Inbreeding and purging at the genomic Level: the Chillingham cattle reveal extensive,non‐random SNP heterozygosity

Local breeds of livestock are of conservation significance as components of global biodiversity and as reservoirs of genetic variation relevant to the future sustainability of agriculture. One such rare historic breed, the Chillingham cattle of northern England, has a 350‐year history of isolation and inbreeding yet shows no diminution of viability or fertility. The Chillingham cattle have not been subjected to selective breeding. It has been suggested previously that the herd has minimal genetic variation. In this study, high‐density SNP genotyping with the 777K SNP chip showed that 9.1% of loci on the chip are polymorphic in the herd, compared with 62–90% seen in commercial cattle breeds. Instead of being homogeneously distributed along the genome, these loci are clustered at specific chromosomal locations. A high proportion of the Chillingham individuals examined were heterozygous at many of these polymorphic loci, suggesting that some loci are under balancing selection. Some of these frequently heterozygous loci have been implicated as sites of recessive lethal mutations in cattle. Linkage disequilibrium equal or close to 100% was found to span up to 1350 kb, and LD was above r² = 0.25 up to more than 5000 kb. This strong LD is consistent with the lack of polymorphic loci in the herd. The heterozygous regions in the Chillingham cattle may be the locations of genes relevant to fitness or survival, which may help elucidate the biology of local adaptation in traditional breeds and facilitate selection for such traits in commercial cattle.     

The use of cattle Bos taurus for restoring and maintaining holarctic landscapes: Conclusions from a long‐term study (1946–2017) in northern England

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Calf Diseases and Mortality in Swedish Dairy Herds

A survey of the mortality and morbidity affecting calves during the first 3 months of life was carried out. Results are reported from 131 herds with altogether 5,050 calvings. These herds kept individual calf cards for all calves born. The incidences of abortions and stillborn calves were 0.6% and 3.6%, respectively. During the period 0-90 days the mortality and morbidity were 2.6% and 11.0%, respectively. The frequencies of enteritis and pneumonia in calves were 7.2% and 0.8%. Mortality and morbidity were influenced by breed, season, age of the dam and time of first colostrum. The frequencies of abortions, stillborn calves, mortality and morbidity varied considerably between herds. Herd factors influencing mortality and morbidity during different periods of time were: herd size, yield, zero-grazing, whether the calf was allowed to feed by suckling, the design of the calf pens, and previous incidence of infectious enteritis in the herd. On average, both mortality and morbidity in calves were low, though in certain herds, temporarily high frequencies were registered.     

Unique mitochondrial DNA in highly inbred feral cattle

The Chillingham herd of wild Northumbrian cattle remains viable despite over 300 years of in-breeding and a near-homozygous nuclear genome. Here we report the complete mitochondrial DNA sequence using ultra-deep next generation sequencing. Random population sampling of ~10% of the extant herd identified a single mtDNA haplotype harbouring a unique bovine variant present in all other higher mammals (m.11789C/Y421H) which may contribute to their survival.     

Pre-weaning management of calves on commercial dairy farms and its influence on calf welfare and mortality

Welfare and management of calves is of increasing interest and also influences performance of these animals in later life. The aim of this study was to assess management and environmental conditions under which pre-weaned dairy calves are reared on commercial Irish dairy farms. We included 47 spring-calving, pasture-based herds in this study. Herd and animal-specific data, such as mortality rate, age and breed, were gathered from all participants via the HerdPlus® database. Information pertaining to management practices was collected by conducting an interview with the principal calf rearer, while an assessment of calf housing facilities was conducted to identify conditions calves were reared in. The environmental assessment included measurements of space allowance per calf, as well as feeding equipment hygiene. To assess calf behaviour video observations were used, while accounting for the number of calves present in a group and the space available per calf. Faecal samples were also collected to determine the presence of enteric pathogens among calves. To compare calf space allowance, group size and presence of enteric pathogens early and late in the calving season each farm was visited twice. Calf mortality was not associated with either herd size, space allowance per calf or post-colostrum feeding practices. Higher calf mortality was identified among herds which reported experiencing an on-set of calf pneumonia during weeks 8 to 10 of the calving season. This study demonstrates that factors associated with calf welfare on commercial Irish dairy farms (e.g. space allowance, mortality rate) are independent of herd size. Some management practices however, such as methods used for treating health issues can affect rates of calf mortality experienced. Calf mortality, for example, was lower in herds which treated diarrhoea cases by administering electrolytes, while continuing to offer milk. Behavioural observations indicate that smaller group sizes could promote expression of positive behaviours, potentially resulting from an overall improvement in welfare. Space allowance per calf was not associated with observed behaviour frequencies. We also identified that similar rates of calf mortality are experienced across herds of different sizes.     

