Investigating the population structure and genetic diversity of Arabian horses in Oman using SNP markers.

Arabian horses were selected for metabolic efficiency, beauty, efficiency and endurance. Therefore, Bedouins have for centuries traced their prized horses' ancestries. With the establishment of the World Arabian Horse Organization (WAHO), registration of Arabian horses became centralized and countries worldwide registered them in its database. Most existing Arabian horses in Oman today were imported after the 1970s and are predominantly flat-racing Arabians. This work aimed at revealing the genetic background and diversity of Omani Arabian horses by comparing them with Arabian horses from a diverse genetic background. To that end, we genotyped 63 randomly sampled Arabian horses from Oman using the Illumina Equine SNP70. For comparison, SNP genotypes of 12 Saudi Arabian horses, 27 French, 77 Egyptian, 11 Polish and 36 US Arabians were included in the study. We additionally included 17 Thoroughbred horses and 21 horses representing large and small breeds as an outgroup. Our MDS analysis and phylogenetic analysis showed that the Arabian horses in Oman cluster primarily with French Arabian horses, with a few horses clustering within the Polish/US Arabians. The French Arabian horse cluster was the closest to the Thoroughbred horses. Amongst the Arabian horses, plink average genomic inbreeding levels were highest in the Egyptian Arabian (0.169) followed by the Saudi Arabian horses (0.137) and lowest in the Omani and French Arabian horses, -0.041 and -0.079 respectively. To our knowledge, this is the first report on the genetic background and diversity of Arabian horses in Oman. Our results demonstrated a definite subpopulation structure among Arabian horses and this information should advise future decision-making on Arabian horse breeding.

Genome-wide association study of equine herpesvirus type 1-induced myeloencephalopathy identifies a significant single nucleotide polymorphism in a platelet-related gene.

Equine herpesvirus type 1 (EHV-1)-induced myeloencephalopathy (EHM) is a neurologic disease of horses that represents one outcome of infection. The neurologic form of disease occurs in a subset of infected horses when virus-induced endothelial cell damage triggers vasculitis and subsequent ischemic insult to the central nervous system. EHM causes considerable animal suffering and economic loss for the horse industry. Virus polymorphisms have been previously associated with disease outcome but cannot fully explain why only some horses develop EHM. This study investigated the role of host genetics in EHM. DNA samples were collected from 129 horses infected with EHV-1 (61 that developed EHM and 68 in which disease resolved without the development of neurologic signs) during natural outbreaks or experimental infections. A genome-wide association study (GWAS) was performed to investigate host genetic variations associated with EHM. Genotyping was performed using the Illumina SNP50 and SNP70 arrays and a custom Sequenom array. Mixed linear model (MLM) analysis using a recessive model identified one marker that surpassed the threshold for genome-wide significance (P<0.001) after Bonferroni correction. The marker (BIEC2_946397) is in an intron of the tetraspanin 9 (TSPAN9) gene, which is expressed in endothelial cells and platelets. The GWAS identified a region in the horse genome that is associated with EHM in the sample population and thus warrants further exploration. Understanding the contribution of host genetic variation to the development of EHM will enhance our knowledge of disease pathophysiology, and lead to improved strategies for treating individual cases and managing outbreaks.

Use of rumination and activity monitoring for the identification of dairy cows with health disorders: Part II. Mastitis.

