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DOAJ Open Access 2025
Estimation of Breeding Values by Various Sire Evaluation Methods for Selection of Sires in Crossbred Cattle

Shashikant, C. V. Singh, R. S. Barwal et al.

The study was conducted from January to November, 2022 at G.B. Pant University of Agriculture and Technology, Pantnagar, with the objective of ranking sires based on first lactation traits. The breeding values of 66 crossbred sires were evaluated for age at first calving, first lactation length, and first lactation milk yield using Best Linear Unbiased Prediction, Least Squares Method, and Restricted Maximum Likelihood methods. The average breeding values for age at first calving were 1153.41 days (Best Linear Unbiased Prediction), 1152.25 days (Least Squares Method), and 1153.93 days (Restricted Maximum Likelihood); for first lactation length, 340.51 days (Best Linear Unbiased Prediction), 353.24 days (Least Squares Method), and 354.04 days (Restricted Maximum Likelihood); and for first lactation milk yield, 3348.81 kg (Best Linear Unbiased Prediction), 3602.34 kg (Least Squares Method), and 3612.37 kg (Restricted Maximum Likelihood). Significant and highest Spearman's rank and Pearson correlation coefficients were observed between LSM and REML for the first lactation length and milk yield, indicating that these methods were highly correlated and equally accurate for ranking sires. Sire no. 15 showed consistently high breeding values for age at first calving across all methods, securing the top rank for this trait. For the first lactation length, sire no. 23 ranked first with BLUP, while sire no. 59 led in LSM and REML. Different sires topped the rankings for first lactation milk yield in each method. Overall, 4–5% of top-ranked sires maintained similar ranks across evaluation methods, providing insights into sire performance.

Social Sciences, Agriculture
DOAJ Open Access 2025
Properties of Grassland Habitats in Organic and Conventional Farms Located in Mountainous Areas—A Case Study from the Western Sudetes

Krzysztof Solarz, Agnieszka Dradrach, Marta Czarniecka-Wiera et al.

Organic farming is becoming increasingly important in agricultural production, especially in mountain and foothill areas. In organic farms, unlike conventional ones, no mineral fertilization or chemical plant protection is used, which often limits the economic efficiency of production. It is commonly believed that conventional farming poses a threat to biodiversity due to the use of mineral fertilization, chemical plant protection, and highly productive crop varieties, and the products obtained are in many respects of lower quality than those from organic farms. The aim of this work is to compare the quality and fertility of soils and the biodiversity of grasslands in organic and conventional farms, using the example of a foothill area within the commune of Kamienna Góra located in the Western Sudetes. Thirty-three areas representing 11 farms that produce dairy cattle in a grazing system were selected for analysis. The properties of soils in organic and conventional farms and their nutrient status did not differ significantly, except for the content of available potassium, which was higher in the group of organic farms. This fact seems to be related to the type of parent rock. All soils had acidic, slightly acidic, or strongly acidic pH levels. The greatest differences between pastures in organic and conventional farms concerned the sward species composition and biodiversity indices. Grasslands in organic farms were much richer in species, which was reflected by the species richness (SR) index and the F-fidelity index. The species inventoried clearly formed two groups that are characteristic of organic and conventional grasslands. The greater biodiversity of grasslands in organic farms did not have a significant effect on the fodder value of the sward, which should be considered good, allowing producers to participate in short supply chains. However, in all farms, regardless of their type, it would be advisable to carry out gentle liming.

Agriculture (General)
DOAJ Open Access 2023
Effect of Creep Feeding Supplementation on Growth Performance and Metabolic Characteristics of Nellore Heifers

Robert T. da Paixão, Edenio Detmann, Marcos I. Marcondes et al.

