Effects of steam-flaked grains on foals' growth and faecal microbiota.

BACKGROUND: There is little objective information concerning the effect of steam-flaked grains on foal's growth performance and faecal microbiota. To determine the effects of steam-flaked grains on foal's growth performance and faecal microbiota, faecal samples were collection from 18 foals which had been fed either corn, oat or barley diets over the 60 days of the experiment. Body weight and conformation measurements were collected. Next-generation sequencing of the V3 + V4 region of the 16 S rRNA gene was used to assess the microbial composition of faeces. Alpha diversity, Venn graph, Relative abundance and beta diversity are presented. RESULTS: There was a significantly higher larger increase in the body weight of those foals fed barley compared to either corn or oats. There were also significant changes in the Alpha diversity of the gut microbiota. The Shannon and Simpson indices were significantly higher in the barley fed group than those fed corn or oats. The Chao1 index was significantly higher in the oat fed group than the corn or barley fed groups. There were significant changes in the relative abundance of bacteria in the microbiota in terms of phylum, family and genus. The histogram of LDA value distribution showed that the 12 statistically different biomarkers of the bacteria were present. Tax4Fun function annotation clustering heat map showed that functional information was detected from 26 species of bacteria in faecal samples from the foals. CONCLUSIONS: Differences by starch sources were found in overall growth of the foals and in the faecal microbiota if either supplementary corn, oat or barley was fed. Further studies are required to determine the potential impact of the changes in the microbiota on the health and development of foals fed cereal starch of different sources.

Research article expression of surfactant protein-A and D, and CD9 in lungs of 1 and 30 day old foals.

BACKGROUND: Respiratory diseases are a major cause of morbidity and mortality in the horses of all ages including foals. There is limited understanding of the expression of immune molecules such as tetraspanins and surfactant proteins (SP) and the regulation of the immune responses in the lungs of the foals. Therefore, the expression of CD9, SP-A and SP-D in foal lungs was examined. RESULTS: Lungs from one day old (n = 6) and 30 days old (n = 5) foals were examined for the expression of CD9, SP-A, and SP-D with immunohistology and Western blots. Western blot data showed significant increase in the amount of CD9 protein (p = 0.0397) but not of SP-A and SP-D at 30 days of age compared to one day. Immunohistology detected CD9 in the alveolar septa and vascular endothelium but not the bronchiolar epithelium in the lungs of the foals in both age groups. SP-A and SP-D expression was localized throughout the alveolar septa including type II alveolar epithelial cells and the vascular endothelium of the lungs in all the foals. Compared to one day old foals, the expression of SP-A and SP-D appeared to be increased in the bronchiolar epithelium of 30 day old foals. Pulmonary intravascular macrophages were also positive for SP-A and SP-D in 30 days old foals and these cells are not developed in the day old foals. CONCLUSIONS: This is the first data on the expression of CD9, SP-A and SP-D in the lungs of foals.

SNPs analysis of height traits in Ningqiang pony.

Ningqiang pony is one of the five pony breeds in China and is listed as a rare species. It is, therefore, meaningful to conduct stature research on this breed for its efficient reproduction, utilization and protection. This study is based on four SNP variants of adjacent LCORL/NCAPG, HMGA2, ZFAT and LASP1 genes, which have been found to be associated with horse height, and then, the 4 SNP loci in 22 Ningqiang ponies were analyzed. The results showed that there were genetic variations at the four loci in Ningqiang pony, there was a SNP on LCORL/NCAPG, HMGA2 and ZFAT gene all including T allele and C allele and LASP1 including A allele and G allele. Further data analysis revealed that LCORL/NCAPG variant harbor the allele T and LASP1 variant harbor the allele G were significantly related to body height (p < 0.05). These findings suggested that the two SNP mutations within the LCORL/NCAPG and LASP1 genes could be considered as a screening marker for the body height of Ningqiang pony and could provide a new strategy for breeding and protect the rare germplasm resources.

Estrogens Regulate Placental Angiogenesis in Horses.

