High genetic connectivity and introgression from domestic reindeer characterize northern Alaska caribou herds

Defining genetic populations and detecting hybridization with introduced or domestic taxa are two major concerns for the conservation of population-level diversity. We studied the genetic population structure of large, migratory caribou herds (Rangifer tarandus granti) on Alaska’s North Slope and their potential hybridization with introduced domestic reindeer (R. t. tarandus). Using a population genetics approach, we determined: (1) whether the four caribou herds could be differentiated; (2) how distance and population size appear to drive genetic population structure; and (3) how contact with reindeer has affected the genetic identity of herds. Samples from four caribou herds (n = 245) and reindeer (n = 67) were analyzed at 19 microsatellite loci. We found that North Slope caribou are isolated by distance, with no differentiation among herd pairs except for the most geographically distant herds (F _st  = 0.003, Jost’s D = 0.023; P-values < 0.001). We detected reindeer-caribou admixture in all populations except Kodiak Island, including 8 % of individuals in caribou herds and 14 % of individuals in Seward Peninsula reindeer herds. However, considering the stable or increasing trend in North Slope herds, reindeer introgression has had no apparent deleterious effect on herd demographics. Our findings indicate long-term genetic exchange among North Slope caribou herds when their ranges overlap, and suggest that herd size may influence susceptibility to reindeer introgression. As North Slope herd ranges are increasingly altered by industrial development, this study can provide a baseline for detecting potential future impacts to what are currently large, diverse, and naturally evolving herds.     

Genetic characterization and founder effect analysis of recently introduced Salers cattle breed population

Salers are a native French breed used for beef and dairy production that has expanded to all the continents. The Salers breed was introduced to the north of Spain in 1985 with only 15 individuals from France and has successfully increased to over 20 000 animals. Although over time new animals have been imported from France for breeding, it is possible that the limiting number of founder animals could have resulted in a reduction of the genetic diversity found in Spanish Salers. Thus, the purpose of the present study has been to characterize the genetic diversity of Salers breed in Spain and evaluate a possible founder effect due to reduced number of the first reproducers. A total of 403 individuals from 12 Salers herds were analyzed using 12 microsatellite markers and compared with phylogenetically and geographically close related Blonde d’Aquitaine, Limousin and Charolais French breeds but also other 16 European breeds. Microsatellites in Salers were polymorphic, with a mean allelic richness of 5.129 and an expected heterozygosity of 0.621 across loci (0.576 to 0.736 among all breeds). Average observed heterozygosity was 0.618. All the loci fit the Hardy–Weinberg (HW) equilibrium except TGLA227 locus due to a significant deficit of heterozygotes in only one of the herds, probably attributable to a sampling effect. When all loci were combined, Salers inbreeding coefficient did not differ statistically from 0 (F_IS=0.005), indicating not significant excess or deficit of heterozygotes (P=0.309). Based in allelic distribution, Salers revealed a frequency of 0.488 in BM2113-131 and 0.064 in BM2113-143 diagnostic alleles, which are specific to the African zebu. These zebu alleles are also found in some French breeds, supported by STR data previously postulated hypothesis of a migration route through Mediterranean route by which North African cattle may have left a genetic signature in southern Europe. Phylogenetic tree and population structure analyses could unambiguously differentiate Salers cattle from the other populations and 10% of the total genetic variability could be attributed to differences among breeds (mean R_ST=0.105; P<0.01). Mutation-drift equilibrium tests (sign test and Wilcoxon’s sign rank test) were in correspondence to the absence of founder effect when Bonferroni was applied. Gene diversity previously reported in French Salers was comparable with the observed in our population. Thus, high genetic diversity in Spanish Salers highlights the resources of this population, which looks toward future breeding and selection programs.     

