Comparison of Conformation and Movement Characteristics in Dressage and Jumping Sport Warmblood Mares Based on Point Evaluation and Linear Scoring System.

The aim of this study was to analyze the influence of factors on the results of 100-point judging systems, linear scoring and basic measurements, as well as differences between systems for dressage and jumping warmblood mares. The research covered official data on 1547 warmblood mares. Analysis of variance and phenotypic correlations (Pearson and partial) were used. The analysis showed that sport type significantly influenced 1/3 of biometric measurements, 2/9 traits on the 100-point system and 7/37 of linear scored traits. The influence of horse type evaluation is more significant in linear scoring than in the 100-point evaluation, which provides an argument for using the first system in breeding. In the linear evaluation for warmblood mares grouped as jumping or dressage, the most significant differences (p < 0.001) were noted between the traits of shoulder position, line of the loins and shape of the croup. In the point-based evaluation, differences (p < 0.05) were found in forelimbs and walking, as well as chest circumference in basic measurements. None of the traits in the two evaluation systems is identical to any other (r > 0.8). The comparison of systems showed meaningful correlations only between general traits. The differences between sport types of warmblood mares were smaller than expected. More objective traits should be discovered to increase accuracy in discriminating between horse types.

Some Genetic and Environmental Effects on Equine Asthma in Polish Konik Horses.

Current knowledge of the genetic and environmental backgrounds of equine asthma seems to be insufficient, especially for primitive horse breeds. The main objectives of this study were to estimate the effects of sex, birth period, stud, parentage line and inbreeding on asthma morbidity in Polish Konik horses. Records of 274 horses (housed in two studs) were analysed. These animals were allocated to maternal and paternal lines. Individual inbreeding coefficients were extracted from the additive relationship matrix. Horses underwent diagnosis based on observation of the basic symptoms (high frequency of coughing and excessive nasal discharge). Subsequently, some horses (28 individuals) were clinically examined to confirm the earlier observations. Generally, no significant effects of parentage line on heaves morbidity were identified by the use of logistic regression, although the Pearson's chi-squared test had shown that individuals of some maternal and paternal lines had a predisposition to severe equine asthma. It was concluded that the individual inbreeding level is not associated with the incidence of EA, but a significant effect of the maternal inbreeding coefficient may be observed. It was also found that there is some variability in the incidence of this disease between studs.

Genetic Background of the Polish Primitive Horse (Konik) Coat Color Variation-New Insight into Dun Dilution Phenotypic Effect.

Only the blue dun coat color, produced by the action of the dun allele on the background of a black base coat, is officially permitted in the Polish primitive horse (PPH, Konik) breed, yet the population is not visually homogenous and various coat color shades occur. Herein, the molecular background of PPH coat color was studied based on genotyping of known causative variants in equine coat color-related genes (ASIP, MC1R, TBX3, SLC36A1, SLC45A2, PMEL17, and RALY). Additionally, screening for the new polymorphisms was conducted for the ASIP gene coding sequence and the TBX3 1.6-kb insert (associated with the dun dilution). We did not observe the champagne, silver, or cream color dilution variants in the PPH breed. A significant association (P < 0.01) was recorded for the genotype in TBX3 gene 1.6 kb in/del and the degree of dun coat dilution, demonstrating that the dominant action of the dun mutation is not fully penetrant. In addition to the effect of the 1.6 kb in/del zygosity, variants within the TBX3 insert were significantly associated with PPH coat color variability (P < 0.01), suggesting the presence of an additional allele at this locus. Finally, we identified a high frequency (35%) of genetically bay dun-colored PPH individuals that are officially recorded as blue (black base coat) duns. We propose that the difficulty in distinguishing these 2 phenotypes visually is due to an independent locus upstream of the ASIP gene, which was recently described as darkening the typical bay pigmentation shade.

Genes encoding equine ß-lactoglobulin (LGB1 and LGB2): Polymorphism, expression, and impact on milk composition.

ß-lactoglobulin is one of the most abundant milk whey proteins in many mammal species, including the domestic horse. The aim of this study was to screen for polymorphism in the equine LGB1 and LGB2 gene sequences (all exons, introns, and 5'-flanking region) and to assess potential relationship of particular genotypes with gene expression levels (measured in milk somatic cells) and milk composition traits (protein, fat, lactose, and total ß-lactoglobulin content). Direct DNA sequencing analysis was performed for twelve horse breeds: Polish Primitive Horse (PPH), Polish Coldblood Horse (PCH), Polish Warmblood Horse (PWH), Silesian, Hucul, Fjording, Haflinger, Shetland Pony, Welsh Pony, Arabian, Thoroughbred, and Percheron-and revealed the presence of 83 polymorphic sites (47 and 36 for LGB1 and LGB2 genes, respectively), including eight that were previously unknown. Association analysis of the selected polymorphisms, gene expression, and milk composition traits (conducted for the PPH, PCH, and PWH breeds) showed several statistically significant relationships; for example, the two linked LGB1 SNPs (rs1143515669 and rs1144647991) were associated with total milk protein content (p < 0.01). Our study also confirmed that horse breed had significant impact on both gene transcript levels (p < 0.01) and on milk LGB content (p < 0.05), whereas an influence of lactation period was seen only for gene relative mRNA abundances (p < 0.01).