The objective of this paper is to evaluate the effects of creep feeding supplementation during the preweaning phase on the growth performance and metabolic characteristics of Nellore heifers. Forty-two female Nellore calves (age = 100 ± 25 d; initial body weight (BW) = 113.4 ± 16.6 kg) were randomly assigned to the following treatments: control, where calves received mineral mix supplementation (<i>n</i> = 21); supplemented in creep feeding, where calves received 6 g/kg BW of a concentrate supplement (<i>n</i> = 21) during a period of 140 d. In the postweaning phase, all heifers received 6 g/kg BW of a concentrate supplement during a period of 210 d. Supplemented heifers had a greater average daily gain (ADG) than control heifers during the preweaning phase and, consequently, were heavier at weaning and at the end of the growing phase (<i>p</i> < 0.05). However, preweaning supplementation did not influence (<i>p</i> > 0.05) the body measurements or BW at the end of the growing period. Greater (<i>p</i> < 0.05) rib fat was observed in supplemented heifers. Concentrations of metabolites were not affected by preweaning supplementation (<i>p</i> > 0.05). Thus, supplementing heifers in the preweaning phase improved growth performance of weaning and body adiposity.

Nutrition. Foods and food supply
DOAJ Open Access 2022
Screening of Bovine Tissue-Specific Expressed Genes and Identification of Genetic Variation Within an Adipose Tissue-Specific lncRNA Gene

Sihuan Zhang, Han Xu, Enhui Jiang et al.

Global classification of bovine genes is important for studies of biology and tissue-specific gene editing. Herein, we classified the tissue-specific expressed genes and uncovered an important variation in the promoter region of an adipose tissue-specific lncRNA gene. Statistical analysis demonstrated that the number of genes specifically expressed in the brain was the highest, while it was lowest in the adipose tissues. A total of 1,575 genes were found to be significantly higher expressed in adipose tissues. Bioinformatic analysis and qRT-PCR were used to uncover the expression profiles of the 23 adipose tissue-specific and highly expressed genes in 8 tissues. The results showed that most of the 23 genes have higher expression level in adipose tissue. Besides, we detected a 12 bp insertion/deletion (indel) variation (rs720343880) in the promoter region of an adipose tissue-specific lncRNA gene (LOC100847835). The different genotypes of this variation were associated with carcass traits of cattle. Therefore, the outcomes of the present study can be used as a starting point to explore the development of cattle organs and tissues, as well as to improve the quality of cattle products.

Veterinary medicine
DOAJ Open Access 2022
Incidence of Aflatoxin M<sub>1</sub> in Milk and Milk Products from Punjab, Pakistan, and Estimation of Dietary Intake

Shahzad Zafar Iqbal, Muhammad Waqas, Sidra Latif

In the present study, 124 samples of milk and milk products were analyzed for the presence of aflatoxin M<sub>1</sub> (AFM<sub>1</sub>), which were purchased from the central cities of Punjab, Pakistan. The analysis was carried out using reverse-phase liquid chromatography, which was equipped with a fluorescence detector. The results showed that 66 samples (53.8%) of raw milk and milk products were found to be contaminated with detectable levels of AFM<sub>1</sub> above ≤50 ng/L, and 24.2% of the samples had levels of AFM<sub>1</sub> higher than the permissible limit of the European Union (EU; 50 ng/kg). In total, 53.6% of the raw milk, 57.8% of the UHT (ultra-heat-temperature) milk, 45% of the powdered milk, 57.1% of the yogurt, 55.5% of the cheese, and 50% of the buttermilk samples had levels higher than the LOD, i.e., 4 ng/L. The highest mean of 82.4 ± 7.8 ng/kg of AFM<sub>1</sub> was present in the positive samples of raw milk. The highest dietary intake of AFM<sub>1</sub> was found in infants’ milk (5.35 ng/kg/day), UHT milk (1.80 ng/kg/day), powdered milk (5.25 ng/kg/day), and yogurt (1.11 ng/kg/day). However, no dietary intake was detected in the cheese and butter milk samples used for infants. The results from the undertaken work are beneficial for establishing rigorous limits for AFB<sub>1</sub> in animal feed, especially considering the high prevalence rate of hepatitis cases in the central cities of Punjab, Pakistan.

Dairy processing. Dairy products
DOAJ Open Access 2022
<i>Moringa oleifera</i> and Propolis in Cattle Nutrition: Characterization of Metabolic Activities in the Rumen In Vitro

Mubarik Mahmood, Hasan Ersin Samli, Arife Sener-Aydemir et al.