A sufficient vascular network within the feto-maternal interface is necessary for placental function. Several pregnancy abnormalities have been associated with abnormal vascular formations in the placenta. We hypothesized that growth and expansion of the placental vascular network in the equine (Equus caballus) placenta is regulated by estrogens (estrogen family hormones), a hormone with a high circulating concentration during equine gestation. Administration of letrozole, a potent and specific inhibitor of aromatase, during the first trimester (D30 to D118), decreased circulatory estrone sulfate concentrations, increased circulatory testosterone and androstenedione concentrations, and tended to reduce the weight of the fetus (p < 0.1). Moreover, the gene expression of CYP17A1 was increased, and the expression of androgen receptor was decreased in the D120 chorioallantois (CA) of letrozole-treated mares in comparison to that of the control mares. We also found that at D120, the number of vessels tended to decrease in the CAs with letrozole treatment (p = 0.07). In addition, expression of a subset of angiogenic genes, such as ANGPT1, VEGF, and NOS2, were altered in the CAs of letrozole-treated mares. We further demonstrated that 17ß-estradiol increases the expression of ANGPT1 and VEGF and increases the angiogenic activity of equine endothelial cells in vitro. Our results from the estrogen-suppressed group demonstrated an impaired placental vascular network, suggesting an estrogen-dependent vasculogenesis in the equine CA during the first trimester.

Analysis of the miRNA transcriptome during testicular development and spermatogenesis of the Mongolian horse.

Numerous studies have shown that microRNAs (miRNAs) are essential for testicular development and spermatogenesis. In order to further characterise these physiological processes, three immature and three mature testes of the Mongolian horse were collected and six libraries were established. Using small RNA sequencing technology, 531 mature miRNAs were identified, including 46 novel miRNAs without previously ascribed functions. Among the 531 miRNAs, 421 were expressed in both immature and mature libraries, 65 miRNAs were found solely in immature testis libraries and 45 miRNAs were found solely in mature testis libraries. Furthermore, among the miRNAs that were identified in both immature and mature libraries, 107 were significantly differentially expressed (corrected P value (padj)<0.05). Among the miRNAs that were only expressed in immature testes, two miRNAs were differentially expressed, whereas among the miRNAs that were only expressed in mature testes, nine miRNAs were differentially expressed. Comprehensive analysis of miRNA and mRNA expression profiles predicted 107 miRNA-mRNA interaction sites. Gene ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis of the predicted target genes suggested roles of the differentially expressed miRNAs in testicular development and spermatogenesis. These findings identify miRNAs as key factors in the development of the testes and spermatogenesis in the Mongolian horse, which may also help us to understand the mechanisms of fertility in related mammalian species.

The impact of artificial selection on morphological integration in the appendicular skeleton of domestic horses.

The relationships between the different component parts of organisms, such as the sharing of common development or function, produce a coordinated variation between the different traits. This morphological integration contributes to drive or constrain morphological variation and thus impacts phenotypic diversification. Artificial selection is known to contribute significantly to phenotypic diversification of domestic species. However, little attention has been paid to its potential impact on integration patterns. This study explores the patterns of integration in the limb bones of different horse breeds, using 3D geometric morphometrics. The domestic horse is known to have been strongly impacted by artificial selection, and was often selected for functional traits. Our results confirm that morphological integration among bones within the same limb is strong and apparently partly produced by functional factors. Most importantly, they reveal that artificial selection, which led to the diversification of domestic horses, impacts covariation patterns. The influence of selection on the patterns of covariation varies along the limbs and modulates bone shape, likely due to a differential ligament or muscle development. These results highlight that, in addition to not being constrained by a strong morphological integration, artificial selection has modulated the covariation patterns according to the locomotor specificities of the breeds. More broadly, it illustrates the interest in studying how micro-evolutionary processes impact covariation patterns and consequently contribute to morphological diversification of domestic species.

Effect of linseed supplementation and slaughter age on meat quality of grazing cross-bred Galician x Burguete foals.

BACKGROUND: The aim of this study was to assess the effect of finishing diet (control concentrate vs. linseed concentrate) and slaughter age (13 vs. 26 months) on meat and nutritional quality of foal meat. For this study, 46 foals from crossing Galicia Mountain x Burguete breeds were used. RESULTS: The obtained results showed that slaughter age had an influence on chemical composition and colour parameters. Foals slaughtered at the age of 13 months had lower content of intramuscular fat and higher cholesterol contents than those slaughtered at 26 months of age. Regarding colour parameters, older foals showed the highest values of redness and lowest myoglobin contents. Finishing diet had a low effect on the majority of parameters evaluated. Foals fed with linseed presented lower shear force values than those fed with control concentrate. Fatty acid and amino acid contents were hardly influenced by finishing diet, whereas slaughter age effect had a high impact on fatty acid profile. Older animals showed lowest SFA values and n-6/n-3 ratio. CONCLUSION: Older animals presented the best meat quality. Diet had low effect in meat quality and could be related to the short time during finishing diet was administered and the low amount of linseed in the experimental diet. © 2017 Society of Chemical Industry.