Evaluation of productivity of sexually precocious Nelore heifers

The objectives of the present study were to investigate the influence of yearling weight on the occurrence of early pregnancy and to determine differences between precocious and non-precocious heifers in terms of pre- and postnatal calf mortality, calf weight and height, mature cow weight, and stayability of the cow in the herd. Data from 26 977 females of a Nelore herd that participated in the breeding season between 1986 and 2004 were analyzed. The influence of yearling weight on sexual precocity and differences between precocious and non-precocious heifers in pre- and postnatal calf mortality and stayability were analyzed using the GENMOD procedure of the SAS program. Differences in the growth traits between precocious and non-precocious animals were estimated by contrast analysis. Three groups were analyzed for postnatal mortality: first calving of the heifers, calves born from the third calving and all offspring of the cow. In order to have a standardized calving to conception period for all females (precocious and non-precocious), calves born from the second calving were not included in the analysis. This was necessary because the first calving to conception period (days open) of precocious heifers was longer than for non-precocious due to farm reproductive management. No differences in postnatal mortality rates, from the third calving, were observed between the two groups of heifers studied. Analysis of all offspring of the dams showed a 9% higher probability of death of calves born to precocious heifers compared with calves born to non-precocious heifers. With respect to stayability, precocious heifers presented 33% greater odds to remain in the herd until 5 and 6 years of age and 28% greater odds to remain in the herd until 7 years when compared with non-precocious heifers. Precocious heifers weaned calves (205 days) significantly heavier than non-precocious ones, 1.410 and 0.797 kg considering the weaning weights of all offspring and of the third calving, respectively. With respect to sexual precocity, the results suggest that the probability of heifers to become pregnant at 16 months of age increases with increasing weight. However, heifers weighing more than 240 kg present practically the same pregnancy probability. Nevertheless, exposure of heifers during the early breeding season is recommended for beef cattle herds raised in tropical regions in view of the numerous benefits demonstrated here.     

Studies on the Decline of Bovine Virus Diarrhoea Virus (BVD V) Maternal Antibodies and Detectability of BVDV in Persistently Infected Calves

Persistently infected (PI) animals play a significant role in spread and transmission of bovine virus diarrhoea virus (B VD V) (Duffell & Harkness 1985). The identification and removal of PI cattle from the herd is of great importance in the control of BVDV. Although PI animals often show various degrees of growth retardation and unthrifty appearance, a significant proportion is clinically normal. PI animals are often seronegative (Duffell & Harkness 1985), but calves may be tested seropositive because of the presence of maternal immunity (Meyling & Jensen 1988). The passively derived BVDV antibodies may interfere with the ability to detect virus. Considering the importance of early recognition of PI calves, it is essential to determine the earliest time when PI animals can safely be diagnosed in the herd.     