Boar culling and mortality in commercial swine breeding herds

The objectives of this study were to measure culling rate and mortality rate of boars; to compare boar life day (BLD: days from birth date to removal date), boar herd life day (BHLD: days from herd entry date to removal date) and herd entry age of boars between high-performing herds and ordinary herds (herd groups); to examine herd measurements for BLD, BHLD and boar age at herd entry; and to observe removal patterns and survival curves for boars by herd groups. This study used 2474 records of individual boars born in 108 herds from 2000 to 2003. Two herd groups were formed on the basis of the upper 25th percentile of pigs weaned per mated female per year (2001-2005). Mixed-effects models and survival analysis were performed. Means of BLD and BHLD (±S.E.M.) were 984 ± 9.5 and 781 ± 8.4 d, respectively. Annualized culling rate and mortality rate were 0.411 and 0.035 boars per 365 BHLD, respectively. Boars in high-performing herds had 51 higher BLD and 62 higher BHLD than those in ordinary herds (P < 0.01). High-performing herds had 32 d lower entry ages than ordinary herds (P < 0.01). Herd measurements such as herd mortality and herd size were not associated with both BLD and BHLD. The hazards in survival analysis were associated with herd groups (P < 0.05). Measurements in the present study provide benchmarks for boar removal in commercial herds.     

Genetic diversity and networks of exchange: a combined approach to assess intra-breed diversity

Background

Cryopreservation of three endangered Belgian sheep breeds required to characterize their intra-breed genetic diversity. It is assumed that the genetic structure of a livestock breed depends mostly on gene flow due to exchanges between herds. To quantify this relation, molecular data and analyses of the exchanges were combined for three endangered Belgian breeds.

Methods

For each breed, between 91 and 225 sheep were genotyped with 19 microsatellites. Genetic differentiations between breeds and among herds within a breed were evaluated and the genetic structure of the breeds was described using Bayesian clustering (Structure). Exchanges of animals between 20, 46 and 95 herds according to breed were identified via semi-directed interviews and were analyzed using the concepts of the network theory to calculate average degrees and shortest path lengths between herds. Correlation between the Reynolds’ genetic distances and the shortest path lengths between each pair of herds was assessed by a Mantel test approach.

Results

Genetic differentiation between breeds was high (0.16). Overall Fst values among herds were high in each breed (0.17, 0.11 and 0.10). Use of the Bayesian approach made it possible to identify genetic groups of herds within a breed. Significant correlations between the shortest path lengths and the Reynolds’ genetic distances were found in each breed (0.87, 0.33 and 0.41), which demonstrate the influence of exchanges between herds on the genetic diversity. Correlation differences between breeds could be explained by differences in the average degree of the animal exchange networks, which is a measure of the number of exchanges per herd. The two breeds with the highest average degree showed the lowest correlation. Information from the exchange networks was used to assign individuals to the genetic groups when molecular information was incomplete or missing to identify donors for a cryobank.

Conclusions

A fine-scale picture of the population genetic structure at the herd level was obtained for the three breeds. Network analysis made it possible to highlight the influence of exchanges on genetic structure and to complete or replace molecular information in establishing a conservation program.     

Herd- and sow-related risk factors for lameness in organic and conventional sow herds

Lameness in sows is an animal welfare problem which also presents an economic challenge to pig producers. Information about the prevalence of herd lameness in organic sows is relatively scarce. The first objective of this study was to establish the prevalence of lameness and to identify risk factors associated with sow lameness in Danish outdoor organic sow herds by analysing the association between risk factors at both sow and herd level using clinical records of lameness. A total of 1850 sows from nine organic herds were included in the study. Second, the study examined differences in the prevalence of sow lameness between outdoor organic and indoor conventional herds. An additional aim here was to identify risk factors associated with clinical records of sow lameness in Danish sow herds by analysing the association between risk factors with lameness at sow and herd level. One thousand and fifty four gestation sows from 44 indoor conventional and nine organic sow herds were included in this study. The nine organic herds were visited twice: once in summer/autumn 2011, and once in winter/spring 2012. In winter/spring 2011, a total of 44 indoor conventional herds were visited. Risk factors included in the study were clinical parameters and factors related to the production system. Sows were examined visually by one of four trained observers. The organic sows were assigned scores for lameness, body condition, hoof length, bursitis, abscesses and leg wounds, while the conventional sows were assigned scores for lameness, body condition and bursitis. A multivariable analysis was carried out by logistic regression with the herd and observer as random effects. The average herd lameness prevalence in gestation and lactation sows in organic herds was 11% in summer/autumn and 4.6% in winter/spring. ‘Wounds, bursitis and abscess’ on legs (OR=4.7, P<0.001) and body condition score >3 (OR=1.79, P=0.008) were associated with increased risk of lameness in Danish organic sow herds. Season (winter/spring v. summer/autumn) lowered the risk of lameness (OR=0.37, P<0.001). Average prevalence of lameness in gestation sow herds in winter/spring in conventional herds was 24.4%, and in organic herds it was 5.4%. An organic sow had a decreased risk of lameness (OR=0.28, P<0.001) as compared with a conventional sow. Bursitis was associated with increased risk of lameness (OR=2.08, P=0.002) regardless of the production system (i.e. whether the herd was organic or conventional).     

