Association between a genetic index for digital dermatitis resistance and the presence of digital dermatitis, heel horn erosion and interdigital hyperplasia in Holstein cows.

Digital dermatitis (DD) is a polybacterial disease endemic to most UK dairy farms. It poses a major financial and welfare threat and is characterized by high incidence and recurrence rates. We aimed to investigate the association between the UK estimated breeding value for resistance to digital dermatitis, the Digital Dermatitis Index (DDI) and the frequency of DD, heel horn erosion (HHE), and interdigital hyperplasia (IH) in a population of Holstein dairy cows. We enrolled and genotyped 2,352 cows from 4 farms in a prospective cohort study. Foot lesion records were recorded by veterinary surgeons for each animal at 4 time points during a production cycle, starting at approximately 2 mo before calving and ending in late lactation. Importantly, these records were not used in the calculation of the DDI. Lesion records were matched to the animal's own DDI (n = 2,101) and their sire's DDI (n = 1,812). Digital Dermatitis Index values in our study population ranged from -1.41 to +1.2 and were transformed to represent distance from the mean expressed in standard deviations. The relationship between the DDI and the presence of DD was investigated using a logistic regression model, with farm, parity, and a farm-parity interaction fitted as covariates. A multivariable logistic regression model was fitted to evaluate the relationship between HHE and DDI with farm fitted as a covariate. Finally, a univariable logistic regression model with DDI as explanatory variable was used to investigate the relationship between IH and DDI. The odds ratio of an animal being affected by DD was 0.69 for one standard deviation (SD) increase in the animal's DDI (95% confidence interval (CI) = 0.63-0.76). The odds of HHE and IH were 0.69 (95%CI = 0.62-0.76) and 0.58 (95%CI = 0.49-0.68) respectively for one SD increase in DDI. The adjusted probability of DD was 32% (95% CI = 27-36%) for cows with mean DDI value of 0 while it was 24% (95% CI = 20-29%) in cows with a DDI value of +1. Sire DDI breeding values were standardized in the same way and then binned into terciles creating an ordinal variable representing bulls of high, medium, and low genetic merit for DD resistance. The daughters of low genetic merit bulls were at 2.05 (95% CI = 1.60-2.64), 1.96 (95% CI = 1.53-2.50), and 2.85 (95% CI = 1.64-5.16) times greater odds of being affected by DD, HHE, and IH respectively compared with the daughters of high genetic merit bulls. The results of this study highlight the potential of digital dermatitis genetic indexes to aid herd management of DD, and suggest that breeding for resistance to DD, alongside environmental and management control practices, could reduce the prevalence of the disease.

Genetic profile of adaptive immune traits and relationships with parasite resistance and productivity in Scottish Blackface sheep.

Gastrointestinal (GI) parasites cause significant production losses in grazing ruminants which can be mitigated by breeding animals resistant to disease. Lymphocyte cytokine production and parasite-specific Immunoglobulin A (IgA) are adaptive immune traits associated with immunity to GI parasites. To explore the utility of these traits for selective breeding purposes, this study estimated the genetic parameters of the immune traits in sheep and assessed their relationship with disease and productivity traits. Whole blood stimulation assays were performed on 1 040 Scottish Blackface lambs at two months of age in 2016-2017. Blood was stimulated with either pokeweed mitogen (PWM), a non-specific activator of lymphocytes, and Teladorsagia circumcincta (T-ci) larval antigen to activate parasite-specific T lymphocytes. The type of adaptive immune response was determined by quantifying production of cytokines interferon-gamma (IFN-γ), interleukin (IL)-4, and IL-10, which relate to T-helper type (Th) 1, Th2 and regulatory T cell responses, respectively. Serum T-ci specific IgA was also quantified. Heritabilities were estimated for each immune trait by univariate analyses. Genetic and phenotypic correlations were estimated between different immune traits, and between immune traits vs. disease and productivity traits that were recorded at three months of age. Disease phenotypes were expressed as faecal egg counts (FEC) of nematode parasites (Strongyles and Nematodirus), faecal oocyst counts (FOC) of coccidian parasites, and faecal soiling score; production was measured as lamb live weight. Significant genetic variation was observed in all immune response traits. Heritabilities of cytokine production varied from low (0.14 ± 0.06) to very high (0.77 ± 0.09) and were always significantly greater than zero (P < 0.05). IgA heritability was found to be moderate (0.41 ± 0.09). Negative associations previously identified between IFN-γ production and FOC, and IL-4 production and strongyle FEC, were not evident in this study, potentially due to the time-lag between immune and parasitology measures. Instead, a positive genetic correlation was found between FOC and PWM-induced IFN-γ production, while a negative genetic correlation was found between FOC and T-ci induced IL-10. Live weight was negatively genetically correlated with IFN-γ responses. Overall, IFN-γ and IL-4 responses were positively correlated, providing little evidence of cross-regulation of Th1 and Th2 immunity within individual sheep. Furthermore, T-ci specific IgA was highly positively correlated with PWM-induced IL-10, indicating a possible role for this cytokine in IgA production. Our results suggest that while genetic selection for adaptive immune response traits is possible and may be beneficial for parasite control, selection of high IFN-γ responsiveness may negatively affect productivity.