Effects of a novel missense polymorphism within the SIGLEC5 gene on fertility traits in Holstein-Friesian cattle.

The aim of the study was to find functional polymorphism within two exons of the SIGLEC5 (sialic acid-binding Ig-like lectin-5) gene and to examine its effects on the production and fertility traits of cows and bulls. Two hundred seventytwo Holstein-Friesian cows and 574 bulls were included in the study. Novel missense polymorphism (A > G) within exon 3 causing substitution of amino acid arginine by glutamate in position 260 of SIGLEC5 protein (R260Q) was identified by sequencing and digestion by restriction enzyme Msp I. Basic production and fertility traits of cows and estimated breeding values (EBV) of bulls were analysed. The study demonstrated a significant association of SIGLEC5 R260Q polymorphism with days open and calving interval in cows as well as with breeding value for calving interval in bulls. An opposite effect of SIGLEC5 alleles for production and fertility traits was observed: the allele G increased the breeding value for the protein yield, while the allele A increased the breeding value for the calving interval. The current study suggests the involvement of SIGLEC5 R260Q polymorphism in biological processes related to fertility traits. This finding can be applied as a biomarker for a genetic improvement programme in Holstein-Friesian cattle.

5'-flanking variants of equine casein genes (CSN1S1, CSN1S2, CSN2, CSN3) and their relationship with gene expression and milk composition.

Genes encoding casein proteins are important candidates for milk composition traits in mammals. In the case of the domestic horse, our knowledge of casein genes is limited mainly to coding sequence variants. This study involved screening for polymorphism in 5'-flanking regions of four genes encoding equine caseins (CSN1S1, CSN1S2, CSN2, and CSN3) and making a preliminary assessment of their effect on the gene expression (on the mRNA and protein levels) and milk composition traits in selected horse breeds. Altogether, 23 polymorphisms (21 described previously SNPs and two novel InDels) were found in the studied sequences, the majority of which are common in various horse breeds. Statistical analysis revealed that some are putatively associated with gene expression or milk composition - for example, the c.-2047_-2048insAT polymorphism (CSN1S1) turns out to be related to the total milk protein content in Polish Primitive Horse (p < 0.05), whereas c.-2105C>G SNP (CSN2) is related to beta-casein relative mRNA level and milk lactose concentration in the Polish Coldblood Horse breed (p < 0.05). We have also found significant effects of horse breed and lactation time-point on gene expression and mare's milk composition. Our study indicates that the 5'-regulatory regions of genes encoding casein proteins are interesting targets for functional studies of their expression and the composition traits of mare's milk.

Identification of genome regions determining semen quality in Holstein-Friesian bulls using information theory.

Use of information theory can be an alternative statistical approach to detect genome regions and candidate genes that are associated with livestock traits. The aim of this study was to verify the validity of the SNPs effects on some semen quality variables of bulls using entropy analysis. Records from 288 Holstein-Friesian bulls from one AI station were included. The following semen quality variables were analyzed: CASA kinematic variables of sperm (total motility, average path velocity, straight line velocity, curvilinear velocity, amplitude of lateral head displacement, beat cross frequency, straightness, linearity), sperm membrane integrity (plazmolema, mitochondrial function), sperm ATP content. Molecular data included 48,192 SNPs. After filtering (call rate = 0.95 and MAF = 0.05), 34,794 SNPs were included in the entropy analysis. The entropy and conditional entropy were estimated for each SNP. Conditional entropy quantifies the remaining uncertainty about values of the variable with the knowledge of SNP. The most informative SNPs for each variable were determined. The computations were performed using the R statistical package. A majority of the loci had relatively small contributions. The most informative SNPs for all variables were mainly located on chromosomes: 3, 4, 5 and 16. The results from the study indicate that important genome regions and candidate genes that determine semen quality variables in bulls are located on a number of chromosomes. Some detected clusters of SNPs were located in RNA (U6 and 5S_rRNA) for all the variables for which analysis occurred. Associations between PARK2 as well GALNT13 genes and some semen characteristics were also detected.

Characterization of the Polish Primitive Horse (Konik) maternal lines using mitochondrial D-loop sequence variation.