<i>Moringa oleifera</i> by-products such as seed cake and leaves are protein-rich ingredients, while raw propolis has the potential to influence ruminal protein metabolism. These substances are also known to be sources of functional compounds. With these properties, they could modulate ruminal fermentation activities. Using the rumen simulation technique, we investigated ruminal fermentation and the antioxidant properties of four dietary treatments. These included a control diet (CON) without supplementation; the CON diet top-dressed on a dry matter (DM) basis, either with moringa seed cake (MSC, containing 49% crude protein (CP)), moringa leaf powder (ML, containing 28% CP), or raw propolis (PRO, 3% CP). MSC, ML, and PRO accounted for 3.8, 7.4, and 0.1% of the total diet DM, respectively. Both ML and MSC resulted in 14 and 27% more ammonia concentration, respectively than CON and PRO (<i>p</i> < 0.05). MSC increased the propionate percentage at the expense of acetate (<i>p</i> < 0.05). Both ML and MSC decreased methane percentages by 7 and 10%, respectively, compared to CON (<i>p</i> < 0.05). The antioxidant capacity of the moringa seed cake, moringa leaf powder, and raw propolis were 1.14, 0.56, and 8.56 mg Trolox/g DM, respectively. However, such differences were not evident in the fermentation fluid. In conclusion, the supplementation of moringa seed cake desirably modulates rumen microbial activities related to protein and carbohydrate metabolism.

DOAJ Open Access 2021
Characterization of the Biodistribution of a Silica Vesicle Nanovaccine Carrying a Rhipicephalus (Boophilus) microplus Protective Antigen With in vivo Live Animal Imaging

Karishma T. Mody, Bing Zhang, Xun Li et al.

Development of veterinary subunit vaccines comes with a spectrum of challenges, such as the choice of adjuvant, antigen delivery vehicle, and optimization of dosing strategy. Over the years, our laboratory has largely focused on investigating silica vesicles (SVs) for developing effective veterinary vaccines for multiple targets. Rhipicephalus microplus (cattle tick) are known to have a high impact on cattle health and the livestock industry in the tropical and subtropical regions. Development of vaccine using Bm86 antigen against R. microplus has emerged as an attractive alternative to control ticks. In this study, we have investigated the biodistribution of SV in a live animal model, as well as further explored the SV ability for vaccine development. Rhodamine-labeled SV-140-C18 (Rho-SV-140-C18) vesicles were used to adsorb the Cy5-labeled R. microplus Bm86 antigen (Cy5-Bm86) to enable detection and characterization of the biodistribution of SV as well as antigen in vivo in a small animal model for up to 28 days using optical fluorescence imaging. We tracked the in vivo biodistribution of SVs and Bm86 antigen at different timepoints (days 3, 8, 13, and 28) in BALB/c mice. The biodistribution analysis by live imaging as well as by measuring the fluorescent intensity of harvested organs over the duration of the experiment (28 days) showed greater accumulation of SVs at the site of injection. The Bm86 antigen biodistribution was traced in lymph nodes, kidney, and liver, contributing to our understanding how this delivery platform successfully elicits antibody responses in the groups administered antigen in combination with SV. Selected tissues (skin, lymph nodes, spleen, kidney, liver, and lungs) were examined for any cellular abnormalities by histological analysis. No adverse effect or any other abnormalities were observed in the tissues.

DOAJ Open Access 2021
A meta-analysis of effects of dietary seaweed on beef and dairy cattle performance and methane yield.

Ian J Lean, Helen M Golder, Tianna M D Grant et al.