Higher preweaning mortality in free farrowing pens compared with farrowing crates in three commercial pig farms

If loose-housed farrowing systems are to be an alternative to traditional farrowing crates, it is important that they can deliver the same production results as can be achieved in farrowing crates under commercial conditions. The aim of this study was to compare preweaning mortality in farrowing crates and free farrowing pens (FF-pens) within herds that had both systems. The study was conducted over 2 years in three commercial Danish herds that had FF-pens as well as traditional farrowing crates in their farrowing unit. Piglet mortality was analysed in two periods: before litter equalisation and after litter equalisation. Linear models were used to analyse effects of housing (crate or pen), herd (Herd A, B or C), parity (parities 1, 2, 3 to 4 or 5 to 8) as well as the effect of number of total born piglets on mortality before litter equalisation, and the effect of equalised litter size on piglet mortality after litter equalisation. All corresponding interactions were included in the models. Before litter equalisation piglet mortality was higher (P<0.001) in pens (13.7%) than in crates (11.8%). Similarly, piglet mortality after litter equalisation was higher in pens than in crates in all three herds, but the difference between pens and crates were dissimilar (P<0.05) in the different herds. In addition, piglet mortality, both before (P<0.001) and after litter equalisation (P<0.001), grew with increasing parity of the sows. Mortality before litter equalisation moreover increased with increasing number of total born piglets per litter (P<0.001), and mortality after equalisation increased when equalised litter size increased (P<0.001). No significant interactions were detected between housing and parity or housing and litter size for any of the analysed variables. In conclusion, there is knowledge how to design pens for free farrowing; but this study showed a higher preweaning mortality in the FF-pen. Nonetheless a noteworthy proportion of the sows in the FF-pens delivered results comparable to those farrowing in crates. This indicates that FF-pens are not yet a robust type of housing for farrowing sows.     

Merging and characterising phenotypic data on conventional and rare traits from dairy cattle experimental resources in three countries

This study set out to demonstrate the feasibility of merging data from different experimental resource dairy populations for joint genetic analyses. Data from four experimental herds located in three different countries (Scotland, Ireland and the Netherlands) were used for this purpose. Animals were first lactation Holstein cows that participated in ongoing or previously completed selection and feeding experiments. Data included a total of 60 058 weekly records from 1630 cows across the four herds; number of cows per herd ranged from 90 to 563. Weekly records were extracted from the individual herd databases and included seven traits: milk, fat and protein yield, milk somatic cell count, liveweight, dry matter intake and energy intake. Missing records were predicted with the use of random regression models, so that at the end there were 44 weekly records, corresponding to the typical 305-day lactation, for each cow. A total of 23 different lactation traits were derived from these records: total milk, fat and protein yield, average fat and protein percentage, average fat-to-protein ratio, total dry matter and energy intake and average dry matter intake-to-milk yield ratio in lactation weeks 1 to 44 and 1 to 15; average milk somatic cell count in lactation weeks 1 to 15 and 16 to 44; average liveweight in lactation weeks 1 to 44; and average energy balance in lactation weeks 1 to 44 and 1 to 15. Data were subsequently merged across the four herds into a single dataset, which was analysed with mixed linear models. Genetic variance and heritability estimates were greater (P < 0.05) than zero for all traits except for average milk somatic cell count in weeks 16 to 44. Proportion of total phenotypic variance due to genotype-by-environment (sire-by-herd) interaction was not different (P > 0.05) from zero. When estimable, the genetic correlation between herds ranged from 0.85 to 0.99. Results suggested that merging experimental herd data into a single dataset is both feasible and sensible, despite potential differences in management and recording of the animals in the four herds. Merging experimental data will increase power of detection in a genetic analysis and augment the potential reference population in genome-wide association studies, especially of difficult-to-record traits.     