Scrotal size of yearling sires and early calving in beef herds: epidemiological investigation of possible causal pathways

Scrotal circumference has been recommended as a clinical test for predicting the fertility potential of yearling bulls. The objectives of this study were to determine if scrotal size of yearling bulls influences herd fertility and to investigate specific causal pathways. Calving records from 44 herds enrolled in the Beef Herd Improvement Plan were selected from the data base for 1984 to 1989. Logistic regression was used to model the event of calving within the first 3 wk of the calving season as a function of scrotal circumference, herd size, age and the interactions of scrotal circumference with age, scrotal circumference with herd size, and herd size with age and the random effects of herd. The odds of cows calving in the first 3 weeks of the calving season were lower in large herds (>30 vs 20 to 30 calves born per season) and with younger yearling bulls (12 to 15 vs. 16 to 18 months of age). Early calving was not associated with scrotal circumference, or the interactions scrotal circumference with herd size and scrotal circumference with age (p > 0.15). It was concluded that the female:male ratio and age of bull both affected the odds of a cow calving early, but neither of the associations was altered by selection for bulls with a larger scrotal circumference, and therefore scrotal circumference is not included in either of the 2 causal pathways.     

Evaluation of Potential Factors Predisposing Livestock to Predation by Jaguars

ABSTRACT Depredation of livestock by large carnivores is an important but poorly understood source of human-carnivore conflict. We examined patterns of livestock depredation by jaguars (Panthera onca) and pumas (Puma concolor) on a ranch-wildlife reserve in western Brazil to assess factors contributing to prey mortality. We predicted jaguars would kill a greater proportion of calves than yearling and adult cattle and that proximity to suitable habitat would increase mortality risk. We further speculated that exposure to predation risk would promote livestock grouping and increased movement distance. We recorded 169 cattle mortality incidents during 2003–2004, of which 19% were due to predation by jaguars and pumas. This level of mortality represented 0.2–0.3% of the total livestock holdings on the ranch. Jaguars caused most (69%) cattle predation events, and survival in allotments was lower for calves than for other age classes. Forest proximity was the only variable we found to explain patterns of livestock mortality, with predation risk increasing as distance to forest cover declined. Due to low predation risk, cattle movement patterns and grouping behavior did not vary relative to level of spatial overlap with radiocollared jaguars. The overall effect of predation on cattle was low and livestock likely constituted an alternative prey for large cats in our study area. However, selection of calves over other age cohorts and higher predation risk among cattle in proximity to forest cover is suggestive of selection of substandard individuals. Cattle ranchers in the Pantanal region may reduce cattle mortality rates by concentrating on losses due to nonpredation causes that could be more easily controlled.     

Seroepidemiology of bovine viral diarrhoea virus (BVDV) in the Adamawa Region of Cameroon and use of the SPOT test to identify herds with PI calves

Bovine viral diarrhoea, caused by the bovine viral diarrhoea virus (BVDV) in the Pestivirus genus of the Flaviviridae, is one of the most important diseases of cattle world wide causing poor reproductive performance in adult cattle and mucosal disease in calves. In addition it causes immunosuppression and increased susceptibility to other infections, the impact of which is uncertain, particularly in sub-Saharan Africa where animals are exposed to a much wider range and higher intensity of infections compared to Europe. There are no previous estimates of the seroprevalence of BVDV in cattle in Cameroon. This paper describes the serological screening for antibodies to BVDV and antigen of BVDV in a cattle population in the Adamawa Region of Cameroon in 2000. The estimates of herd-level and within herd seroprevalences adjusted for test imperfections were 92% and 30% respectively and 16.5% of herds were classed as having a persistently infected calf (PI) in the herd within the last year based on the "spot" test approach. There was evidence of clustering of herds with PI calves across the north and west of the Region which corresponds with the higher cattle density areas and of self-clearance of infection from herds. A multivariable model was developed for the risk of having a PI calf in the herd; proximity to antelope, owning a goat, mixing with > 10 other herds at grazing and the catchment area of the veterinary centre the herd was registered at were all significant risk factors. Very little is known about BVDV in sub-Saharan Africa and these high seroprevalences suggest that there is a large problem which may be having both direct impacts on fertility and neonate mortality and morbidity and also indirect effects through immunosuppression and susceptibility to other infections. Understanding and accounting for BVDV should be an important component of epidemiological studies of other diseases in sub-Saharan Africa.     