Genome-wide association studies of parasite resistance, productivity and immunology traits in Scottish Blackface sheep.

Gastrointestinal parasitism represents a global problem for grazing ruminants, which can be addressed sustainably by breeding animals to be more resistant against infection by parasites. The aim of this study was to assess the genetic architecture underlying traits associated with gastrointestinal parasite resistance, immunological profile and production in meat sheep, and identify and characterise candidate genes affecting these traits. Data on gastrointestinal parasite infection (faecal egg counts for Strongyles (FECS) and Nematodirus (FECN) and faecal oocyst counts for Coccidia, along with faecal soiling scores (DAG), characterised by the accumulation of faeces around the perineum) and production (live weight (LWT)) were gathered from a flock Scottish Blackface lambs at three and four months of age. Data on the immune profile were also collected from a subset of these lambs at two and five months of age. Immune traits included the production of Interferon-γ (IFN-γ), Interleukin (IL)-4 and IL-10 following stimulation of whole blood with pokeweed mitogen (PWM) or antigen from the gastric parasite Teladorsagia circumcincta (T-ci), and serum levels of T. circumcincta-specific immunoglobulin A (IgA). Animals were genotyped with genome-wide DNA arrays, and a total of 1 766 animals and 45 827 Single Nucleotide Polymorphisms (SNPs) were retained following quality control and imputation. Genome-wide association studies were performed for 24 traits. The effects of individual markers with significant effects were estimated, and the genotypic effect solutions were used to estimate additive and dominance effects, and the proportion of additive genetic variance attributed to each SNP locus. A total of 15 SNPs were associated at least at a suggestive level with FECS, FECN, DAG, IgA, PWM-induced IFN-γ and IL-4, and T-ci-induced IL-10. This study uncovered 52 genes closely related to immune function in proximity to these SNPs. A number of genes encoding C-type lectins and killer cell lectin-like family members were close to a SNP associated with FECN, while several genes encoding IL-1 cytokine family members were found to be associated with IgA. Potential candidate genes belonging to or in close proximity with the Major Histocompatibility Complex (MHC) were revealed, including Homeostatic Iron Regulator and butyrophilin coding genes associated with IFN-γ(PWM), and IL-17 coding genes associated with IgA. Due to the importance of the MHC in the control of immune responses, these genes may play an important role in resistance to parasitic infections. Our results reveal a largely complex and polygenic genetic profile of the studied traits in this Scottish Blackface sheep population.

Variation in protein metabolism biomarkers during the transition period and associations with health, colostrum quality, reproduction, and milk production traits in Holstein cows.

The aims of this study were to assess (1) the variation of protein metabolism biomarkers and factors affecting them during the transition period, (2) the association of each biomarker with skeletal muscle reserves and their changes, and (3) the association of these biomarkers with postpartum health, colostrum quality, reproduction, and milk production. For this purpose, 238 multiparous Holstein cows from 6 herds were used in a prospective cohort study. Plasma concentrations of 3-methylhistidine (3-MH) and 1-methylhistidine (1-MH) and serum concentrations of total protein (TP), albumin (ALB), urea nitrogen (BUN), and creatinine (SCR) were determined for each cow at -21, -7, 7, 21, and 28 d relative to calving. Clinical diseases were recorded during the first 28 d postcalving, and presence of subclinical ketosis (scKET) was investigated at 7 and 21 d. Colostrum quality was estimated by Brix refractometry. Reproduction data by 150 d in milk (DIM) and milk production records were also available. Linear mixed models including the fixed effects of time point, herd, parity, body condition score (-21 d), duration of dry period and postparturient diseases were fitted to assess the variation in each biomarker's concentration. The association between the biomarkers' concentration during the prepartum period with the odds for each postparturient disease and for a combined trait (CD_1-28), defined as the presence of at least one clinical condition during the first 28 d after calving, were assessed with separate binary logistic models for time points -21 d and -7 d. The relationship of each biomarker's concentration with longissimus dorsi thickness (LDT) and the changes in LDT (ΔLDT) was assessed with pairwise correlations. Separate general linear models were used to assess the association of each biomarker with colostrum Brix values and milk production traits. Finally, the associated hazard for first artificial insemination (AI) and for pregnancy by 150 DIM (PREG_150DIM) was assessed with Cox proportional hazard models, whereas odds for pregnancy to the first AI (PREG_1stAI) were assessed with binary logistic models. The level of 3-MH was affected mainly by herd, time points, and their interaction. Higher 3-MH was associated with increased odds for metritis and CD_1-28, increased hazard for PREG_150 DIM and with increased milk production. 1-Methylhistidine was affected mainly by herd, scKET and occurrence of displaced abomasum. Higher 1-MH was associated with better colostrum quality, increased odds for scKET, increased hazard for first AI by 150 DIM and with decreased milk production. Both 3-MH and 1-MH were weakly to moderately negatively correlated with LDT and moderately to strongly negatively correlated with ΔLDT at the corresponding time periods. Additionally, higher TP was associated with increased odds for metritis and CD_1-28 and increased milk production, while higher ALB was associated with increased odds for scKET and increased milk production. Moreover, higher BUN was associated with decreased odds for scKET, increased odds for PREG_1stAI and increased milk production. Higher SCR was associated with decreased odds for retained fetal membranes, metritis, and CD_1-28. Periparturient protein metabolism is significantly associated with postpartum health, colostrum quality, reproduction, and milk production; mechanisms involved require further investigation.