The objectives of this study were to evaluate (1) the performance of an automated health-monitoring system (AHMS) to identify cows with mastitis based on an alert system (health index score, HIS) that combines rumination time and physical activity; (2) the number of days between the first HIS alert and clinical diagnosis (CD) of mastitis by farm personnel; and (3) the daily rumination time, physical activity, and HIS patterns around CD. Holstein cows (n=1,121; 451 nulliparous and 670 multiparous) were fitted with a neck-mounted electronic rumination and activity monitoring tag (HR Tags, SCR Dairy, Netanya, Israel.) from at least -21 to 80 d in milk (DIM). Raw data collected in 2-h periods were summarized per 24 h as daily rumination and activity. An HIS (0 to 100 arbitrary units) was calculated daily for individual cows with an algorithm that used rumination and activity. A positive HIS outcome was defined as an HIS of <86 units during at least 1 d from -5 to 2 d after CD. Blood concentrations of nonesterified fatty acids, ß-hydroxybutyrate, total calcium, and haptoglobin were also determined in a subgroup of cows (n=459) at -11±3, -4±3, 0, 3±1, 7±1, 14±1, and 28±1 DIM. The sensitivity of the HIS was 58% [95% confidence interval (CI): 49, 67] for all cases of clinical mastitis (n=123), and 55% (95% CI: 46, 64; n=114) and 89% (95% CI: 68, 100; n=9) for cases of mastitis alone or concurrent with other health disorders, respectively. Among clinical cases, sensitivity was 80.7% (95% CI: 67, 97) for cases caused by Escherichia coli (n=31) and ranged from 45 to 48% for cases caused by gram-positive bacteria (n=39; Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis, Streptococcus spp., Staphylococcus spp., and Trueperella pyogenes), Staphylococcus aureus (n=11), or cases with no bacterial growth (n=25). Days between the first HIS <86 and CD were -0.6 (95% CI: -1.1, -0.2) for all cases of mastitis. Cows diagnosed with mastitis had alterations of their rumination, activity, HIS patterns, and reduced milk production around CD depending on the type of mastitis case. Cows with mastitis also had some alterations of their calcium and haptoglobin concentrations around calving. The AHMS used in this study was effective for identifying cows with clinical cases of mastitis caused by E. coli and cows with another disease occurring during an event of mastitis, but it was less effective in identifying cows with mastitis not caused by E. coli.

Use of rumination and activity monitoring for the identification of dairy cows with health disorders: Part III. Metritis.

The objectives of this study were to evaluate (1) the performance of an automated health-monitoring system (AHMS) to identify cows with metritis based on an alert system (health index score, HIS) that combines rumination time and physical activity; (2) the number of days between the first HIS alert and clinical diagnosis (CD) of metritis by farm personnel; and (3) the daily rumination time, physical activity, and HIS patterns around CD. In this manuscript, the overall performance of HIS to detect cows with all disorders of interest in this study [ketosis, displaced abomasum, indigestion (companion paper, part I), mastitis (companion paper, part II), and metritis] is also reported. Holstein cattle (n=1,121; 451 nulliparous and 670 multiparous) were fitted with a neck-mounted electronic rumination and activity monitoring tag (HR Tags, SCR Dairy, Netanya, Israel) from at least -21 to 80 d in milk (DIM). Raw data collected in 2-h periods were summarized per 24 h as daily rumination and activity. An HIS (0 to 100 arbitrary units) was calculated daily for individual cows with an algorithm that used rumination and activity. A positive HIS outcome was defined as an HIS of <86 units during at least 1 d from -5 to 2 d after CD. Blood concentrations of nonesterified fatty acids, ß-hydroxybutyrate, total calcium, and haptoglobin were determined in a subgroup of cows (n=459) at -11±3, -4±3, 0, 3±1, 7±1, 14±1, and 28±1 DIM. The overall sensitivity of HIS was 55% for all cases of metritis (n=349), but it was greater for cows with metritis and another disorder (78%) than for cows with metritis only (53%). Cows diagnosed with metritis and flagged based on HIS had substantial alterations in their rumination, activity, and HIS patterns around CD, alterations of blood markers of metabolic and health status around calving, reduced milk production, and were more likely to exit the herd than cows not flagged based on the HIS and cows without disease, suggesting that cows flagged based on the HIS had a more severe episode of metritis. Including all disorders of interest for this study, the overall sensitivity was 59%, specificity was 98%, positive predictive value was 58%, negative predictive value was 98%, and accuracy was 96%. The AHMS was effective for identifying cows with severe cases of metritis, but less effective for identifying cows with mild cases of metritis. Also, the overall accuracy and timing of the AHMS alerts for cows with health disorders indicated that AHMS that combine rumination and activity could be a useful tool for identifying cows with metabolic and digestive disorders, and more severe cases of mastitis and metritis.