The Polish Primitive Horse (PPH, Konik) is a Polish native horse breed managed through a conservation program mainly due to its characteristic phenotype of a primitive horse. One of the most important goals of PPH breeding strategy is the preservation and equal development of all existing maternal lines. However, until now there was no investigation into the real genetic diversity of 16 recognized PPH dam lines using mtDNA sequence variation. Herein, we describe the phylogenetic relationships between the PPH maternal lines based upon partial mtDNA D-loop sequencing of 173 individuals. Altogether, 19 mtDNA haplotypes were detected in the PPH population. Five haplotypes were putatively novel while the remaining 14 showed the 100% homology with sequences deposited in the GenBank database, represented by both modern and primitive horse breeds. Generally, comparisons found the haplotypes conformed to 10 different recognized mtDNA haplogroups (A, B, E, G, J, M, N, P, Q and R). A multi-breed analysis has indicated the phylogenetic similarity of PPH and other indigenous horse breeds derived from various geographical regions (e.g., Iberian Peninsula, Eastern Europe and Siberia) which may support the hypothesis that within the PPH breed numerous ancestral haplotypes (found all over the world) are still present. Only in the case of five maternal lines (Bona, Dzina I, Geneza, Popielica and Zaza) was the segregation of one specific mtDNA haplotype observed. The 11 remaining lines showed a higher degree of mtDNA haplotype variability (2-5 haplotypes segregating in each line). This study has revealed relatively high maternal genetic diversity in the small, indigenous PPH breed (19 haplotypes, overall HapD = 0.92). However, only some traditionally distinguished maternal lines can be treated as genetically pure. The rest show evidence of numerous mistakes recorded in the official PPH pedigrees. This study has proved the importance of maternal genetic diversity monitoring based upon the application of molecular mtDNA markers and can be useful for proper management of the PPH conservation program in the future.

Variability of lysozyme and lactoferrin bioactive protein concentrations in equine milk in relation to LYZ and LTF gene polymorphisms and expression.

BACKGROUND: Equine milk is considered to be an interesting product for human nutrition, mainly owing to its low allergenicity and significant amounts of bioactive proteins, including lysozyme (LYZ) and lactoferrin (LTF). The present study assessed the effect of genetic factors on LYZ and LTF concentration variability in mare's milk. RESULTS: Significant effects of horse breed and lactation stage on milk LYZ and LTF contents were observed. The highest level of LTF and the lowest concentration of LYZ were recorded for the Polish Warmblood Horse breed. The highest amounts of both proteins were found for the earliest investigated time point of lactation (5th week). Altogether 13 (nine novel) polymorphisms were found in the 5'-flanking regions of both genes, but they showed no significant relationship with milk LYZ and LTF contents. Several associations were found between selected SNPs and the LYZ gene relative transcript level. CONCLUSION: While the present study indicated the existence of intra- and interbreed variability of LYZ and LTF contents in mare's milk, this variation is rather unrelated to the 5'-flanking variants of genes encoding both proteins. This study is a good introduction for broader investigations focused on the genetic background for variability of bioactive protein contents in mare's milk. © 2016 Society of Chemical Industry.

Characterization of equine CSN1S2 variants considering genetics, transcriptomics, and proteomics.

Currently, research interest is increasing in horse milk composition and its effect on human health. Despite previously published studies describing the presence of intra- and interbreed variability of equine milk components, no investigations have focused on the genetic background of this variation. Among horse caseins and the genes encoding them, least is known about the structure and expression of the α-S2 casein gene, CSN1S2. Herein, based on direct sequencing of the equine CSN1S2 coding sequence, we describe the presence of 51-bp insertion-deletion (in/del) polymorphism, which significantly changes the protein sequence (lack or presence of 17-amino acid serine-rich peptide). Bioinformatic analysis revealed that the observed in/del polymorphism spanned exactly 2 exons; therefore, we hypothesized that we were observing different CSN1S2 splicing isoforms. However, further investigation indicated that the detected sequence variation was caused by a large (1.3-kb) deletion in the genomic DNA. We found that the polymorphic forms (A, longer; B, shorter; KP658381 and KP658382 GenBank records, respectively) were unevenly distributed among different horse breeds (the highest frequency of variant B was observed in coldblood horses and Haflingers). We propose that the analyzed polymorphism is associated with CSN1S2 expression level (the highest expression was recorded for individuals carrying the BB genotype), which was much more pronounced for milk CSN1S2 protein content than for relative transcript abundance (measured in milk somatic cells). Our results provide insight into the equine CSN1S2 structure and lay a foundation for further functional analyses regarding, for example, allergenicity or physiochemical properties of the observed CSN1S2 variants.

Inbreeding and Offspring Sex Ratio in the Pygmy Hippopotamus (Cheoropsis liberiensis) Population Kept in Zoological Gardens.

The aim of this study was to estimate the inbreeding level and its impact on offspring sex ratio in the pygmy hippopotamus population kept in zoological gardens. Records of pygmy hippopotamus born between 1873-2013 were extracted from the international studbook. Totally, 1357 individuals originating from 148 breeding units were included (individuals with unknown sex were omitted). The offspring sex ratio is defined as the number of sons to the total number of progeny of each dam and sire. Spearman's rank correlation was employed to examine the relationships between the inbreeding level and offspring sex ratio. Inbreeding coefficients and individual increase in inbreeding coefficients (included as a linear co-variable) were examined as well as the geographic region and birth period using general linear models. The average inbreeding coefficient was 5.39%. The following sex proportion was observed for the inbred population: 57% and 43% for females and males, respectively. A significant relationship between inbreeding level of parents and their offspring sex ratio were estimated for European zoological gardens, whereas in others geographic regions the dependencies were insignificant.