Genome-wide association study of health and production traits in meat sheep.

Genotypes are currently widely used in animal breeding programmes to enhance the speed of genetic progress. With sufficient data, a Genome-Wide Association Study (GWAS) can be performed to identify informative markers. The aim of this study was to investigate the genetic background of health (footrot and mastitis) and production (birth weight, weaning weight, scan weight, and fat and muscle depth) traits using the available phenotypic and Single Nucleotide Polymorphism (SNP) data collected on the UK Texel sheep population. Initially, 10 193 genotypes were subject to quality control, leaving 9 505 genotypes for further analysis. Selected genotypes, recorded on four different Illumina chip types from low density (15 k SNPs) to high density (606 006 SNPs), were imputed to a subset of 45 686 markers from 50 k array, distributed on 27 chromosomes. Phenotypes collected on 32 farms across the UK for footrot and mastitis and extracted from the UK National database (iTexel) for the production traits were used along with pre-estimated variance components to obtain de-regressed breeding values and used to perform GWAS. Results showed three SNPs being significant on the genome-wise level ('OAR8_62240378.1' on chromosome 8 for birth weight, 's14444.1' on chromosome 19 for weaning weight and 's65197.1' on chromosome 23 for scan weight). Fourteen subsequent SNPs were found to be significant at the chromosome-wise level. These SNPs are located within or close to previously reported QTLs impacting on animal health (such as faecal egg count or somatic cell count) and production (such as body or carcass weight and fat amount). These results indicate that the studied traits are highly polygenic with complex genetic architecture.

Identification of temporal patterns of environmental heat stress of Holstein dairy heifers raised in Mediterranean climate during their in-utero and post-natal life periods and modelling their effects on age at first calving.

A retrospective study was conducted to evaluate temporal patterns of environmental heat stress during the in-uterus period of development (IUP) and the 3-month post-natal (PN) period of dairy heifers, and to estimate their association with the age at first calving (AFC). Data from 30 dairy herds in Northern Greece including 9098 heifers were extracted from National Cattle Database. Data (2005-2019) regarding 230,100 farm-specific ambient daily temperature and relative humidity records, were obtained from ERA5-Land. Average monthly Temperature-Humidity-Index values (THI; low≤68, and high>68) were calculated and matched for each heifer to their IUP and PN. Subsequently, Cluster Analysis was used with monthly THIs as predictors to allocate heifers to THI clusters. The association of clusters with AFC was assessed with Generalized Linear Mixed Model analysis, an extended form of multiple linear regression. Finally, 8 Heat Stress Clusters (HSC; namely HSC-1 to HSC-8) were identified. Compared to HSC-8 (8th-9th IUP months and 1st PN month) heifers of HSC-5 (4th-7th IUP months) and HSC-6 (6th-8th IUP months) calved 13.8 and 17.8 days later, respectively (P < 0.01-0.001). Moreover, when AFC was treated as a binary variable, heifers of HSC-5 and HSC-6 had 1.15 and 1.34 (P < 0.01-0.001) higher risk of calving for the first time later than 787 days compared to HSC-8, respectively.

Novel genomic markers and genes related to reproduction in prolific Chios dairy sheep: a genome-wide association study.