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.     

Connectedness among herds of beef cattle bred under natural service

Background

A procedure to measure connectedness among herds was applied to a beef cattle population bred by natural service. It consists of two steps: (a) computing coefficients of determination (CDs) of comparisons among herds; and (b) building sets of connected herds.

Methods

The CDs of comparisons among herds were calculated using a sampling-based method that estimates empirical variances of true and predicted breeding values from a simulated n-sample. Once the CD matrix was estimated, a clustering method that can handle a large number of comparisons was applied to build compact clusters of connected herds of the Bruna dels Pirineus beef cattle. Since in this breed, natural service is predominant and there are almost no links with reference sires, to estimate CDs, an animal model was used taking into consideration all pedigree information and, especially, the connections with dams. A sensitivity analysis was performed to contrast single-trait sire and animal model evaluations with different heritabilities, multiple-trait animal model evaluations with different degrees of genetic correlations and models with maternal effects.

Results

Using a sire model, the percentage of connected herds was very low even for highly heritable traits whereas with an animal model, most of the herds of the breed were well connected and high CD values were obtained among them, especially for highly heritable traits (the mean of average CD per herd was 0.535 for a simulated heritability of 0.40). For the lowly heritable traits, the average CD increased from 0.310 in the single-trait evaluation to 0.319 and 0.354 in the multi-trait evaluation with moderate and high genetic correlations, respectively. In models with maternal effects, the average CD per herd for the direct effects was similar to that from single-trait evaluations. For the maternal effects, the average CD per herd increased if the maternal effects had a high genetic correlation with the direct effects, but the percentage of connected herds for maternal effects was very low, less than 12%.

Conclusions

The degree of connectedness in a bovine population bred by natural service mating, such as Bruna del Pirineus beef cattle, measured as the CD of comparisons among herds, is high. It is possible to define a pool of animals for which estimated breeding values can be compared after an across-herds genetic evaluation, especially for highly heritable traits.     

A cross-sectional study to collect risk factors associated with stillbirths in pig herds

The aim of this study was to identify risk factors for stillborn piglets at herd level in commercial pig herds. A written questionnaire, containing semi-open questions directly or indirectly related to stillborn piglets, was sent to 250 randomly selected pig herds (>150 sows) in northern Belgium. In total 111/250 questionnaires were returned (response rate of 44.4%) and 107 were valid for analysis. The average reported frequency of stillbirth was 7.5% (S.D. 2.8%). The relationship between risk factors and stillbirths was evaluated with a generalized linear effects model with the percentage of stillborn piglets as outcome variable. Type of breed used on the farm was significantly (P < 0.01) associated with the percentage of stillborn piglets. A high temperature in the farrowing unit (≥22 °C compared to <22 °C) was associated with significantly (P < 0.01) more stillbirths, whereas showering sows with warm water before parturition resulted in significantly less stillbirths (5.8%) than no showering (7.7%) (P < 0.01) and was not significantly different from showering with cold water (7.0%) (P = 0.26). When supervision of farrowing was performed occasionally, significantly more stillbirths (8.1%) were observed in comparison with no attending to farrowing (6.5%) (P < 0.01) or frequent supervision of farrowing (6.9%) (P < 0.01). Significant interactions were found between breed and showering sows prior parturition or supervision of sows at parturition, and between temperature in the farrowing unit at parturition and showering procedure of the sows. In conclusion, this study has clearly demonstrated that breed is a major factor involved in the frequency of stillbirth. Additionally, some management practices before or at parturition may reduce the number of stillborn piglets.     