Whole-genome sequencing reveals a potential causal mutation for dwarfism in the Miniature Shetland pony.

The Miniature Shetland pony represents a horse breed with an extremely small body size. Clinical examination of a dwarf Miniature Shetland pony revealed a lowered size at the withers, malformed skull and brachygnathia superior. Computed tomography (CT) showed a shortened maxilla and a cleft of the hard and soft palate which protruded into the nasal passage leading to breathing difficulties. Pathological examination confirmed these findings but did not reveal histopathological signs of premature ossification in limbs or cranial sutures. Whole-genome sequencing of this dwarf Miniature Shetland pony and comparative sequence analysis using 26 reference equids from NCBI Sequence Read Archive revealed three probably damaging missense variants which could be exclusively found in the affected foal. Validation of these three missense mutations in 159 control horses from different horse breeds and five donkeys revealed only the aggrecan (ACAN)-associated g.94370258G>C variant as homozygous wild-type in all control samples. The dwarf Miniature Shetland pony had the homozygous mutant genotype C/C of the ACAN:g.94370258G>C variant and the normal parents were heterozygous G/C. An unaffected full sib and 3/5 unaffected half-sibs were heterozygous G/C for the ACAN:g.94370258G>C variant. In summary, we could demonstrate a dwarf phenotype in a miniature pony breed perfectly associated with a missense mutation within the ACAN gene.

Seasonal fluctuations in body weight during growth of Thoroughbred racehorses during their athletic career.

BACKGROUND: Domesticated horses adapt to environmental conditions through seasonal fluctuations in their metabolic rate. The seasonal change of metabolic rates of domesticated horses in pastures is documented. However, there are few investigations on seasonal body weight change of domesticated horses housed in stables, which are provided constant energy intake throughout the year. Both seasonal changes and gain in body weight of racehorses during their athletic career is known to a lesser extent because their body weight are not measured in most countries. Here, we used a seasonal-trend decomposition method to conduct a time series analysis of body weight of Thoroughbred racehorses participating in flat races held by the Japan Racing Association from 1 January 2002 to 31 December 2014. RESULTS: We acquired 640,431 body weight measurements for race starts and included 632,540 of these in the time series analysis. Based on seasonal component analysis, the body weight of male and gelding horses peaked in autumn and winter and reached its nadir in summer. In contrast, the body weight of female horses peaked in autumn and reached the nadir in spring. Based on trend component analysis, most of the increase in body weight was observed when all sexes approached 5 years of age. The slope of the body weight gain was smaller after that, and an approximately 30 kg gain was observed during their careers. CONCLUSION: These results indicate that the body weight of a Thoroughbred racehorse fluctuates seasonally, and that there may be sex differences in energy balance mechanisms. Moreover, the present results suggest that the physiological development of Thoroughbred racehorses is completed just before they reach 5 years of age.

Routine Trimming and Therapeutic Farriery in Foals.

Hoof care in the first few months of life is serious business and should never be taken lightly. Farriery plays a vital role in both the development of the hoof and the conformation of the limb. Management of the feet and limbs during this period will often dictate the success of the foal as a sales yearling or mature sound athlete. A sound foot care program is time-consuming, whereas assembly-line trimming is quick and easy, but the former is much more beneficial.

Nutritional ecology of obesity: from humans to companion animals.

We apply nutritional geometry, a framework for modelling the interactive effects of nutrients on animals, to help understand the role of modern environments in the obesity pandemic. Evidence suggests that humans regulate the intake of protein energy (PE) more strongly than non-protein energy (nPE), and consequently will over- and under-ingest nPE on diets with low or high PE, respectively. This pattern of macronutrient regulation has led to the protein leverage hypothesis, which proposes that the rise in obesity has been caused partly by a shift towards diets with reduced PE:nPE ratios relative to the set point for protein regulation. We discuss potential causes of this mismatch, including environmentally induced reductions in the protein density of the human diet and factors that might increase the regulatory set point for protein and hence exacerbate protein leverage. Economics--the high price of protein compared with fats and carbohydrates--is one factor that might contribute to the reduction of dietary protein concentrations. The possibility that rising atmospheric CO2 levels could also play a role through reducing the PE:nPE ratios in plants and animals in the human food chain is discussed. Factors that reduce protein efficiency, for example by increasing the use of ingested amino acids in energy metabolism (hepatic gluconeogenesis), are highlighted as potential drivers of increased set points for protein regulation. We recommend that a similar approach is taken to understand the rise of obesity in other species, and identify some key gaps in the understanding of nutrient regulation in companion animals.