Genetic architecture of sheep reproduction is increasingly gaining scientific interest due to the major impact on sheep production systems. In the present study, we conducted pedigree-based analyses and genome-wide association studies using the Illumina Ovine SNP50K BeadChip to explore the genetic mechanisms underlying the reproduction of the highly prolific Chios dairy sheep. First lambing age, total prolificacy and maternal lamb survival were selected as representative reproductive traits and estimated as significantly heritable (h2 = 0.07-0.21) with no evident genetic antagonism among traits. We identified novel genome-wide and suggestive significant single-nucleotide polymorphisms (SNPs) on chromosomes 2 and 12 associated with age at first lambing. The new variants detected on chromosome 2 span a region of 357.79 kb with high pairwise linkage disequilibrium estimates (r2 = 0.8-0.9). Functional annotation analysis revealed candidate genes, such as the collagen-type genes and the Myostatin gene, that participate in osteogenesis, myogenesis, skeletal and muscle mass development resembling the functionality of major genes affecting the ovulation rate and prolificacy. Additional functional enrichment analysis associated the collagen-type genes with multiple uterine-related disfunctions, such as cervical insufficiency, uterine prolapse and abnormalities of the uterine cervix. Several genes (e.g., KAZN, PRDM2, PDPN, LRRC28) localised close to the SNP marker on chromosome 12 were grouped in annotation enrichment clusters majorly involved in developmental and biosynthetic pathways, apoptosis, and nucleic acid-templated transcription. Our findings may further contribute to unravel the genomic regions that are important for sheep reproduction and could be incorporated into future selective breeding programmes.

The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions.

BACKGROUND: Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms. RESULTS: We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation. CONCLUSIONS: Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.

Skeletal muscle and adipose tissue reserves and mobilisation in transition Holstein cows: Part 1 Biological variation and affecting factors.

Nutrient deficit during the periparturient period leads to mobilisation of body energy and protein reserves. Research regarding fat reserves and mobilisation is extensive, while, on the contrary, investigation of muscle mobilisation during the periparturient period is limited. The aim of this cohort study was to simultaneously investigate the biological variation of skeletal muscle and subcutaneous fat reserves together with their mobilisation in transition Holstein cows of different herds, using ultrasonography, and to assess potential affecting factors. For this purpose, ultrasound measurements of longissimus dorsi muscle thickness (LDT) and backfat thickness (BFT) from 238 multiparous cows of six dairy farms were obtained at six time points across the transition period (from 21 days pre- to 28 days postpartum). Concentrations of serum creatinine and non-esterified fatty acids were determined in order to confirm the loss of muscle mass and adipose tissue, respectively. Cases of clinical postparturient diseases and subclinical ketosis (scKET) during the first 28 days postcalving were recorded. Cows mobilised on average 32.8% and 37.3% of LDT and BFT reserves, respectively. Large between-cow variation was observed for both the onset and the degree of mobilisation. Time point, initial body condition score and parity were the most important predictors of LDT variation. Cows diagnosed with metritis (MET) had lower LDT postpartum and mobilised more muscle depth compared to cows not diagnosed with MET. Initial BCS, time point, initial BW (estimated by heart girth measurement) and parity were the most important predictors of BFT variation. Cows diagnosed with MET mobilised more backfat between -7d and 7d compared to cows not diagnosed with MET. Cows with scKET mobilised more backfat between 7- and 21 days postpartum compared to healthy ones. Variation of subcutaneous fat and skeletal muscle reserves during the transition period was large and affected by herd and several cow-level factors.

Skeletal muscle and adipose tissue reserves and mobilisation in transition Holstein cows: Part 2 association with postpartum health, reproductive performance and milk production.

The aim of this study was, for the first time, to simultaneously assess the association of skeletal muscle and subcutaneous fat reserves and their mobilisation, measured by ultrasonography, with the incidence of specific postparturient health, reproduction, and milk production traits. For this purpose, ultrasound measurements of longissimus dorsi thickness (LDT) and backfat thickness (BFT) from 238 multiparous cows from 6 dairy farms were obtained at 6 time points during the transition period (from 21 days pre- to 28 days postpartum). In each case, LDT and BFT measurements at each time point and LDT and BFT mobilisation variables at each study period were assessed simultaneously. Cases of specific clinical postparturient diseases and subclinical ketosis were recorded. An additional disease trait was used, defined as the presence or absence of at least one clinical condition after calving (CD_1-28). The associated disease odds with LDT/BFT variables were assessed with binary logistic regression models. The associated hazard for 1st artificial insemination (AI) and for pregnancy by 150 days-in-milk (PREG_150DIM) was assessed with Cox proportional hazard models. Moreover, binary logistic models were used to assess the associated odds for pregnancy to 1stAI (PREG_1stAI). Finally, association with 30d, 100d and 305d milk yield was assessed with linear regression models. Increased muscle depth during transition was negatively associated with odds for metritis and CD_1-28, while associations with odds for subclinical ketosis were inconclusive. Moreover, increased LDT reserves were associated with greater hazard for 1st AI by 150 days-in-milk, but results were inconclusive regarding odds for PREG_1stAI. Increased LDT mobilisation was associated with increased odds for metritis. Increased BFT reserves were positively associated with odds for metritis, CD_1-28 and subclinical ketosis and with decreased hazard for PREG_150DIM. Increased BFT mobilisation was associated with increased odds for subclinical ketosis and with decreased odds for PREG_1stAI and decreased hazard for PREG_150DIM. Cows with moderate BFT reserves performed better. Finally, increased BFT mobilisation during -21d to -7d from parturition was associated with less milk by 30d and 100d. On the contrary, increased BFT mobilisation during -7d to 7d was associated with more milk by 305d. Metabolism of muscle and fat tissue during transition period was differently associated with different postparturient health, reproduction and milk production traits. In general, greater muscle mass and moderate fat reserves with limited muscle and fat mobilisation were associated with better performance.