Questionnaire identifying management practices surrounding calving on spring-calving dairy farms and their associations with herd size and herd expansion

Healthy calves are fundamental to any profitable dairy enterprise. Research to-date, has focused on year-round calving systems which experience many different challenges compared to spring-calving systems. The objective of the present study was to determine the on-farm dry cow, calving, and colostrum management practices of spring-calving dairy production systems, and quantify their associations with herd size and herd expansion status (i.e. expanding or not expanding). Information on these management practices was available from a survey of 262 Irish spring-calving dairy farmers, representative of the Irish national population. Herd expansion in the 2 years before, and the year that the survey was conducted was not associated with any of the management practices investigated. Fifty-three percent of respondents had an average calving season length of 10 to14 weeks with 35% of herds having a longer calving season. Previous research in cattle has documented that both colostrum source and feeding management are associated with the transmission of infectious disease from cow to calf. In the present study 60% of respondents fed calves colostrum from their own dam; however, 66% of those respondents allowed the calf to suckle the dam, 23% of survey respondents fed calves pooled colostrum. Larger herds were more likely (P<0.01) to use pooled colostrum supplies, while smaller herds were more likely (P<0.05) to allow the calf to suckle the dam. The majority (86%) of respondents had stored supplies of colostrum; average-sized herds had the greatest likelihood of storing colostrum (P<0.05), compared to other herd sizes; larger sized herds had a lesser likelihood (P<0.05) of storing colostrum in a freezer, compared to other herd sizes. Although freezing colostrum was the most common method used to store colostrum (54% of respondents), 17% of respondents stored colostrum at room temperature, 29% of which stored it at room temperature for greater than 4 days. The results from the present study indicate that a particular focus needs to be placed on calving and colostrum management because this study has highlighted a number of areas which are below international standards, and may have repercussions for calf health. Furthermore, management practices on larger farms could be improved and, as these represent the future of dairy farming, a focus needs to be placed on them. Expanding herds are not a particular concern as herd expansion, independent of herd size, does not seem to be associated with calving and colostrum management practices on Irish spring-calving dairy herds.     

Drought and recovery: Livestock dynamics among the Ngisonyoka Turkana of Kenya

From 1980–1985, the Turkana District of Kenya experienced both drought and above average rainfall. The effects of a 2-year drought on the livestock population of the nomadic pastoral Ngisonyoka are discussed. Detailed data on mortality rates and offtake are presented for the animals of four herd owners, and the recovery process is followed for the 5-year period for one herd owner. It is concluded that during the drought, 63% of the cattle, 45% of the camels, and 55% of the small stock left the sample herds. The livestock population of one herd had recovered to pre-drought levels 3 years after the drought.     

A model of bovine tuberculosis control in domesticated cattle herds.

A typical strategy for disease control in domesticated animals involves regular field tests and quarantine of infected herds. This prevents disease spread beyond the herd, while slaughter of diseased animals removes the infection from within the herd. A model of bovine tuberculosis (Tb) control in cattle is examined, which includes ''test and slaughter'' combined with herd isolation and vaccination. Herd status is represented by an integral equation expressing the duration of herd isolation. The current Tb situation in New Zealand is used as an example, and vaccination strategy discussed. Extrapolation of existing management strategies indicate that a vaccine of efficacy greater than 96% would be required, reaching 95% of target Tb levels within six years. These results suggest that a complementary strategy of vaccination and vector control may be more promising than vaccination alone.     