Central corneal thickness measurements and ultrasonographic study of the growing equine eye.

OBJECTIVE: The aim of this study was to determine the central corneal thickness (CCT) of healthy equine eyes with high-frequency ultrasound (HF) and ultrasound biomicroscopy (UBM) and to measure the axial dimensions with B-mode ultrasound. Additionally, the influence of the age on the measured dimensions of the globe was analyzed. ANIMALS STUDIED: Fifty warm blood horses (mean age 23.0 ± 21.12 months) were divided into 3 age groups (group 1: 0-6 months; group 2: ≥7-30 months; and group 3: ≥31-78 months). PROCEDURE: Corneal measurements were performed with a 22-MHz and a 50-MHz transducer. Crystalline lens thickness (CLT), vitreous chamber depth (VCD), and axial globe length (AGL) were measured at a frequency of 10 MHz. Anterior chamber depth (ACD) was calculated. The eyes were measured under general anesthesia nonrelated to this study. RESULTS: The mean CCT of 50 eyes was 818 ± 41 µm. The mean values ± SD in mm for axial dimensions were AGL 34.7 ± 2.7, ACD 3.4 ± 0.7, CLT 10.0 ± 0.9, and VCD of 20.4 ± 1.5. A positive correlation with increasing age was found for all dimensions. No significant differences were found between the gender and the left or right eye. CONCLUSION: HF and UBM are valuable high-resolution imaging tools for CCT measurements in horses. The here-obtained values support previous findings that a positive correlation with increasing age exists for CCT, ACD, CLT, VCD, and AGL in horse.

Assessing the Role of Free-Roaming Horses in a Social-Ecological System.

Management actions concerning free-roaming horses attract controversy in many areas. In the Chilcotin region of British Columbia, Canada, social and cultural values influence debates about management of free-roaming horses and perceptions of their ecological impacts. A dearth of current, empirical research on the role and impacts of horses in local ecosystems results in management decisions being informed largely by studies from other ecoregions and locations, which may not accurately represent local ecological, social, cultural, and economic influences. We initiated the first socio-ecological study of horse sub-populations, their grazing habitat, and past management approaches affecting current conditions in the ?Elegesi Qayuse Wild Horse Preserve in Xeni Gwet'in (Tsilhqot'in) First Nations' territory. This exploratory study used mixed methods including a review of literature and unpublished data, assessment of vegetation in core grazing habitat, and exploration of local ecological and cultural knowledge and perceptions. Plant community composition and abundance in core grazing habitat of the Wild Horse Preserve are consistent with a structurally sound ecosystem. Socio-cultural factors are important for managers to consider in effective decision-making concerning horse populations.

Improving environmental management on small-scale farms: perspectives of extension educators and horse farm operators.

Although the number of small-scale farms is increasing in North America and Europe, few studies have been conducted to better understand environmental management in this sector. We investigate this issue by examining environmental management on horse farms from both the perspective of the "expert" extension educator and horse farm operator. We conducted a Delphi survey and follow-up interviews with extension educators in Indiana and Kentucky. We also conducted interviews and farm assessments with 15 horse farm operators in the two states. Our results suggest a disconnection between the perceptions of extension educators and horse farm operators. Extension educators believed that operators of small horse farms are unfamiliar with conservation practices and their environmental benefits and they found it difficult to target outreach to this audience. In the interviews with horse farm operators, we found that the majority were somewhat familiar with conservation practices like rotational grazing, soil testing, heavy use area protection, and manure composting. It was not common, however, for practices to be implemented to generally recognized standards. The horse farm respondents perceived these practices as interrelated parts of a system of farm management that has developed over time to best deal with the physical features of the property, needs of the horses, and available resources. Because conservation practices must be incorporated into a complex farm management system, traditional models of extension (i.e., diffusion of innovations) may be inappropriate for promoting better environmental management on horse farms.

Cell and matrix modulation in prenatal and postnatal equine growth cartilage, zones of Ranvier and articular cartilage.

