Development of Epigenetic Clocks for Key Ruminant Species

Robust biomarkers of chronological age have been developed in humans and model mammalian species such as rats and mice using DNA methylation data. The concept of these so-called “epigenetic clocks” has emerged from a large body of literature describing the relationship between genome-wide methylation levels and age. Epigenetic clocks exploit this phenomenon and use small panels of differentially methylated cytosine (CpG) sites to make robust predictions of chronological age, independent of tissue type. Here, we present highly accurate livestock epigenetic clocks for which we have used the custom mammalian methylation array “HorvathMammalMethyl40” to construct the first epigenetic clock for domesticated goat (Capra hircus), cattle (Bos taurus), Red (Cervus elaphus) and Wapiti deer (Cervus canadensis) and composite-breed sheep (Ovis aries). Additionally, we have constructed a ‘farm animal clock’ for all species included in the study, which will allow for robust predictions to be extended to various breeds/strains. The farm animal clock shows similarly high accuracy to the individual species’ clocks (r > 0.97), utilizing only 217 CpG sites to estimate age (relative to the maximum lifespan of the species) with a single mathematical model. We hypothesise that the applications of this livestock clock could extend well beyond the scope of chronological age estimates. Many independent studies have demonstrated that a deviation between true age and clock derived molecular age is indicative of past and/or present health (including stress) status. There is, therefore, untapped potential to utilize livestock clocks in breeding programs as a predictor for age-related production traits.

Case Report: A Case of Caprine Arthritis Encephalitis in Dairy Goat Farms in South Korea

One Saanen dairy goat (Capra aegagrus hircus) farm in Korea reported that some goats showed clinical signs such as arthritis, paralysis, carpal joint swelling, and even death. We monitored clinical signs and pathological lesions. In the laboratory, we confirmed caprine arthritis encephalitis virus (CAEV) infection by polymerase chain reaction (PCR). We examined all the dairy goats on the farm and found that many of them were positive. In conclusion, CAEV infection was detected in the majority of the goats in this farm, and it induced severe clinical signs impacting productivity and causing important economic shortfalls. We need to regularly investigate all dairy goat farms, and, more importantly, inspection of the quarantine stage should be required before importation. Interestingly, we found all negative results in Korean native black goats (Capra hircus linnaeus).

Dairy goat welfare in semi-intensive production systems and drought conditions

The region of Coquimbo has the highest percentage of goats (Capra hircus) in Chile and is severely affected by droughts. This can lead to environmental challenges such as limited water and forage availability when goats are kept in natural grasslands. The objective of this study was to assess the welfare of dairy goats in semi-intensive production systems under drought conditions. The study was carried out in La Serena city, region of Coquimbo, Chile and 22 semi-intensive dairy goat farms were assessed using the Animal Welfare Indicators protocol. In each evaluation, the following indicators and information were gathered: physical and behavioural indicators of animal welfare, farmers' sociodemographic information, farm facilities, husbandry practices and management of the farm, and farmers' perception of animal welfare. Of the goats evaluated (n = 446), the vast majority had a body condition score (BCS) considered normal (n = 349; 78.25%). The main welfare problems were poor hair condition, faecal soiling, overgrown claws and improper disbudding or dehorning. The majority of farmers (96%) considered it 'rather important' or 'very important' to handle their goats in a gentle manner, expressing concern about the welfare of their animals and considering pain as a negative experience for goats. A lower than expected percentage of very thin animals (low BCS) were seen, considering the drought conditions and the forage shortage that affects the region, and no animals were observed with signs of thermal stress. The semi-intensive production systems could be an alternative to pasture-based systems to overcome environmental challenges.

Characterization of Triatomine Bloodmeal Sources Using Direct Sanger Sequencing and Amplicon Deep Sequencing Methods

Knowledge of host associations of blood-feeding vectors may afford insights into managing disease systems and protecting public health. However, the ability of methods to distinguish bloodmeal sources varies widely. We used two methods—Sanger sequencing and amplicon deep sequencing—to target a 228 bp region of the vertebrate CYTB gene and determine hosts fed upon by triatomines (n = 115) collected primarily in Texas, USA. Direct sanger sequencing of PCR amplicons was successful for 36 samples (31%). Sanger sequencing revealed 15 distinct host species, which included humans, domestic animals (Canis lupus familiaris, Ovis aries, Gallus gallus, Bos taurus, Felis catus, and Capra hircus), wildlife (Rattus rattus, Bufo nebulifer, Sciurus carolinensis, Sciurus niger, Odocoileus virginianus), and captive animals (Panthera tigris, Colobus spp., Chelonoidis carbonarius). Samples sequenced by the Sanger method were also subjected to Illumina MiSeq amplicon deep sequencing. The amplicon deep sequencing results (average of 302,080 usable reads per sample) replicated the host community revealed using Sanger sequencing, and detected additional hosts in five triatomines (13.9%), including two additional blood sources (Procyon lotor, Bassariscus astutus). Up to four bloodmeal sources were detected in a single triatomine (Bufo nebulifer, Homo sapiens, Canis lupus familiaris, and Sciurus carolinensis). Enhanced understanding of vector-host-parasite networks may allow for integrated vector management programs focusing on highly-utilized and highly-infected host species.