There has been considerable interest in the use of red seaweed, and in particular Asparagopsis taxiformis, to increase production of cattle and to reduce greenhouse gas emissions. We hypothesized that feeding seaweed or seaweed derived products would increase beef or dairy cattle performance as indicated by average daily gain (ADG), feed efficiency measures, milk production, and milk constituents, and reduce methane emissions. We used meta-analytical methods to evaluate these hypotheses. A comprehensive search of Google Scholar, Pubmed and ISI Web of Science produced 14 experiments from which 23 comparisons of treatment effects could be evaluated. Red seaweed (Asparagopsis taxiformis) and brown seaweed (Ascophyllum nodosum) were the dominant seaweeds used. There were no effects of treatment on ADG or dry matter intake (DMI). While there was an increase in efficiency for feed to gain by 0.38 kg per kg [standardized mean difference (SMD) = 0.56; P = 0.001] on DerSimonian and Laird (D&L) evaluation, neither outcome was significant using the more rigorous robust regression analysis (P >0.06). The type of seaweed used was not a significant covariable for ADG and DMI, but A. nodosum fed cattle had lesser feed to gains efficiency compared to those fed A. taxiformis. Milk production was increased with treatment on weighted mean difference (WMD; 1.35 ± 0.44 kg/d; P <0.001); however, the SMD of 0.45 was not significant (P = 0.111). Extremely limited data suggest the possibility of increased percentages of milk fat (P = 0.040) and milk protein (P = 0.001) on (D&L) WMD evaluation. The limited data available indicate dietary supplementation with seaweed produced a significant and substantial reduction in methane yield by 5.28 ± 3.5 g/kg DMI (P = 0.003) on D&L WMD evaluation and a D&L SMD of -1.70 (P = 0.001); however, there was marked heterogeneity in the results (I2 > 80%). In one comparison, methane yield was reduced by 97%. We conclude that while there was evidence of potential for benefit from seaweed use to improve production and reduce methane yield more in vivo experiments are required to strengthen the evidence of effect and identify sources of heterogeneity in methane response, while practical applications and potential risks are evaluated for seaweed use.

Medicine, Science
DOAJ Open Access 2021
Mo¬lecular evidence and epidemiology of “Candidatus Mycoplasma haemobos” among cat-tle in Peninsular Malaysia using the 16S rRNA gene

S. D. Ola-Fadunsin, D. A. Abdullah, F. I. Gimba et al.

Haemotropic Mycoplasma infection among cattle has not been seriously looked into, despite the fact it is associated with poor weight gain and depression. One thousand and forty-five blood samples from apparently healthy cattle from forty-three farms within the entire Peninsular Malaysia were exa¬mined over a one-year period. Using polymerase chain reaction to amplify the 16S rRNA gene, the presence of “Candidatus Mycoplasma haemobos” as one of the haemotropic Mycoplasma species that affects cattle in the country was detected. Forty-seven percent of the sampled population was positive for “C. M. haemobos”, with the antigen present in all herds sampled. Breed of cattle, gender, age, production type, physiological status, herd size, management system, farm size, farm age, prophylac-tic treatment against blood parasites, presence of ticks, frequency of de-ticking, zone, closeness to forest, closeness to waste area, closeness to human settlement and closeness to body of water were all significantly associated (P<0.05) with the detection of “C. M. haemobos”. The findings from this study will be pivotal in government policy on this blood Mycoplasma infection, as the study happens to be the first comprehensive molecular survey of the microorganism in the country.

Veterinary medicine
DOAJ Open Access 2021
Retrospective Evaluation of Claw Lesions, Inflammatory Markers, and Outcome after Abomasal Rolling in Cattle with Left Displacement of the Abomasum

Theresa Tschoner, Yury Zablotski, Melanie Feist

Lameness is often diagnosed in cattle with left displacement of the abomasum (LDA). Laterality of lying has an effect on the etiology of LDA, and lame cows prefer to lie on the affected limb. The objective of this study was to investigate the possible association between laterality of claw lesion and presence of LDA. The medical records of 252 cattle presented with a diagnosis of LDA and subjected to a diagnostic examination of claw lesions over a period of 11 years (2009–2019), were analyzed retrospectively. Data were evaluated for presence and localization of claw lesion, concentrations of inflammatory markers, and abomasal rolling as therapy. At least one claw lesion was diagnosed in 46.4% of cattle. There was no association between laterality of claw lesion and LDA. Presence of claw lesion or oral drench and/or analgesic treatment did not have an effect on occurrence of relapse. A high number of cattle was diagnosed with both LDA and claw lesions. Focus should lie on preventing painful claw lesions in the dry and the early post-partum period. The high recurrence rate after abomasal rolling suggests that abomasal rolling should only be considered as a therapy for temporary relief, and surgical procedures should be discussed with farmers.

Veterinary medicine, Zoology
DOAJ Open Access 2021
Assessing the role of livestock and sympatric wild ruminants in spreading antimicrobial resistant Campylobacter and Salmonella in alpine ecosystems

Johan Espunyes, Oscar Cabezón, Andrea Dias-Alves et al.