Evaluation of production efficiencies at pasture of lactating suckler cows of diverse genetic merit and replacement strategy

Feed costs account for the largest proportion of direct cost within suckler beef production systems. By identifying the cow type with enhanced capability of converting grazed herbage to beef output across lactations, suckler cow systems would become more efficient and sustainable. The objective of this study was to estimate grass DM intake (GDMI) and production efficiency among lactating suckler cows of diverse genetic merit for the national Irish maternal index (Replacement Index) which includes cow efficiency components such as milk yield and feed intake. Data from 131 cows of diverse genetic merit within the Replacement Index, across two different replacement strategies (suckler or dairy sourced), were available over two grazing seasons. Milk yield, GDMI, cow live weight (BW) and body condition score (BCS) were recorded during early, mid and late-lactation, with subsequent measures of production efficiency extrapolated. Genetic merit had no significant effect on any variables investigated, with the exception of low genetic merit (LOW) cows being 22 kg heavier in BW than high genetic merit (HIGH) cows (P < 0.05). Beef cows were 55 kg heavier in BW (P < 0.001), had a 0.31 greater BCS (P < 0.05) and 0.30 Unité Fourragère Lait (UFL) greater energy requirement for maintenance compared to dairy sourced beef × dairy crossbred (BDX) cows (P < 0.001). The BDX had 0.8 kg greater GDMI, produced 1.8 kg more milk (P < 0.001), had a 0.8 UFL greater energy requirement for lactation and produced weanlings that were 17 kg heavier in BW than beef cows (P < 0.05). Subsequent efficiency variables of milk per 100 kg BW (P < 0.001), milk per kg GDMI (P < 0.001) and GDMI per 100 kg BW (P < 0.001) were more favourable for BDX. The correlations examined showed GDMI had moderate positive correlations (P < 0.001) with intake per 100 kg BW, net energy intake per kg milk yield, RFI and intake per 100 kg calf weaning weight but was weakly negatively correlated to milk yield per kg GDMI (P < 0.001). No difference was observed across genetic merit for beef cows for any of the traits investigated. Results from the current study showed that, while contrasting replacement strategies had an effect on GDMI and production efficiency, no main effect was observed on cows diverse in genetic merit for Replacement Index. Nonetheless, utilising genetic indexes in the suckler herd is an important resource for selecting breeding females for the national herd and phenotypic performance generated from this study can be included in future genetic evaluations to improve reliability of genetic values.     

Pig carcass tail lesions: the influence of record keeping through an advisory service and the relationship with farm performance parameters

Tail lesions are important pig welfare indicators that could be recorded during meat inspection as they are more visible on the carcass than on the live animal. Tail biting is associated with reduced performance in the bitten pig, but it is not clear whether problems with tail biting are reflected in general farm performance figures. Farm advisory services aim to improve farm productivity which could be associated with improvements in pig welfare. Record keeping forms an integral part of such advisory services. The aim of this study was to examine the influence of record keeping in the Teagasc eProfit Monitor (ePM herds) on the prevalence of tail lesion severity scores in Irish slaughter pigs. In addition, we investigated associations between the prevalence of tail lesion scores and production parameters at farm level in ePM herds. Pigs were observed after scalding/dehairing and tail lesion score (0 to 4), sex and farm identification were recorded. Tail lesion scores were collapsed into none/mild lesions (score ⩽1), moderate lesions (score 2) and severe lesions (score ⩾3). The effect of record keeping (ePM herd) on the different tail lesion outcomes was analysed at batch level using the events/trials structure in generalized linear mixed models (PROC GLIMMIX). Spearman’s rank correlations were calculated between average tail lesion score of a batch and production parameters. A total of 13 133 pigs were assessed from 73 batches coming from 61 farms. In all, 23 farms were identified as ePM herds. The average prevalence of moderate tail lesions was 26.8% and of severe tail lesions was 3.4% in a batch. Batches coming from ePM herds had a lower prevalence of moderate tail lesions than non-ePM herds (P<0.001). Average tail lesion score was negatively associated with age (P<0.05) and weight (P<0.05) at sale/transfer of weaners, and tended to be positively associated with the number of finishing days (P=0.06). In addition, the prevalence of severe tail lesions was negatively associated with average daily gain in weaners (P<0.05) and tended to do so with average daily gain in finishers (P=0.08). This study provides the first indication that record keeping through an advisory service may help to lower the risk of tail biting, which is associated with improved farm performance.     