The Complexity of the Ovine and Caprine Keratin-Associated Protein Genes

Sheep (Ovis aries) and goats (Capra hircus) have, for more than a millennia, been a source of fibres for human use, be it for use in clothing and furnishings, for insulation, for decorative and ceremonial purposes, or for combinations thereof. While use of these natural fibres has in some respects been superseded by the use of synthetic and plant-based fibres, increased accounting for the carbon and water footprint of these fibres is creating a re-emergence of interest in fibres derived from sheep and goats. The keratin-associated proteins (KAPs) are structural components of wool and hair fibres, where they form a matrix that cross-links with the keratin intermediate filaments (KIFs), the other main structural component of the fibres. Since the first report of a complete KAP protein sequence in the late 1960s, considerable effort has been made to identify the KAP proteins and their genes in mammals, and to ascertain how these genes and proteins control fibre growth and characteristics. This effort is ongoing, with more and more being understood about the structure and function of the genes. This review consolidates that knowledge and suggests future directions for research to further our understanding.

Behaviour, temperature and terrain slope impact estimates of energy expenditure using oxygen and dynamic body acceleration

The energy used by animals is influenced by intrinsic (e.g. physiological) and extrinsic (e.g. environmental) factors. Accelerometers within biologging devices have proven useful for assessing energy expenditures and their behavioural context in free-ranging animals. However, certain assumptions are frequently made when acceleration is used as a proxy for energy expenditure, with factors, such as environmental variation (e.g. ambient temperature or slope of terrain), seldom accounted for. To determine the possible interactions between behaviour, energy expenditure and the environment (ambient temperature and terrain slope), the rate of oxygen consumption ($${\dot{\text{V}}\text{O}}_{2}$$ V ˙ O 2 ) was measured in pygmy goats (Capra hircus aegarus) using open-flow indirect calorimetry. The effect of temperature (9.7–31.5 °C) on resting energy expenditure was measured. The relationship between $${\dot{\text{V}}\text{O}}_{2}$$ V ˙ O 2 and dynamic body acceleration (DBA) was measured at different walking speeds (0.8–3.0 km h−1) and on different inclines (0, + 15°, − 15°). The daily behaviour of individuals was measured in two enclosures: enclosure A (level terrain during summer) and enclosure B (sloped terrain during winter) and per diem energy expenditures of behaviours estimated using behaviour, DBA, temperature, terrain slope and $${\dot{\text{V}}\text{O}}_{2}$$ V ˙ O 2 . During rest, energy expenditure increased below 22 °C and above 30.5 °C. $${\dot{\text{V}}\text{O}}_{2}$$ V ˙ O 2 (ml min−1) increased with DBA when walking on the level. Walking uphill (+ 15°) increased energetic costs three-fold, whereas walking downhill (− 15°) increased energetic costs by one third. Based on these results, although activity levels were higher in animals in enclosure A during summer, energy expenditure was found to be significantly higher in the sloped enclosure B in winter (means of enclosures A and B: 485.3 ± 103.6 kJ day−1 and 744.5 ± 132.4 kJ day−1). We show that it is essential to account for extrinsic factors when calculating animal energy budgets. Our estimates of the impacts of extrinsic factors should be applicable to other free ranging ungulates.

Molecular Detection and Genotyping of Enterocytozoon bieneusi in Black Goats (Capra hircus) in Yunnan Province, Southwestern China

Enterocytozoon bieneusi is a fungus-like protist that can parasitize in the intestines of humans and various animals causing a threat to public health. However, there has been no data for E. bieneusi prevalence and genotypes in black goats in Yunnan Province, Southwestern China. In this study, 907 fecal samples were collected from black goats in 5 counties from Yunnan Province. The prevalence and genotypes of E. bieneusi were examined by nested PCR amplification targeting the nuclear internal transcribed spacer (ITS). Multi-locus sequence typing (MLST) was used to further examine the potential occurrence of genetic segregation. The overall prevalence of E. bieneusi in black goats in Yunnan Province was 10.3% (93/907). Statistical analysis revealed that E. bieneusi prevalence was significantly associated with the region, age and gender of black goats (p < 0.001). Four new genotypes (CYG-1, CYG-2, CYG-3, CYG-4) and 11 known genotypes (CHG1, CHG2, CHG3, CHG5, CHG28, J, D, BEB6, Wildboar3, CD6, SDD1) of E. bieneusi were identified. At the microsatellite and minisatellite loci, 15, 2, 17, and 33 sequences were obtained, respectively, forming one new multi-locus genotype (MLG27). Phylogenetic analysis revealed that all 15 genotypes were clustered into group 1 and group 2, with zoonotic potential. This is the first report of E. bieneusi prevalence and genotypes in black goats in Yunnan Province, China. Effective control strategies and measures should be taken to reduce the risk of E. bieneusi transmission between black goats, other animals, and humans.