Abstract Background Livestock play an important role as reservoir of enteric pathogens and antimicrobial resistance (AMR), a health and economic concern worldwide. However, little is known regarding the transmission and maintenance of these pathogens at the wildlife-livestock interface. In this study, we assessed the occurrence, genetic diversity and AMR of Campylobacter spp. and Salmonella spp. shed by sympatric free-ranging livestock and a wild herbivore in an alpine ecosystem. Results Campylobacter spp. was isolated from 23.3 % of cattle and 7.7 % of sheep but was not isolated from horses nor Pyrenean chamois (Rupicapra pyrenaica). Campylobacter jejuni was the most frequent species. A high genetic diversity and certain host specificity of C. jejuni isolates was observed. The main AMR detected in Campylobacter isolates was to nalidixic acid (88.2 %), ciprofloxacin (82.4 %) and tetracycline (82.4 %); only 11.7 % of the isolates were pan-susceptible and 17.6 % were multi-resistant. Salmonella ser. Newport was isolated only from one Pyrenean chamois and was pan-susceptible. Conclusions Results show that free-ranging cattle and sheep are spreaders of Campylobacter as well as their AMR strains in the alpine environment. Therefore, contaminated alpine pastures or streams may constitute a source for the dissemination of AMR enteropathogens. However, apparently, alpine wild ungulates such as Pyrenean chamois play a negligible role in the epidemiology of zoonotic enteropathogens and AMR, and are not potential bioindicators of the burden of alpine environments.

Veterinary medicine
DOAJ Open Access 2020
Betaine Supplementation Improves the Production Performance, Rumen Fermentation, and Antioxidant Profile of Dairy Cows in Heat Stress

Ali Mujtaba Shah, Jian Ma, Zhisheng Wang et al.

The aim of the current research was to investigate the effects of betaine (Bet) supplementation on the production performance, rumen fermentation, digestibility, and serum indexes of dairy cows. Thirty healthy Holstein cows with the same parity (milk production = 22 ± 2.5 kg) were randomly selected and divided into three groups. One group served as a control group (CON; no betaine); the other two groups were Bet1 (15 g/d per cow) and Bet2 (30 g/d per cow). All cows were fed regularly three times a day at 06:00, 14:00, and 22:00 h. Cows received the formulate diet, and water was provided ad libitum. The experiment lasted for 60 days during the summer season. Results showed that the dry matter intake, milk protein, and fat of Bet1 cows was significantly higher (<i>p</i> < 0.05) than that in other groups. The content of volatile fatty acid (VFA) in Bet1 was significantly higher (<i>p</i> < 0.05) than CON. Consistent with VFA, a similar trend was found in acetate, while propionate exhibited an opposite trend. Compared to other groups, the microbial protein (MCP) concentrations of Bet1 increased (<i>p</i> < 0.05). The apparent digestibility of dry matter (DM), organic matter (OM), crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF) of Bet1 was significantly higher (<i>p</i> < 0.05) than CON. The serum concentration of total antioxygenic capacity (T-AOC) in Bet1 and Bet2 was significantly increased (<i>p</i> < 0.05). Furthermore, the contents of malonaldehyde (MDA) and superoxide dismutase (SOD) in Bet2 were higher (<i>p</i> < 0.05) than that in other groups. Compared to CON and Bet2, Bet1 significantly increased (<i>p</i> < 0.05) the serum concentrations of glucose. Therefore, it is practicable to feed betaine to lactating cows to improve their performance in heat stress.

Veterinary medicine, Zoology
DOAJ Open Access 2019
Bovine Foamy Virus: Shared and Unique Molecular Features In Vitro and In Vivo

Magdalena Materniak-Kornas, Juan Tan, Anke Heit-Mondrzyk et al.