Use of rumination and activity monitoring for the identification of dairy cows with health disorders: Part I. Metabolic and digestive disorders.

The objectives of this study were to evaluate (1) the performance of an automated health-monitoring system (AHMS) to identify cows with metabolic and digestive disorders-including displaced abomasum, ketosis, and indigestion-based on an alert system (health index score, HIS) that combines rumination time and physical activity; (2) the number of days between the first HIS alert and clinical diagnosis (CD) of the disorders by farm personnel; and (3) the daily rumination time, physical activity, and HIS patterns around CD. Holstein cattle (n=1,121; 451 nulliparous and 670 multiparous) were fitted with a neck-mounted electronic rumination and activity monitoring tag (HR Tags, SCR Dairy, Netanya, Israel) from at least -21 to 80 d in milk (DIM). Raw data collected in 2-h periods were summarized per 24 h as daily rumination and activity. A HIS (0 to 100 arbitrary units) was calculated daily for individual cows with an algorithm that used rumination and activity. A positive HIS outcome was defined as a HIS of <86 during at least 1 d from -5 to 2 d after CD. Blood concentrations of nonesterified fatty acids, ß-hydroxybutyrate, total calcium, and haptoglobin were determined in a subgroup of cows (n=459) at -11±3, -4±3, 0, 3±1, 7±1, 14±1, and 28±1 DIM. The sensitivity of the HIS was 98% [95% confidence interval (CI): 93, 100] for displaced abomasum (n=41); 91% (95% CI: 83, 99) for ketosis (n=54); 89% (95% CI: 68, 100) for indigestion (n=9); and 93% (95% CI: 89, 98) for all metabolic and digestive disorders combined (n=104). Days (mean and 95% CI) from the first positive HIS <86 and CD were -3 (-3.7, -2.3), -1.6 (-2.3, -1.0), -0.5 (-1.5, 0.5), and -2.1 (-2.5, -1.6) for displaced abomasum, ketosis, indigestion, and all metabolic and digestive disorders, respectively. The patterns of rumination, activity, and HIS for cows flagged by the AHMS were characterized by lower levels than for cows without a health disorder and cows not flagged by the AHMS from -5 to 5 d after CD, depending on the disorder and parameter. Differences between cows without health disorders and those flagged by the AHMS for blood markers of metabolic and health status confirmed the observations of the CD and AHMS alerts. The overall sensitivity and timing of the AHMS alerts for cows with metabolic and digestive disorders indicated that AHMS that combine rumination and activity could be a useful tool for identifying cows with metabolic and digestive disorders.

Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region.

Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.

Disclosing the origin and diversity of Omani cattle.

Among all livestock species, cattle have a prominent status as they have contributed greatly to the economy, nutrition and culture from the beginning of farming societies until the present time. The origins and diversity of local cattle breeds have been widely assessed. However, there are still some regions for which very little of their local genetic resources is known. The present work aimed to estimate the genetic diversity and the origins of Omani cattle. Located in the south-eastern corner of the Arabian Peninsula, close to the Near East, East Africa and the Indian subcontinent, the Sultanate of Oman occupies a key position, which may enable understanding cattle dispersal around the Indian Ocean. To disclose the origin of this cattle population, we used a set of 11 polymorphic microsatellites and 113 samples representing the European, African and Indian ancestry to compare with cattle from Oman. This study found a very heterogenic population with a markedly Bos indicus ancestry and with some degree of admixture with Bos taurus of African and Near East origin.