Association of post-partum serum Ca patterns with reproduction in Holstein cows.

The objective of this study was to evaluate the effects of subclinical hypocalcemia (SCHCa) patterns on reproductive performance in dairy cows. In a prospective observational study 916 cows from 9 herds were blood sampled on DIMs 1, 2, 4 and 8; Ca concentration was measured with atomic absorption and SCHCa was defined as Ca ≤ 2.09 mmol/L. Cluster analysis revealed 2 normocalcemic (NORM and HIGH) and five hypocalcemic (SCH-1 to 5) clusters. Cows in cluster NORM (n = 151) had mean day-to-day serum Ca (DIMs 1-8) between 2.24 and 2.41 mmol/L, and cows in HIGH (n = 167) between 2.42 and 2.53 mmol/L. Cows in SCH-1 (n = 130) and SCH-2 (n = 102) had transient and mostly mild SCHCa on day 1 and day 2, respectively. Cows in SCH-3 (n = 123) had mostly severe SCHCa on days 1 and 2, extending to day 4. Cows in SCH-4 (n = 120) and SCH-5 (n = 145) had SCHCa which culminated on days 4 and 8, respectively. Information on reproductive outcomes including pregnancy status by 120 and 200 DIM and days open were retrieved from farm records. Median (±SE) days to 1st artificial insemination (AI) until 120 DIM estimated with Kaplan-Meier analysis for cows in SCH-3, SCH-4 and SCH-5 were 100.0 ± 7.2, 109.0 ± 6.6 and 120.0 ± 3.2, respectively, and were statistically significantly higher from those in NORM and HIGH (91.0 ± 3.4 and 87 ± 3.7, respectively). Mean days (±SE) to detected pregnancy until 200 DIM estimated with Kaplan-Meier analysis for cows in SCH-3 were 161.2 ± 4.8 and were statistically significantly higher from those in clusters NORM and HIGH (155.5 ± 4.2 and 151.6 ± 4.3, respectively). The association of Ca clusters with the odds of detected pregnancy for the 1st insemination until 120 and 200 DIM was evaluated with Linear Mixed Models. Odds for pregnancy by 120 DIM did not differ among clusters, however, cows in clusters SCH-3 and SCH-5 had lower odds for pregnancy by 200 DIM compared to HIGH (OR = 0.55, P = 0.02, and OR = 0.49, P = 0.004, respectively). Covariate adjusted survival curves generated by multivariable Cox proportional hazards model revealed that: a) clusters SCH-3 and SCH-5 had the highest (36% and 38%, respectively), while NORM and HIGH the lowest (16% and 17%, respectively) proportion of cows not inseminated for the 1st time by 120 DIM, b) compared to HIGH, cows in SCH-5 had a lower hazard of pregnancy by 120 DIM (HR = 0.42, P = 0.005), c) the proportion of open cows by 200 DIM for NORM and HIGH were 57% and 47%, respectively, while for SCH-3 and SCH-5 66% and 68%, respectively, and d) compared to HIGH, SCH-3 (HR = 0.54, P = 0.008) and SCH-5 (HR = 0.50, P = 0.001) presented the lowest hazard for pregnancy by 200 DIM. In conclusion, cows that during the entire first week after calving were continuously normocalcemic had the best reproductive performance, while those of SCH-3 and SCH-5 the worst.

Discovery of hidden pedigree errors combining genomic information with the genomic relationship matrix in Texel sheep.

Genomic variants such as Single Nucleotide Polymorphisms and animal pedigree are now used widely in routine genetic evaluations of livestock in many countries. The use of genomic information not only can be used to enhance the accuracy of prediction but also to verify pedigrees for animals that are extensively managed using natural mating and enabling multiple-sire mating groups to be used. By so doing, the rate of genetic gain is enhanced, and any bias associated with incorrect pedigrees is removed. This study used a set of 8 764 sheep genotypes to verify the pedigree based on both the conventional opposing homozygote method as well as a novel method when combined with the inclusion of the genomic relationship matrix (GRM). The genomic relationship coefficients between verified pairs of animals showed on average a relationship of 0.50 with parent, 0.25 with grandparent, 0.13 with great grandparent, 0.50 with full-sibling and 0.27 with half-sibling. Minimum obtained values from these verified pairs were then used as thresholds to determine the pedigree for unverified pairs of animals, to detect potential errors in the pedigree. Using a case study from a population partially genotyped UK sheep, the results from this study illustrate a powerful way to resolve parentage inconsistencies, when combining the conventional 'opposing homozygote' method using genomic information together with GRM for pedigree checking. In this way, previously undetected pedigree errors can be resolved.