Formation of synovial joints includes phenotypic changes of the chondrocytes and the organisation of their extracellular matrix is regulated by different factors and signalling pathways. Increased knowledge of the normal processes involved in joint development may be used to identify similar regulatory mechanisms during pathological conditions in the joint. Samples of the distal radius were collected from prenatal and postnatal equine growth plates, zones of Ranvier and articular cartilage with the aim of identifying Notch signalling components and cells with stem cell-like characteristics and to follow changes in matrix protein localisation during joint development. The localisation of the Notch signalling components Notch1, Delta4, Hes1, Notch dysregulating protein epidermal growth factor-like domain 7 (EGFL7), the stem cell-indicating factor Stro-1 and the matrix molecules cartilage oligomeric matrix protein (COMP), fibromodulin, matrilin-1 and chondroadherin were studied using immunohistochemistry. Spatial changes in protein localisations during cartilage maturation were observed for Notch signalling components and matrix molecules, with increased pericellular localisation indicating new synthesis and involvement of these proteins in the formation of the joint. However, it was not possible to characterise the phenotype of the chondrocytes based on their surrounding matrix during normal chondrogenesis. The zone of Ranvier was identified in all horses and characterised as an area expressing Stro-1, EGFL7 and chondroadherin with an absence of COMP and Notch signalling. Stro-1 was also present in cells close to the perichondrium, in the articular cartilage and in the fetal resting zone, indicating stem cell-like characteristics of these cells. The presence of stem cells in the articular cartilage will be of importance for the repair of damaged cartilage. Perivascular chondrocytes and hypertrophic cells of the cartilage bone interface displayed positive staining for EGFL7, which is a novel finding and suggests a role of EGFL7 in the vascular infiltration of growth cartilage.

The influence of nutrition on the insulin-like growth factor system and the concentrations of growth hormone, glucose, insulin, gonadotropins and progesterone in ovarian follicular fluid and plasma from adult female horses (Equus caballus).

BACKGROUND: Feed intake affects the GH-IGF system and may be a key factor in determining the ovarian follicular growth rate. In fat mares, the plasma IGF-1 concentration is high with low GH and a quick follicular growth rate, in contrast to values observed in thin mares. Nothing is known regarding the long-term effects of differential feed intake on the IGF system. The objective of this experiment was to quantify IGFs, IGFBPs, GH, glucose, insulin, gonadotropin and progesterone (P4) in blood and in preovulatory follicular fluid (FF) in relation to feeding levels in mares. METHODS: Three years prior to the experiment, Welsh Pony mares were assigned to a restricted diet group (R, n = 10) or a well-fed group (WF, n = 9). All mares were in good health and exhibited differences in body weight and subcutaneous fat thickness. Follicular development was scanned daily and plasma was also collected daily. Preovulatory FF was collected by ultrasound-guided follicular aspiration. Hormone levels were assayed in FF and plasma with a validated RIA. RESULTS: According to scans, the total number of follicles in group R was 53% lower than group WF. Insulin and IGF-1 concentrations were higher in WF than in R mares. GH and IGF-2 concentrations were lower in plasma from WF mares than from R mares, but the difference was not significant in FF. The IGFBP-2/IGFBP-3 ratio in FF was not affected by feeding but was dramatically increased in R mare plasma. No difference in gonadotropin concentration was found with the exception of FSH, which was higher in the plasma of R mares. On the day of puncture, P4 concentrations were not affected by feeding but were higher in preovulatory FF than in plasma. CONCLUSIONS: The bioavailability of IGF-1 or IGF-2, represented by the IGFBP2/IGFBP3 ratio, is modified by feed intake in plasma but not in FF. These differences partially explain the variability in follicular growth observed between well-fed mares and mares on restricted diets.

No effect of moderate or high concentrate allowance on growth parameters in weanling Warmblood foals fed late-cut haylage as forage.

Two groups of Warmblood foals from the Bavarian federal stud participated in the study beginning from the age of approximately 6 months. The foals were offered a late 1st cut of haylage, oats and foal starter feed. For 2 months after weaning, group 'R' (15 foals) received an amount of oats to provide a total digestible energy supply meeting the recommendations of the German Society of Nutrition Physiology (GfE), whereas the other group 'A' (16 foals) was offered a higher amount of oats (surplus of approximately 1.3 kg/animal/day). Concentrates were fed individually twice daily; total daily haylage intake of all foals together was recorded. In both groups, individual concentrate intake, body weight (BW), body condition score (BCS) and several growth parameters were documented. Both groups showed an absolutely parallel development of the measured growth parameters and of BW and BCS. BW and BCS increased above the recommendations of GfE and Hois. The amount of concentrates offered was not ingested completely in both groups. The average metabolisable energy (ME) intake from concentrates amounted to 30.3 and 32.1 MJ ME/animal/day (group 'R') and 38.7 and 38.2 MJ ME/animal/day (group 'A') for the 7th and 8th month respectively. The mean haylage intake of all foals together equalled 26.2 MJ ME/animal/day. The parallel development of all documented growth parameters in both groups leads to the assumption that higher concentrate intake must have caused lower intake of haylage and vice versa, thus resulting in an overall comparable energy intake for each foal, independently of energy source. The calculated average daily energy intake for all foals together amounted to 60.5 and 61.4 MJ ME/animal for the 7th and 8th month. The mean crude protein intake in both groups together amounted to 640 and 647 g/animal/day for the 7th and 8th month.

