequenced for phylogenetic analysis to elucidate the evolutionary linkages and origin. Full genome examination of novel strain RVA/Human-wt/PAK/PAK99/2010/G6P[1] revealed the unique genotype assemblage: G6-P[1]-I2-R2-C2-M2-A3-N2-T6-E2-H1. The evolutionary analyses of VP7, VP4, NSP1 and NSP3 gene segments revealed that PAK99 clustered with bovine, or cattle-like rotavirus strains from other closely related species, in the genotypes G6, P[1], A3 and T6 respectively. Gene segments VP6, VP1, VP2, VP3, NSP2 and NSP4 all possessed the DS-1-like bovine genotype 2 and bovine (-like) RVA strains instead of RVA strains having human origin. However, the NSP5 gene was found to cluster closely with contemporary human Wa-like rotavirus strains of H1 genotype. This is the first report on bovine-human (Wa-like reassortant) genotype constellation of G6P[1] strain from a human case in Pakistan (and the second description worldwide). Our results emphasize the significance of incessant monitoring of circulating RVA strains in humans and animals for better understanding of RV evolution.

Multilocus analysis reveals further genetic differences between Tritrichomonas foetus from cats and cattle

Tritrichomonas foetus isolates from feline and bovine origin has been previously shown to carry a certain degree of genetic heterogeneity. Here, novel candidate molecular markers were developed by means of multilocus sequence typing of the gap2 gene (encoding for T. foetus glyceraldehyde-3-phosphate dehydrogenase), ITS region, the TR7/TR8 variable-length repeat and microsatellite genotyping. These markers were used to characterize T. foetus field isolates from bulls and domestic cats and to compare phylogenetically with the following ATCC isolates: T. foetus isolated from cattle and pig (syn. Tritrichomonas suis), Tritrichomonas mobilensis, Tetratrichomonas gallinarum and Pentatrichomonas hominis. Among them, TFMS10 and TFMS7 were found to be the most polymorphic markers. Moreover, an 809 bp fragment of the gap2 gene was successfully amplified from all the trichomonads included in this study and the sequence analysis revealed differences between T. foetus porcine and feline genotypes and T. mobilensis in comparison to the bovine T. foetus ATCC isolate. The TR7/TR8 repeat pattern was not reproducible, being only consistent the fragments of approximately 110 and 217 bp. Sequence analysis of the latter revealed the existence of 3 SNPs resulting in 98.6 % homology between bovine and feline isolates. A search for similar sequences was carried out to develop a Restriction Length Fragment Polymorphism analysis. A 503 bp region, named TF1, revealed the existence of two BbvI restriction enzyme sites that were able to generate different length fragments for T. foetus feline and bovine isolates. Finally, the neighbour-joining analyses showed that T. foetus porcine genotype clusters together with bovine genotype, whereas T. mobilensis and the feline genotype form a separate cluster.

Effect of bovine genotype on innate immune response of heifers to repeated lipopolysaccharide (LPS) administration

This pilot study provides a preliminary assessment of the impact of genotype on acute innate immune pro-inflammatory, metabolic and endocrine responses to repeated lipopolysaccharide (LPS) administered to growing heifers. Heifers (n = 4/genotype) were from unselected (stable milk yield since 1964, UH) or contemporary (CH) Holstein cows that differed in milk yield (6200 vs 11,100 kg milk/305 d) or from contemporary Black Angus (CA) cows bred to contemporary Red Angus bulls. Heifers were challenged with iv administration of 0.5 μg LPS/kg body weight on day 1 (Challenge 1) and d 5 (Challenge 2) of study to assess endotoxin tolerance. Plasma was collected at -1, -0.5, 0, 1, 2, 3, 4, 6, 8, and 24 h relative to each LPS administration. Rectal body temperature (BT) was measured before each blood sampling and at 5 and 7 h. Data were analyzed by repeated measures with sampling time as the repeated effect. Each genotype had at least one pro-inflammatory response that indicated it might have a more robust response than the other genotypes. The CH heifers had a greater TNF-α response, UH heifers had greater IL-6 and XO responses and CA heifers had greater BT and SAA response to LPS than the other genotypes. There was a genotype by time by interaction as cortisol peaked earlier in CH and UH than in CA heifers. Glucose response was less in CA and insulin response was greater in CH heifers. Endotoxin tolerance to LPS was evident as pro-inflammatory, cortisol, glucose and insulin responses were less during Challenge 2 than during Challenge 1. Differences among genotypes during Challenge 1 were eliminated during Challenge 2 except for the greater SAA response in CA heifers and indicate the potential for differential impacts of genotype on the development of endotoxin tolerance. Specific reasons for these effects of genotype are not clear from these data but the results support the hypothesis for differential innate immune signaling among these bovine genotypes.