Genome-wide analysis reveals selection signatures for body size and drought adaptation in Liangzhou donkey

Liangzhou donkey is a domestic animal breed distributed on the edge of the Tengger Desert in Gansu Province of China. It has small body size and strong adaptability to dry environments. Here, we sequenced 10 Liangzhou donkey genomes and compared them to the 55 genomes of 8 representative donkey breeds worldwide. The population structure analysis revealed that Liangzhou donkey harboured the ancestry with the Asian domestic donkeys (0.863) and European domestic donkeys (0.137). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the genetic diversity in Liangzhou donkey. In addition, we analyzed the genetic basis of the small body size and drought adaptation of Liangzhou donkey by using F_st, θπ-ratio, XP-EHH, CLR and θπ methods. We found that the NCAPG-LCORL on chromosome 3 may be a candidate region for small body size trait of Liangzhou donkey. The CYP4A11 gene located on chromosome 5 showed strong sign of selection sweep. CYP4A11 can convert arachidonic acid into 19(S)-HETE, which can promote water reabsorption in renal tubule and enhance the ability of Liangzhou donkey to adapt to dry environment. These results contribute to a better understanding of the underlying population structure of Liangzhou donkeys and provides a valuable resource for future research on donkey breeding in response to climate change.     

The relationship between consecutive pregnancies in Thoroughbred mares. Does the location of one pregnancy affect the location of the next, is this affected by mare age and foal heat to conception interval or related to pregnancy success

Delayed uterine involution is a major cause of early reproductive failure in mares. Involution is affected by mare age, and foaling to covering interval. Involution rates vary between the previously non-gravid horn (PNGH), which recovers the quicker, and the previously gravid horn (PGH). Location of a pregnancy and its likely success may, therefore, be affected by its location relative to the previous pregnancy. This study aimed to determine: (i) the location of concepti in consecutive pregnancies; (ii) whether this varies with mare age or foaling to conception interval; (iii) whether location in relation to the previous pregnancy affects success. 1383 Thoroughbred mares were monitored by ultrasonic scanning during oestrus and early pregnancy. Significantly (p < 0.01) more pregnancies were located in the PNGH (79.2%) than the PGH (20.8%). The number of pregnancies in PGH significantly increased with mare age (p < 0.01) and foaling to conception interval (p < 0.05). Significantly (p < 0.001) more pregnancies located in the PGH (16.5%) failed, than those in the PNGH (4.6%). It can be concluded that most pregnancies locate in the PNGH where their chances of success are greatest. The larger number of pregnancies locating in the PGH in older mares and those with shorter foaling to conception intervals may in part account for the higher conceptus mortality rates in such mares. Hence breeding older mares on alternate years and maximising foaling to conception interval may improve reproductive success. Alternatively termination of pregnancies located in the PGH followed by timely recovering may be justifiable as might ET in older mares covered close to foaling.     