A study on the use of thermal imaging as a diagnostic tool for the detection of digital dermatitis in dairy cattle.

Our aims were to (1) determine how interdigital skin temperature (IST), measured using infrared thermography, was associated with different stages of digital dermatitis (DD) lesions and (2) develop and validate models that can use IST measurements to identify cows with an active DD lesion. Between March 2019 and March 2020, infrared thermographic images of hind feet were taken from 2,334 Holstein cows across 4 farms. We recorded the maximum temperature reading from infrared thermographic images of the interdigital skin between the heel bulbs on the hind feet. Pregnant animals were enrolled approximately 1 to 2 mo precalving, reassessed 1 wk after calving, and again at approximately 50 to 100 d postpartum. At these time points, IST and the clinical stage of DD (M-stage scoring system: M1-M4.1) were recorded in addition to other data such as the ambient environmental temperature, height, body condition score, parity, and the presence of other foot lesions. A mixed effect linear regression model with IST as the dependent variable was fitted. Interdigital skin temperature was associated with DD lesions; compared to healthy feet, IST was highest in feet with M2 lesions, followed by M1 and M4.1 lesions. Subsequently, the capacity of IST measurements to detect the presence or absence of an active DD lesion (M1, M2, or M4.1) was explored by fitting logistic regression models, which were tested using 10-fold validation. A mixed effect logistic regression model with the presence of active DD as the dependent variable was fitted first. The average area under the curve for this model was 0.80 when its ability to detect presence of active DD was tested on 10% of the data that were not used for the model's training; an average sensitivity of 0.77 and an average specificity of 0.67 was achieved. This model was then restricted so that only explanatory variables that could be practically recorded in a nonresearch, external setting were included. Validation of this model demonstrated an average area under the curve of 0.78, a sensitivity of 0.88, and a specificity of 0.66 for 1 of the time points (precalving). Lower sensitivity and specificity were achieved for the other 2 time points. Our study adds further evidence to the relationship between DD and foot skin temperature using a large data set with multiple measurements per animal. Additionally, we highlight the potential for infrared thermography to be used for routine on-farm diagnosis of active DD lesions.

Genetic parameters of animal traits associated with coccidian and nematode parasite load and growth in Scottish Blackface sheep.

Gastrointestinal parasitism is a global problem for grazing ruminants which can be addressed in a sustainable way through breeding animals to be more resistant to disease. This study estimates the genetic parameters of common and new disease phenotypes associated with natural nematode and coccidian infection in Scottish Blackface sheep to underpin future genetic improvement strategies for parasite control. Data on faecal egg counts (FEC) from different species of strongyle parasites and faecal oocyst counts (FOC) from coccidian parasites were collected on 3-month-old lambs together with a faecal soiling score in the breech area dagginess (DAG) and live weight (LWT). Faecal count data were obtained for Strongyles (FECS), Nematodirus (FECN) and Coccidia (FOC). Data from 3 731 lambs sampled between 2011 and 2017 were included. Faecal egg counts and DAG records were log-transformed prior to analysis. Data were analysed using linear mixed models. Average age at sampling was 92 days with a mean LWT of 24.5 kg. Faecal soiling was not evident in 69% of lambs. Coccidia were the most prevalent parasite (99.5%), while Strongyles and Nematodirus had a prevalence of 95.4% and 72.7%, respectively. Heritability estimates (±SE) were 0.16 ±â€¯0.03, 0.17 ±â€¯0.03, 0.09 ±â€¯0.03, 0.09 ±â€¯0.03 and 0.33 ±â€¯0.04 for FECS, FECN, FOC, DAG and LWT, respectively. Strongyles faecal egg count had a strong and positive genetic correlation with FECN (0.74 ±â€¯0.09) and a moderate positive correlation with FOC (0.39 ±â€¯0.15) while DAG was negatively genetically correlated with LWT (-0.33 ±â€¯0.15). The significant positive genetic correlations between FECS, FECN and FOC at 3 months of age show that co-selection of sheep for resistance to these different parasites is feasible. Selection for increased resistance to parasite infection is not expected to adversely affect live BW, as no significant antagonistic genetic correlations were found between LWT and FEC. There were significant antagonistic phenotypic and genetic relationships between DAG and LWT being -0.19 ±â€¯0.02 and -0.33 ±â€¯0.15, respectively, indicating that the expression of the manifestation of disease in lambs may be a more meaningful indicator of the impact of parasite burden on productivity.