Three monophyletic clusters in Retortamonas species isolated from vertebrates

Retortamonas spp. has been reported as an intestinal parasite among various host organisms, including humans; however, its intra-genus molecular diversity has not yet been elucidated. Haplotypes of the 18S small subunit ribosomal RNA locus (1836–1899 bp) of Retortamonas spp. from humans (n = 8), pigs (n = 6), dogs (n = 1), goats (n = 16), water buffalos (n = 23), cattle (n = 7), rats (n = 3), and chickens (n = 5) were analyzed with references isolated from non-human mammals, amphibians, and insects. Phylogenetic and network analyses revealed a statistically supported three cluster formation among the vertebrate-isolated haplotypes, while insect-isolated haplotypes were independently clustered with Chilomastix. In the clade of vertebrate isolates, assemblage A (amphibian genotype), which included the amphibian references, was addressed as an out-group of the other clusters. Assemblage B (mammalian and chicken genotype) included most haplotypes from various mammals including humans with the haplotypes isolated from a chicken. Human isolates were all classified into this assemblage, thus assemblage B might correspond to R. intestinalis. Assemblage C (bovine genotype), which included specific haplotypes from water buffalos and cattle, was addressed as a sister lineage of assemblage B. Among the diversified haplotypes of assemblage B, a specific haplotype, which was identified from multiple host mammals (humans, dogs, pigs, cattle, water buffalos, elks, goats, and rats), indicates the potential zoonotic transmission of the Retortamonas among them. The genotyping classification of retortamonads could contribute to a better understanding of its molecular epidemiology, especially among humans and related host organisms.

Sanitation of Staphylococcus aureus genotype B-positive dairy herds: A field study

Staphylococcus aureus is one of the most widespread mastitis pathogens infecting dairy cattle worldwide. In Switzerland, different bovine genotypes of Staph. aureus have been identified, and genotype B (GTB) was demonstrated to be a highly contagious subtype, causing herd problems in cattle. As the efficacy of antibiotic therapy against Staph. aureus is not satisfactory, the most promising strategy for controlling this udder pathogen is the implementation of specific sanitation programs for affected farms. The aim of the present longitudinal study was the field evaluation of 2 analytical approaches for the sanitation of Staph. aureus GTB-positive dairy herds. We compared a new real-time quantitative PCR (qPCR) assay based on the detection of the unique target gene adlb with classical bacteriology. Sanitation was successfully achieved using both analytical methods, but the qPCR approach showed some main advantages, namely the use of clean (instead of aseptically collected) milk samples facilitates sample collection in terms of time and costs, enabling the sampling of entire herds during a regular milking procedure and by the farm staff. The high inclusivity and exclusivity of the new target gene adlb enable very specific detection of only the genotype of interest. Because of the very high diagnostic sensitivity of qPCR, each GTB-positive cow can be correctly identified at any time point during lactation, allowing farmers to continuously update milking groups to prevent transmission during milking. Milk sample analysis becomes more objective, faster, less expensive, and more suitable for routine application, enabling the sanitation of even big herds in short time.

Mechanisms regulating follicle selection in ruminants: lessons learned from multiple ovulation models.

Selection of a single dominant follicle from a cohort of growing follicles is a unique biological process, a key step in female reproductive function in monovular species, and lies at the core of reproductive technologies in cattle. Follicle growth and the number of follicles that ovulate are regulated by precise endocrine, paracrine, and autocrine mechanisms. Most of our current understanding about follicle selection focuses on the role of FSH, LH, and the IGF family in follicle growth and selection of the dominant follicle. However, more recently the role of members of the TGF-ß family has been highlighted, particularly in high fecundity genotypes in sheep. Intercellular signaling between the oocyte and granulosa cells (GC) regulates proliferation and differentiation due to actions of bone morphogenetic protein 15 (BMP15) and growth and differentiation factor 9 (GDF9) within the follicle. Mutations that either knockout or reduce the activity of BMP15 or GDF9 have been found to increase ovulation rate in heterozygotes and generally cause severe follicle abnormalities in homozygotes. A mutation in the intracellular kinase domain of the BMPR1B receptor (Booroola fecundity gene) increases ovulation rate in heterozygotes with further increases in ovulation in homozygotes. The physiological mechanisms linking these mutations to increased ovulation rates are still not well defined. A recently identified high fecundity bovine genotype, Trio, causes increased expression of SMAD6, an intracellular inhibitor of the BMP15/GDF9 signalling pathways. This bovine model has provided insights into the mechanisms associated with selection of multiple dominant follicles and multiple ovulations in carriers of fecundity alleles. The present review focuses on the mechanisms involved in follicle selection in ruminants with a special emphasis on the contribution made by multiple ovulation models in both cattle and sheep. The evaluation of multiple ovulation models in ruminants has allowed us to construct a new physiological model that relates changes in the BMP15/GDF9 signalling pathways to the physiological changes that result in selection of multiple dominant follicles. This model is characterized by acquisition of dominance at a smaller follicle size but at a similar time in the follicular wave with multiple follicles acquiring dominance in a hierarchal sequence, delaying FSH suppression and, thus allowing additional follicles to continue to grow and acquire dominance.