Effects of different winter paddock management of Thoroughbred weanlings and yearlings in the cold region of Japan on physiological function, endocrine function and growth.

Effects of different winter paddock management of Thoroughbred weanlings and yearlings in Hokkaido, Japan, which is extremely cold in winter, on physiological function, endocrine function and growth were investigated. They were divided into two groups; those kept outdoors for 22 hr in the paddock (22hr group) and those kept outdoors for 7 hr in daytime with walking exercise for 1 hr using the horse-walker (7hr+W group), and the changes in daily distance travelled, body temperature (BT), heart rate (HR), HR variability (HRV), endocrine function and growth parameters were compared between the two groups from November at the year of birth to January at 1 year of age. The 7hr+W group could travel almost the same distance as the 22hr group by using the horse-walker. The 22hr group had a lower rate of increase in body weight than the 7hr+W group in January. In addition, lower in BT and HR were observed, and HRV analysis showed an increase in high frequency power spectral density, indicating that parasympathetic nervous activity was dominant. And also, changes in circulating cortisol and thyroxine were not observed despite cold environment. On the other hand, the 7hr+W group had higher prolactin and insulin like growth factor than the 22hr group in January, and cortisol and thyroxine were also increased. Physiological and endocrinological findings from the present study indicate that the management of the 7hr+W group is effective in promoting growth and maintaining metabolism during the winter season.

Investigating age-related differences in muscles of Kazakh horse through transcriptome analysis.

This study conducted transcriptome sequencing on the skeletal muscles of three different anatomical locations across various growth stages to investigate the impact of ages on crucial candidate genes and molecular mechanisms associated with muscle development in Kazakh horses. Sixteen Kazakh horses were selected, and they were divided into four age groups, each with four biological replicates. Tissue samples from the longest dorsal muscle, abdominal muscle, and diaphragm muscle were collected for analysis. The results revealed differential mRNA expression in the longest dorsal muscle between the eight-month group (Group O) and the 10-year group (Group F), with 434 up-regulated and 322 down-regulated genes. In the abdominal muscle, there were 125 up-regulated and 127 down-regulated genes, while in the diaphragm muscle, there were 73 up-regulated and 70 down-regulated genes. In this study, GO enrichment analysis focused on biological processes. KEGG pathway analysis highlighted the Oxidative Phosphorylation pathway for the longest dorsal muscle, annotating 37 differentially expressed genes (DEGs), including ATP5PF, NDUFB8, and ATP5MG, all of which were down-regulated. For the abdominal muscle, the ECM-receptor interaction pathway was enriched, annotating 7 DEGs such as COL4A2, COL4A1, and ITGA5. In the diaphragm muscle, the Hippo signaling pathway was enriched, annotating 6 DEGs, including SERPINE1, RASSF1, and FZD10. This study provides robust data support and a theoretical foundation for a comprehensive understanding of the influence of age on skeletal muscle development in horses.

Analysis of copy number variants by three detection algorithms and their association with body size in horses.

BACKGROUND: Copy number variants (CNVs) have been shown to play an important role in genetic diversity of mammals and in the development of many complex phenotypic traits. The aim of this study was to perform a standard comparative evaluation of CNVs in horses using three different CNV detection programs and to identify genomic regions associated with body size in horses. RESULTS: Analysis was performed using the Illumina Equine SNP50 genotyping beadchip for 854 horses. CNVs were detected by three different algorithms, CNVPartition, PennCNV and QuantiSNP. Comparative analysis revealed 50 CNVs that affected 153 different genes mainly involved in sensory perception, signal transduction and cellular components. Genome-wide association analysis for body size showed highly significant deleted regions on ECA1, ECA8 and ECA9. Homologous regions to the detected CNVs on ECA1 and ECA9 have also been shown to be correlated with human height. CONCLUSIONS: Comparative analysis of CNV detection algorithms was useful to increase the specificity of CNV detection but had certain limitations dependent on the detection tool. GWAS revealed genome-wide associated CNVs for body size in horses.