Subclinical hypocalcaemia follows specific time-related and severity patterns in post-partum Holstein cows.

Hypocalcaemia is a common metabolic disorder of post-parturient dairy cows; enhancement of our knowledge regarding Ca dynamics would improve cow health and welfare. This study investigated the presence of time- and severity-related subclinical hypocalcaemia (SCHCa) patterns in Holstein cows after calving and their association with diseases during the first week of lactation. A total of 938 cows from nine herds were blood sampled on days 1, 2, 4 and 8 post-partum, and serum Ca concentration was measured with atomic absorption. Subclinical ketosis (serum ß-hydroxybutyrate≥1.2 mmol/L) and cases of retained foetal membranes, metritis (MET), mastitis, ketosis and displaced abomasum (DA) were recorded. Using receiver operating characteristic (ROC) analysis, the SCHCa cut-off was identified at serum Ca ≤ 2.09 mmol/L. Hierarchical and two-step cluster analysis classified cows to seven clusters based on test day cow Ca records and overall SCHCa status. Two clusters (NORM and HIGH) included 318 normocalcaemic cows and five clusters (SCH-1 to -5) those that were at least once subclinically hypocalcaemic (n = 620). A second ROC analysis was performed in order to distinguish mild from severe cases of SCHCa in these 620 cows; this cut-off was identified at 1.93 mmol/L. The associated risk of disease with Ca clustership was assessed with generalized linear mixed models. Overall incidence of SCHCa was 66.1%. Clusters SCH-1 and SCH-2 included cows with short-term SCHCa of day 1 and day 2, respectively, while SCH-3 included cows with severe and prolonged SCHCa extending to day 4 and beyond. Clusters SCH-4 and SCH-5 included cows with delayed SCHCa, which culminated on days 4 and 8, respectively. Compared to NORM cows in HIGH had lower risk of MET and no cases of DA. Cows in SCH-3 had higher risk of being diagnosed with retained foetal membranes, DA or any disease during the study period. Cows in SCH-5 had higher risk of being diagnosed with ketosis, subclinical ketosis or any disease. In conclusion, there are multiple normocalcaemic and hypocalcaemic patterns that are differently associated with disease risk.

Genetic analyses of live weight and carcass composition traits in purebred Texel, Suffolk and Charollais lambs.

Lamb live weight is one of the key drivers of profitability on sheep farms. Previous studies in Ireland have estimated genetic parameters for live weight and carcass composition traits using a multi-breed population rather than on an individual breed basis. The objective of the present study was to undertake genetic analyses of three lamb live weight and two carcass composition traits pertaining to purebred Texel, Suffolk and Charollais lambs born in the Republic of Ireland between 2010 and 2017, inclusive. Traits (with lamb age range in parenthesis) considered in the analyses were: pre-weaning weight (20 to 65 days), weaning weight (66 to 120 days), post-weaning weight (121 to 180 days), muscle depth (121 to 180 days) and fat depth (121 to 180 days). After data edits, 137 402 records from 50 372 lambs across 416 flocks were analysed. Variance components were derived using animal linear mixed models separately for each breed. Fixed effects included for all traits were contemporary group, age at first lambing of the dam, parity of the dam, a gender by age of the lamb interaction and a birth type by rearing type of the lamb interaction. Random effects investigated in the pre-weaning and weaning weight analyses included animal direct additive genetic, dam maternal genetic, litter common environment, dam permanent environment and residual variances. The model of analysis for post-weaning, muscle and fat depth included an animal direct additive genetic and litter common environment effect only. Significant direct additive genetic variation existed in all cases. Direct heritability for pre-weaning weight ranged from 0.14 to 0.30 across the three breeds. Weaning weight had a direct heritability ranging from 0.17 to 0.27 and post-weaning weight had a direct heritability ranging from 0.15 to 0.27. Muscle and fat depth heritability estimates ranged from 0.21 to 0.31 and 0.15 to 0.20, respectively. Positive direct correlations were evident for all traits. Results revealed ample genetic variation among animals for the studied traits and significant differences between breeds to suggest that genetic evaluations could be conducted on a per-breed basis.

Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds.

Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina's Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright's fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.

Genetic parameters of colostrum traits in Holstein dairy cows.