Initial insights on the performances and management of dairy cattle herds combining two breeds with contrasting features

Finding ways of increasing animal production with low external inputs and without compromising reproductive performances is a key issue of livestock systems sustainability. One way is to take advantage of the diversity and interactions among components within livestock systems. Among studies that investigate the influence of differences in animals’ individual abilities in a herd, few focus on combinations of cow breeds with contrasting features in dairy cattle herds. This study aimed to analyse the performances and management of such multi-breed dairy cattle herds. These herds were composed of two types of dairy breeds: ‘specialist’ (Holstein) and ‘generalist’ (e.g. Montbeliarde, Simmental, etc.). Based on recorded milk data in southern French region, we performed ANOVA: (i) to compare the performances of dairy herds according to breed-type composition: multi-breed, single specialist breed or single generalist breed and (ii) to test the difference of milk performances of specialist and generalist breed cows (n = 10 682) per multi-breed dairy herd within a sample of 22 farms. The sampled farmers were also interviewed to characterise herd management through multivariate analysis. Multi-breed dairy herds had a better trade-off among milk yield, milk fat and protein contents, herd reproduction and concentrate-conversion efficiency than single-breed herds. Conversely, they did not offer advantages in terms of milk prices and udder health. Compared to specialist dairy herds, they produce less milk with the same concentrate-conversion efficiency but have better reproductive performances. Compared to generalist dairy herds, they produce more milk with better concentrate-conversion efficiency but have worse reproductive performances. Within herds, specialist and generalist breed cows significantly differed in milk performances, showing their complementarity. The former produced more milk for a longer lactation length while the latter produced milk with higher protein and fat contents and had a slightly longer lactation rank. Our results also focus on the farmers’ management of multi-breed dairy herds underlying herd performances. Three strategies of management were identified and structured along two main axes. The first differentiates farmers according to their animal-selection practices in relation with their objectives of production: adapting animal to produce milk with low-feeding inputs v. focussing on milk yield trait to intensify milk production. The second refers to the purpose farmers give to multi-breed dairy herds: milk v. milk/meat production. These initial insights on the performances and management of multi-breed dairy herds contribute to better understanding the functioning of ruminant livestock systems based on individual variability.     

Effects of sire genotype on lamb performance at weaning in extensive sheep systems

A low finishing weight and poor carcass characteristics are major causes of lower incomes in extensive sheep flocks; however, the use of terminal sire crossbreeding would improve lamb performance and carcass traits under these conditions. The aim of this study was to evaluate sire breed effects on the performance of lambs born to Corriedale ewes in extensive sheep systems in Western Patagonia. A total of 10 Corriedale, 10 Dorset, nine Suffolk and seven Texel sires, 16 of which were under a genetic recorded scheme and 20 selected from flocks not participating in genetic improvement programmes, were used across six commercial farms for 2 successive years. Data were collected from 685 lambs of the four resulting genotypes. Overall, Corriedale lambs were 0.47 kg lighter at birth than crossbred lambs (P<0.001). Suffolk and Texel sired lambs required more assistance (P<0.01) at birth than Corriedale or Dorset sired lambs, with Suffolk sired lambs requiring the most assistance (8%). Ewes sired with Suffolk rams had larger (P<0.05) litters than ewes sired with Texel or Corriedale rams. Lamb live weight gain from birth to weaning was higher (P<0.001) in crossbred lambs compared with Corriedale lambs, therefore, crossbred lambs averaged 2.9 kg heavier BW (P<0.001) than Corriedale lambs. A significant sire breed x sire source interaction was detected for lamb live weight gain (P<0.05) and lamb live weight at weaning (P<0.01), showing that the heaviest lambs were from recorded sires, except for Suffolk crossbred lambs. Mortality rate to weaning was increased (P<0.05) in Suffolk cross lambs (31%), with Corriedale lambs showing the lowest (17%) mortality. Terminal sire breeds increased (P<0.001) cold carcass weight, with 13.8, 16.0, 15.2 and 14.9 kg for the Corriedale, Dorset, Suffolk and Texel sired lambs, respectively. Carcass length, kidney knob and channel fat, fat grade, grade rule and fat depth measurements were not affected by sire breed (P>0.05). Carcass conformation was higher in Texel sired lambs compared with Corriedale lambs (P<0.05), with Dorset and Suffolk sired lambs being intermediate. Crossbred lambs showed a greater (P<0.001) eye muscle than Corriedale. Commercial cuts were affected by sire breed, as a result of the Corriedale lambs being smaller and having lighter carcass than crossbred lambs. Significant improvement in lamb weights at weaning and carcass traits could be expected when using a terminal sire on Corriedale ewes in Western Patagonia. However, no advantages were detected with the use of recorded sires under these production systems.     