Ovulation rate, antral follicle count, and circulating anti-Müllerian hormone in Trio allele carriers, a novel high fecundity bovine genotype

High fecundity genotypes in sheep are a valuable model to study the physiological mechanisms underlying follicle selection and the control of ovulation rate. Similar genotypes in cattle had not been described until the recent identification of a major bovine allele, termed Trio, which had a large effect on ovulation rate. The present study was designed to evaluate ovulation rate, antral follicle count (AFC), circulating ant-müllerian hormone (AMH), and the association among these measures in unstimulated and superstimulated Trio carrier cattle. We hypothesized that AFC and AMH would be variable among individual cows but would be similar between Trio carriers and non-carrier control cows and that there would be no association between these measures of follicle numbers and ovulation rate. In experiment 1, ovulation rate was determined during 4 consecutive estrous cycles in Trio carriers (n = 34) and non-carrier controls (n = 27). Ovulation rate, on average, was greater (P < 0.01) in Trio carriers (3.5 ± 0.2) compared to non-carrier controls (1.1 ± 0.1) with ∼70% of carrier cycles (n = 136) having 3–4 ovulations while only ∼5% had single ovulations. In contrast, non-carrier cycles (n = 108) were mostly single ovulation (89%) with none having more than two ovulations. In experiment 2, AFC, determined at wave emergence, was not different (P = 0.54) between Trio carriers (24.5 ± 1.3; n = 45) and non-carrier controls (23.1 ± 0.9; n = 37), and no correlation was found between AFC and mean ovulation rate in either genotype (r = −0.009 and r = −0.07; P > 0.70, respectively). In Experiment 3, circulating AMH was also not different between genotypes (P = 0.65) while correlations were found between AFC and AMH in Trio carriers (r = 0.43; P = 0.05; n = 27) and non-carrier controls (r = 0.78; P < 0.01; n = 19). In experiment 4, AFC and AMH were determined in Trio-carriers (n = 9) in relation to a synchronized follicular wave which was unstimulated or stimulated with exogenous FSH. Stimulation with FSH increased ovulation rate, compared to unstimulated Trio carriers, however no association was found between AFC or AMH and ovulation rate regardless of whether superstimulation with exogenous FSH was used. In conclusion, the novel high fecundity bovine genotype Trio, results in consistent multiple ovulations despite having similar AFC and AMH. Therefore, our results suggest that differences in antral follicle numbers during the final stages of follicle development are not a key component of the mechanism underlying multiple ovulations in Trio carriers.

Follicular waves and hormonal profiles during the estrous cycle of carriers and non-carriers of the Trio allele, a major bovine gene for high ovulation and fecundity

A high fecundity bovine genotype has recently been discovered and genetic mapping indicates evidence for segregation of a major gene with influence on ovulation rate located on bovine chromosome 10. Cattle carrying the high fecundity allele, referred to as the Trio allele, have multiple ovulations while half-sibling, non-carriers generally have single ovulations. The present study was designed to evaluate follicle wave patterns and associated circulating hormones during the estrous cycle of Trio allele carriers (n = 7) and non-carrier half-sib controls (n = 5). We hypothesized that Trio allele carriers would exhibit multiple smaller dominant follicles and greater circulating FSH than non-carrier controls. The proportion of Trio carrier and non-carrier cows with 2 or 3-wave patterns was not different between genotypes with the majority (>70%) exhibiting 3-wave patterns. Trio carriers had greater (P < 0.01) number of ovulations (∼4 vs ∼1 ovulations) and smaller preovulatory follicles (8.9 vs. 14.9 mm; P < 0.01) than non-carrier controls. However, total luteal tissue volume and circulating progesterone, normalized to the initial ovulation or to the onset of luteolysis, were not different between genotypes (P > 0.10). Follicular waves were found to be associated with an FSH surge in both genotypes. Peak FSH concentration at each follicular wave (3-wave patterns) was not different (P > 0.05) between genotypes, but circulating FSH during the decline and nadir, encompassing the day of deviation, was greater (P < 0.05) in Trio carriers. Despite a difference (P = 0.032) in the length of the estrous cycle (23.0 vs. 25.2 d; Trio carrier and non-carriers respectively), the pattern of follicle growth, such as day of wave emergence, day of follicle deviation, and day of maximum diameter of the dominant follicle, when normalized to the FSH surge of each follicular wave were similar in Trio carriers compared to non-carriers although Trio carriers consistently had much smaller-sized follicles (P < 0.05). Thus, decreased follicle size and greater circulating FSH are key components of the mechanism that produces multiple ovulations in cattle that are carriers of the Trio high fecundity allele.