The main objective of this study was to assess the genetic background of colostrum yield and quality traits after calving in Holstein dairy cows. The secondary objective was to investigate genetic and phenotypic correlations among laboratory-based and on-farm-measured colostrum traits. The study was conducted in 10 commercial dairy herds located in northern Greece. A total of 1,074 healthy Holstein cows with detailed pedigree information were examined from February 2015 to September 2016. All cows were clinically examined on the day of calving and scored for body condition. All 4 quarters were machine-milked, and a representative and composite colostrum sample was collected and examined. Colostrum total solids (TS) content was determined on-farm using a digital Brix refractometer. Colostrum fat, protein, and lactose contents were determined using an infrared milk analyzer, and energy content was calculated using National Research Council (2001) equations. Dry period length (for cows of parity ≥2), milk yield of previous 305-d lactation (for cows of parity ≥2), age at calving, parity number, season of calving, time interval between calving and first colostrum milking, and milk yield were recorded. Each trait (colostrum yield and quality traits) was analyzed with a univariate mixed model, including fixed effects of previously mentioned factors and the random animal additive genetic effect. All available pedigrees were included in the analysis, bringing the total animal number to 5,662. Estimates of (co)variance components were used to calculate heritability for each trait. Correlations among colostrum traits were estimated with bivariate analysis using the same model. Mean percentage (±SD) colostrum TS, fat, protein, and lactose contents were 25.8 ± 4.7, 6.4 ± 3.3, 17.8 ± 4.0, and 2.2 ± 0.7%, respectively; mean energy content was 1.35 ± 0.3 Mcal/kg and mean colostrum yield was 6.18 ± 3.77 kg. Heritability estimates for the above colostrum traits were 0.27, 0.21, 0.19, 0.15, 0.22, and 0.04, respectively. Several significant genetic and phenotypic correlations were derived. The genetic correlation of TS content measured on-farm with colostrum protein was practically unity, whereas the correlation with energy content was moderate (0.61). Fat content had no genetic correlation with TS content; their phenotypic correlation was positive and low. Colostrum yield was not correlated genetically with any of the other traits. In conclusion, colostrum quality traits are heritable and can be amended with genetic selection.

Current situations of animal data recording, dairy improvement infrastructure, human capacity and strategic issues affecting dairy production in sub-Saharan Africa.

An online survey on the state of existing dairy data, dairy improvement infrastructure and human capacity in sub-Saharan Africa (SSA) was undertaken with the aim of assessing whether the state of existing animal recording, dairy improvement methods and key issues facing dairy production together with means of addressing the issues differ among countries and regions of SSA. Respondents comprised experts and practitioners in livestock production and genetic resources from research institutes, animal breeding companies, universities, non-governmental organisations and government agricultural ministries. The main dairy farming system in which the respondents were involved was mixed crop-livestock system (30.2%), and this was mainly practised in the private land tenure system (46.3%). Data were analysed using linear model and paired Student t test in R software package. Respondents identified key issues affecting dairy production as poor genetic assessment of imported exotic breeds and crosses in Africa (62.3%), fluctuations in milk prices within both the formal and informal markets (50.9%), no comprehensive sire ranking systems (39.6%), housing and health management regimes which adversely affect milk yield (32.1%), poor market networks for dairy products (25.5%), poor feeding (13.3%), inadequate genetic technologies (9.4%) and poor animal performance recording systems (9.4%). Respondents emphasised the need for updated breeding policies, sire ranking systems, adequate farm management systems, capacity building, across-country collaborations and joint genetic assessments of dairy breeds found in sub-Saharan Africa. The current situation of dairy production though similar for the different countries, differed in order of emphasis and magnitude across the countries and regions in sub-Saharan Africa.

Farmer-preferred traits in smallholder dairy farming systems in Tanzania.

Decisions of breeding schemes in many countries in sub-Saharan Africa tend to be either government or project driven, with a focus on upgrading local breeds. However, there is scant information on the individual animal traits that smallholder farmers prefer. The aim of this study was to examine farmers' preferences of dairy cattle traits using a discrete choice experiment methodology. The study was conducted through visits to 555 randomly selected dairy farms in the sub-humid Eastern coast and temperate Southern highlands of Tanzania. Choices of animal traits were presented to farmers who were asked to evaluate choice alternatives based on attribute levels and finally select the alternative with the highest utility. The choice experiment data were analysed using a conditional logit model. Coefficients for milk yield, fertility, feed requirement, temperament and diseases resistance were overall statistically significant (p < 0.05). In order of perceived importance, farmers were willing to keep a cow with high milk yield (coefficient = 1.43 ± 0.059), good fertility (0.85 ± 0.050), easy temperament (0.76 ± 0.066), low feed requirement (- 0.56 ± 0.092) and enhanced tropical disease resistance (0.48 ± 0.048). The purchase price coefficient was negative (- 0.001 ± 0.0003), indicating that farmers would prefer improved dairy cattle at affordable prices. Farmers' preferred traits were influenced by agro-ecological zone and type of production system (extensive vs intensive). The study provides an opportunity for breeding programme designers to take farmers' preferred dairy traits into serious consideration.