Genetic and non-genetic factors associated with milking order in lactating dairy cows

The ability to rapidly identify temporal deviations of an animal from its norm will be important in the management of individual cows in large herds. Furthermore, predictors of genetic merit for especially health traits are useful to augment the accuracy of selection, and thus genetic gain, in breeding programs. The objective of this study was to estimate the repeatability of milking order and to quantify the contribution of differences in additive genetic variation to phenotypic differences (i.e., heritability). The data used in this study included 9813 herd milk recording test-day records with time of milking from 85,532 cows in 1143 herds across an 8-year period. Milking order was available for both morning and evening milking for each cow with, on average, 3.33 milk test-day records (i.e., 6.66 milking events) per lactation, and on average 1.62 lactations per cow. Variance components for milking order were estimated using animal linear mixed models; covariance components between milking order and milk yield, milk composition and somatic cell score (i.e., logarithm₁₀ somatic cell count) were estimated also using animal linear mixed models. The heritability of milking order was 0.20 indicating partial genetic control of milking order. The repeatability of milking order within test-day, within lactation, and across lactations was 0.63, 0.51, and 0.47, respectively. Milking order was positively (P < 0.001), but weakly, phenotypically correlated with milk yield (r = 0.04), and milk fat concentration (r = 0.01) and negatively (P < 0.001), but weakly, correlated with milk protein concentration (r = −0.02) and somatic cell score (r = −0.05). Milking order was positively (P < 0.05), although weakly, genetically correlated with milk yield (r = 0.07) and negatively (P < 0.05), but also weakly, genetically correlated with somatic cell score (r = −0.08). This study is the first to show a contribution of additive genetics to milking order in dairy cattle but the genetic correlation between milking order and somatic cell score was weak.     

Dietary verbascoside supplementation in donkeys: effects on milk fatty acid profile during lactation,and serum biochemical parameters and oxidative markers

Various uses of donkeys’ milk have been recently proposed for human consumption on the basis of its nutritional characteristics. Improvements in milk fatty acid profile and animal oxidative status can be induced through dietary supplementation of phenolic compounds. The study aimed to evaluate in donkeys the effects of dietary supplementation with verbascoside (VB) on: (i) the fatty acid profile and vitamins A and E contents of milk during a whole lactation, and (ii) blood biochemical parameters and markers of oxidative status of the animals. At foaling, 12 lactating jennies were subdivided into two groups (n 6): control, without VB supplement; VB, receiving a lipid-encapsulated VB supplement. Gross composition, fatty acid profile and vitamins A and E contents in milk were assessed monthly over the 6 months of lactation. Serum total cholesterol, high-density lipoproteins cholesterol and low-density lipoproteins cholesterol, tryglicerides, non-esterified fatty acid, bilirubin, alanine aminotransferase (ALT), aspartate aminotransferase, reactive oxygen metabolites, thiobarbituric acid reactive substances (TBARs), vitamin A and vitamin E were evaluated at 8 days after foaling (D0) and then at D90, D105 and D120 of lactation. In milk, the VB supplementation decreased the saturated fatty acids (P<0.05) and increased the monounsaturated fatty acids (P<0.05), and vitamins A and E (P<0.01) values. On the serum parameters, the VB supplementation decreased total cholesterol (P<0.01), tryglicerides, bilirubin, ALT and TBARs, and increased (P<0.01) vitamin E. In conclusion, the VB dietary supplementation affects the nutritional quality of donkey’s milk with a benefit on the oxidative status and serum lipidic profile of the animals.     

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals’ genomic relationships. The Wright’s fixation F_ST index was also employed to assess herds’ genetic homogeneity and to indirectly estimate past migration rates. The Wright’s fixation F_IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r² and |Dʹ| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed’s formation was as high as 549, was then reduced to 463 in 1981 (end of the breed’s formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F_ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals’ genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.