The retroviral subfamily of <i>Spumaretrovirinae</i> consists of five genera of foamy (spuma) viruses (FVs) that are endemic in some mammalian hosts [1]. Closely related species may be susceptible to the same or highly related FVs. FVs are not known to induce overt disease and thus do not pose medical problems to humans and livestock or companion animals. A robust lab animal model is not available or is a lab animal a natural host of a FV. Due to this, research is limited and often focused on the simian FVs with their well-established zoonotic potential. The authors of this review and their groups have conducted several studies on bovine FV (BFV) in the past with the intention of (i) exploring the risk of zoonotic infection via beef and raw cattle products, (ii) studying a co-factorial role of BFV in different cattle diseases with unclear etiology, (iii) exploring unique features of FV molecular biology and replication strategies in non-simian FVs, and (iv) conducting animal studies and functional virology in BFV-infected calves as a model for corresponding studies in primates or small lab animals. These studies gained new insights into FV-host interactions, mechanisms of gene expression, and transcriptional regulation, including miRNA biology, host-directed restriction of FV replication, spread and distribution in the infected animal, and at the population level. The current review attempts to summarize these findings in BFV and tries to connect them to findings from other FVs.

Microbiology
DOAJ Open Access 2019
Assignment of virus and antimicrobial resistance genes to microbial hosts in a complex microbial community by combined long-read assembly and proximity ligation

Derek M. Bickhart, Mick Watson, Sergey Koren et al.

Abstract We describe a method that adds long-read sequencing to a mix of technologies used to assemble a highly complex cattle rumen microbial community, and provide a comparison to short read-based methods. Long-read alignments and Hi-C linkage between contigs support the identification of 188 novel virus-host associations and the determination of phage life cycle states in the rumen microbial community. The long-read assembly also identifies 94 antimicrobial resistance genes, compared to only seven alleles in the short-read assembly. We demonstrate novel techniques that work synergistically to improve characterization of biological features in a highly complex rumen microbial community.

Biology (General), Genetics
DOAJ Open Access 2016
Efficiency of Livestock Residue Treatment in Geomembrane Digesters

Yanet Pérez González , Milagros C Mata Varela

The efficiency of twelve 10 m3 geomembrane biodigesters to treat swine and cattle residuals was assessed. The study took place at the Cooperative of Credits and Services (CCS) of the municipality of Cumanayagua, Cienfuegos, Cuba. Its goal was to evaluate feasibility of technology implementation in Cuba. The effluent physical and chemical indicators were determined at entry and exit from biodigesters. The biodigesters charged with pig manure were able to remove 75.88% COD, and up to 66-44% SS. Besides, 64.79% of the contaminating organic load was converted into volatile products during biofermentation. Meanwhile, the biodigesters charged with cattle manure removed 60.42% of COD, and up to 67.67% of SS; 61.51% of the organic contaminating load was converted in volatile products. It was concluded that the biodigesters had acceptable efficiency values, and that the technology can be applied in Cuba.

Agriculture (General)
DOAJ Open Access 2014
Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes [v2; ref status: indexed, http://f1000r.es/2x3]

Ted Kalbfleisch, Michael P Heaton

Genomics research in mammals has produced reference genome sequences that are essential for identifying variation associated with disease.  High quality reference genome sequences are now available for humans, model species, and economically important agricultural animals.  Comparisons between these species have provided unique insights into mammalian gene function.  However, the number of species with reference genomes is small compared to those needed for studying molecular evolutionary relationships in the tree of life.  For example, among the even-toed ungulates there are approximately 300 species whose phylogenetic relationships have been calculated in the 10k trees project.  Only six of these have reference genomes:  cattle, swine, sheep, goat, water buffalo, and bison.  Although reference sequences will eventually be developed for additional hoof stock, the resources in terms of time, money, infrastructure and expertise required to develop a quality reference genome may be unattainable for most species for at least another decade.  In this work we mapped 35 Gb of next generation sequence data of a Katahdin sheep to its own species’ reference genome (Ovis aries Oar3.1) and to that of a species that diverged 15 to 30 million years ago (Bos taurus UMD3.1).  In total, 56% of reads covered 76% of UMD3.1 to an average depth of 6.8 reads per site, 83 million variants were identified, of which 78 million were homozygous and likely represent interspecies nucleotide differences. Excluding repeat regions and sex chromosomes, nearly 3.7 million heterozygous sites were identified in this animal vs. bovine UMD3.1, representing polymorphisms occurring in sheep.  Of these, 41% could be readily mapped to orthologous positions in ovine Oar3.1 with 80% corroborated as heterozygous.  These variant sites, identified via interspecies mapping could be used for comparative genomics, disease association studies, and ultimately to understand mammalian gene function.

Medicine, Science

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