Ultracentrifugal studies of sera from cattle vaccinated or naturally infected with Brucella abortus

In conformity with the findings of previous investigators, it was shown by density gradient ultracentrifugation that the antibodies in sera collected from calves shortly after vaccination with Brucella abortus, strain 19, were entirely or mainly rapidly-sedimenting. These macroglobulin (19S or IgM) antibodies showed complement-fixing as well as agglutinative activity with Br. abortus antigen. In later bleedings from the same vaccinated calves, antibodies with an intermediate sedimentation rate, (IgG), were present, as well as IgM. Sera from 15 of 22 non-vaccinated, relatively recent field cases of brucellosis appeared to contain only the IgG class of antibodies. In one herd, however, two cows with IgM only and five with both IgM and IgA were found; all seven of these cattle had been serologically negative before their introduction into this known infected herd a few months earlier. The agglutinative activity of sera from four cases of brucellosis of long standing and from eight cows, 4 to 13 years of age, that had been vaccinated as calves, was confined to the IgG fraction.     

Feral cattle of Swona, Orkney Islands

The feral cattle, currently numbering 33, which inhabit the Orkney island of Swona, are described. Their behaviour while foraging for seaweed is compared with that of sheep, and aspects of their social behaviour and population structure are compared with what has been observed among the Chillingham white cattle.     

Economics of selecting for sex: the most important genetic trait

Over 20,000 calves have resulted from artificial insemination (AI) of cattle with sexed, frozen/thawed sperm in the course of experimentation in several countries, and from commercial sales in the United Kingdom. This technology likely will become commercially available in many countries within a few years. Accuracy of the process is about 90% for either sex, and resulting calves appear to be no different from non-sexed controls in birthweight, mortality, rate of gain, and incidence of abnormalities. The main determinants of the extent of use of sexed sperm will be pregnancy rate and cost. Fertility of low doses (1.5 x 10(6)-2 x 10(6)) of sexed, frozen sperm for AI of heifers usually has been in the range of 70-80% of unsexed sperm at normal doses (10 x 10(6)-20 x 10(6) sperm) in well managed herds; it has been lower in poorly managed herds, and likely will be lower with lactating dairy cows. It is expected that fertility of sexed sperm will increase significantly due to very recent improvements in the hydrodynamics of the sexing process and potential improvements in cryopreservation procedures. It is unclear how sexed sperm will be priced; the cost of sexed sperm for cattle will likely be more than double the cost of unsexed sperm in most markets. The economic benefit of using sexed sperm also will depend on the baseline fertility of the herd since at lower fertility, it takes more doses of semen per calf produced. It is noted that for a small percentage of elite cattle, the economics of using sexed sperm do not depend primarily on increased production or efficiency of producing meat or milk, but rather on factors such as scarcity, tradition, cattle show winnings, and biosecurity during herd expansion. Until sorting efficiencies improve and costs decline, sales likely will be limited primarily to these niche markets. With near normal fertility and a premium for sexing in the range of US$ 10 per insemination dose, sexed sperm likely would become economically and environmentally beneficial for many, if not most populations of cattle being bred by AI.     

Potential population-level effects of increased haulout-related mortality of Pacific walrus calves

Availability of summer sea ice has been decreasing in the Chukchi Sea during recent decades, and increasing numbers of Pacific walruses have begun using coastal haulouts in late summer during years when sea ice retreats beyond the continental shelf. Calves and yearlings are particularly susceptible to being crushed during disturbance events that cause the herd to panic and stampede at these large haulouts, but the potential population-level effects of this mortality are unknown. We used recent harvest data, along with previous assumptions about demographic parameters for this population, to estimate female population size and structure in 2009 and project these numbers forward using a range of assumptions about future harvests and haulout-related mortality that might result from increased use of coastal haulouts during late summer. We found that if demographic parameters were held constant, the levels of harvest that occurred during 1990–2008 would have allowed the population to grow during that period. Our projections indicate, however, that an increase in haulout-related mortality affecting only calves has a greater effect on the population than an equivalent increase in harvest-related mortality distributed among all age classes. Therefore, disturbance-related mortality of calves at coastal haulouts may have relatively important population consequences.     