Cryptosporidium: Identification and Genetic Typing.

Cryptosporidium spp. are obligate protozoan parasites of the gastrointestinal tract of vertebrates, including humans. In the majority of human cases, the diarrheal disease cryptosporidiosis is caused by either the human-adapted species Cryptosporidium hominis or the zoonotic Cryptosporidium parvum 'bovine genotype' (also known as Cryptosporidium pestis). The infectious stage, environmentally resilient Cryptosporidium oocysts, are shed by the infected host. Cryptosporidium parasites are transmitted by the fecal-oral route and are one of the major water-borne pathogens. The cryptic nature of the microscopic Cryptosporidium oocysts coupled with the existence of several host-adapted and zoonotic species requires molecular tools to identify Cryptosporidium spp. in either fecal or environmental samples. This unit describes methods for Cryptosporidium identification and typing using genotyping based on nuclear loci. We also provide a protocol for morphological confirmation of Cryptosporidium oocysts based on antibody labeling of the Cryptosporidium oocyst wall and a protocol for purification of oocysts from fecal material. © 2017 by John Wiley & Sons, Inc.

Deriving Gene Networks from SNP Associated with Triacylglycerol and Phospholipid Fatty Acid Fractions from Ribeyes of Angus Cattle.

The fatty acid profile of beef is a complex trait that can benefit from gene-interaction network analysis to understand relationships among loci that contribute to phenotypic variation. Phenotypic measures of fatty acid profile from triacylglycerol and phospholipid fractions of longissimus muscle, pedigree information, and Illumina 54 k bovine SNP genotypes were utilized to derive an annotated gene network associated with fatty acid composition in 1,833 Angus beef cattle. The Bayes-B statistical model was utilized to perform a genome wide association study to estimate associations between 54 k SNP genotypes and 39 individual fatty acid phenotypes within each fraction. Posterior means of the effects were estimated for each of the 54 k SNP and for the collective effects of all the SNP in every 1-Mb genomic window in terms of the proportion of genetic variance explained by the window. Windows that explained the largest proportions of genetic variance for individual lipids were found in the triacylglycerol fraction. There was almost no overlap in the genomic regions explaining variance between the triacylglycerol and phospholipid fractions. Partial correlations were used to identify correlated regions of the genome for the set of largest 1 Mb windows that explained up to 35% genetic variation in either fatty acid fraction. SNP were allocated to windows based on the bovine UMD3.1 assembly. Gene network clusters were generated utilizing a partial correlation and information theory algorithm. Results were used in conjunction with network scoring and visualization software to analyze correlated SNP across 39 fatty acid phenotypes to identify SNP of significance. Significant pathways implicated in fatty acid metabolism through GO term enrichment analysis included homeostasis of number of cells, homeostatic process, coenzyme/cofactor activity, and immunoglobulin. These results suggest different metabolic pathways regulate the development of different types of lipids found in bovine muscle tissues. Network analysis using partial correlations and annotation of significant SNPs can yield information about the genetic architecture of complex traits.

Whole genome characterization of a G6P[5] rotavirus A strain isolated from a stray cat in Japan

The whole genome of an unusual G6P[5] rotavirus A strain named FRV537, which was isolated from a stray cat in Japan, was characterized to determine its species of origin. The genotype constellation of FRV537 was G6-P[5]-I2-R2-C2-M2-A13-N2- T6-E2-H3. No known feline rotavirus has this genotype constellation; the Japanese equine strain OH-4 is the only known strain that does. While FRV537 shares the same genotype with some feline rotaviruses in all genes except those encoding VP4 and NSP1, none of these genes are closely related to those of known feline rotaviruses. By contrast, G6P[5] is almost exclusively present in bovine rotaviruses. The VP7 and VP4 genes of FRV537 formed a lineage with typical bovine rotaviruses with high bootstrap values. As to the internal capsid and nonstructural gene constellation, three bovine rotavirus strains had a constellation identical to that of FRV537. Moreover, each of the genotypes of FRV537 was found to be a common bovine genotype. In addition to the high nucleotide sequence identities between FRV537 and bovine rotaviruses in each genome segment (≥95%), phylogenetic analysis revealed a close relationship to bovine/artiodactyl rotaviruses. Thus, the molecular and phylogenetic evidence suggests that FRV537 isolated from a stray cat was of bovine rotavirus origin.

Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.