Seroprevalence of Neospora caninum infection in dairy and beef cattle in Spain

In recent years, neosporosis has been identified as a major cause of abortion in dairy and beef cattle. Although the disease has been described worldwide, there is a Jack of information concerning the prevalence of this infection in different cattle production systems. The aim of this study was to investigate the seroprevalence of Neospora caninum infection in a representative area of beef and dairy cattle production in Spain. A cross-sectional study was undertaken in which herds constituted the initial sampling unit and two strata (dairy and beef herds) were considered. Using a 95% level of confidence and setting 5% (beef) and 5.4% (dairy) error limits, 216 beef and 143 dairy herds were randomly selected and sampled. Nine animals (> 1 year old) were randomly sampled in each herd to detect the presence of the infection. A herd was considered infected when at least one animal was seropositive. In total, serum samples from 1121 dairy and 1712 beef animals were collected and tested for specific anti-N. caninum IgG using an ELISA. Specific antibodies were detected in 55.1% (119/216) beef and 83.2% (119/143) dairy herds. Individual prevalences obtained were 17.9% (306/1712) for beef and 35.9% (402/1121) for dairy animals. Presence of N. caninum infection was higher in dairy than in beef herds and the association between infection and the cattle production system (dairy or beef) was statistically significant [(chi2)Y= 29.21, P < 0.001, OR = 4.04 (2.35-6.99)]. Herd size of dairy cattle did not appear to be associated with N. caninum infection. On the contrary, infection was associated with herd size in beef cattle (chi2 = 12.79, P < 0.01). Finally, no association was found between replacement or pasture management and infection in beef herds.     

Preliminary field evidence for the association of clinical mastitis with altered interestrus intervals in dairy cattle

Clinical mastitis and reproductive records from two southern California dairy herds were used in a cross-sectional study to determine the risk of an altered interestrus interval following clinical mastitis. An altered interestrus interval was defined as cycles occurring at either less than 18 day or more than 24-day intervals. The data were stratified by herd to assess herd differences and by lactation number to assess confounding by cow parity. The predominant pathogen isolated from mastitis cases in Herd 1 was Staphylococcus aureus , whereas the predominant pathogens in Herd 2 were gram-negative isolates. Cows in Herd 1 which had coliforms cultured from mastitic milk were excluded in the analysis for comparison with Herd 2. In Herd 1, cows with clinical mastitis were less likely to have an altered interestrus interval (Relative Risk [RR]=0.9; 95% Confidence Interval [CI]=0.6,1.6) than herdmates without clinical mastitis. However, cows in Herd 2 were almost two times more likely to have an altered interestrus interval following an episode of clinical mastitis compared to herdmates without clinical mastitis (RR=1.6; 95% CI=1.3,2.0). Because herd management practices differ and could cause differences in mastitis and reproductive outcomes at the dairies, this preliminary field evidence should be followed by prospective studies of luteal function after clinical coliform mastitis.     

Body mass and winter mortality in red deer calves: disentangling sex and climate effects

Understanding population dynamics of large mammals requires studies of variation in the age and sex–specific demographic parameters over time and the factors causing this variation. Here, we have focused on the variation in body mass of 8-10–month old red deer calves, in relation to climate and sex over a 20-yr period (1977–1997). We investigated the relationship between body mass and over–winter mortality during 1985 and 1986 and thereby, the phenotypic selection on body mass. We found a high variability from year to year in calf body mass. Males were consistently heavier than females. No interaction between sex and year was detected. The body mass of individuals from the same cohort shot during the annual hunting season and snow depth in January each explained ca 20% of the variability in calf body mass. Body mass loss during winter did not differ between sexes, but increased with body mass and varied from year to year. The probability of surviving was strongly related to body mass in each sex. For a given body mass relative to the sex–specific mean, males had a lower probability of survival than females. Hence, males had to be 1 kg larger than their mean in order to achieve the same survival as average-sized females. Our results suggested a directional phenotypic selection on body mass that led to an increasing body mass dimorphism in calves. The strength of this selection and the sex difference in the shape of the selection curve may depend, however, on the severity of winter and on sexual dimorphism in body mass at the beginning of winter.