Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations.

Phenotypic diversity in poultry has been mainly driven by artificial selection and genetic drift. These led to the adaptation to the environment and the development of specific phenotypic traits of chickens in response to their economic use. This study evaluated genetic diversity within and between Russian breeds and populations using Illumina Chicken 60K SNP iSelect BeadChip by analysing genetic differences between populations with Hudson's fixation index (FST statistic) and heterozygosity. We estimated the effect of rare alleles and linkage disequilibrium (LD) on these measurements. To assess the effect of LD on the genetic diversity population, we carried out the LD-based pruning (LD<0.5 and LD<0.1) for seven chicken populations combined (I) or separately (II). LD pruning was specific for different dataset groups. Because of the noticeably large sample size in the Russian White RG population, pruning was substantial for Dataset I, and FST values were only positive when LD<0.1 pruning was applied. For Dataset II, the LD pruning results were confirmed by examining heterozygosity and alleles' frequency distribution. LD between single nucleotide polymorphisms was consistent across the seven chicken populations, except the Russian White RG population with the smallest r2 values and the largest effective population size. Our findings suggest to study variability in each population LD pruning has to be carried separately not after merging to avoid bias in estimates.

Genome-wide association studies of cryostability of semen in roosters.

Conservation of genetic resources by semen cryopreservation is essential for biodiversity conservation and storage of rare poultry breeds. Despite the widespread use of this method not all individuals presentia similar capacity for semen to be used after defrosting. The aim of the current study was to identify SNP markers and linked candidate genes potentially associated with rooster (Gallus gallus) sperm motility after cryopreservation. Genome-wide association studies were performed using 33 roosters from four breeds genotyped using Illumina Chicken 60K SNP BeadChip Calculations were performed using PLINK and EMMAX software. Significant SNP associations rs15557972 (p⟨1.36E-07) on chromosome 10 in the LOXL1 gene and rs15751385 (p⟨6.10E-06) on chromosome 6 in the intron of the ENSGALG00000052127 gene were identified. These findings associated with sperm motility SNPs will help to develop strategies for the selection of valuable individuals and the efficient conservation of the gene pool.

Metafounder approach for single-step genomic evaluations of Red Dairy cattle.

Single-step genomic BLUP (ssGBLUP) is a powerful approach for breeding value prediction in populations with a limited number of genotyped animals. However, conflicting genomic (G) and pedigree (A22) relationship matrices complicate the implementation of ssGBLUP into practice. The metafounder (MF) approach is a recently proposed solution for this problem and has been successfully used on simulated and real multi-breed pig data. Advantages of the method are easily seen across breed evaluations, where pedigrees are traced to several pure breeds, which are thereafter used as MF. Application of the MF method to ruminants is complicated due to multi-breed pedigree structures and the inability to transmit existing unknown parent groups (UPG) to MF. In this study, we apply the MF approach for ssGBLUP evaluation of Finnish Red Dairy cattle treated as a single breed. Relationships among MF were accounted for by a (co)variance matrix (Γ) computed using estimated base population allele frequencies. The attained Γ was used to calculate a relationship matrix A22Γ for the genotyped animals. We tested the influence of SNP selection on the Γ matrix by applying a minor allele frequency (MAF) threshold (ΓMAF) where accepted markers had an MAF ≥0.05. Elements in the ΓMAF matrix were slightly lower than in the Γ matrix. Correlation between diagonal elements of the genomic and pedigree relationship matrices increased from 0.53 (A22) to 0.76 ( A22Γ and [Formula: see text] ). Average diagonal elements of A22Γ and [Formula: see text] matrices increased to the same level as in the G matrix. The ssGBLUP breeding values (GEBV) were solved using either the original 236 or redefined 8 UPG, or 8 MF computed with or without the MAF threshold. For bulls, the GEBV validation test results for the 8 UPG and 8 MF gave the same validation reliability (R2; 0.31) and over-dispersion (0.73, measured by regression coefficient b1). No significant R2 increase was observed in cows. Thus, the MF greatly influenced the pedigree relationship matrices but not the GEBV. Selection of SNP according to MAF had a notable effect on the Γ matrix and made the A22 and G matrices more similar.

Assessing the power of principal components and wright's fixation index analyzes applied to reveal the genome-wide genetic differences between herds of Holstein cows.

BACKGROUND: Due to the advent of SNP array technology, a genome-wide analysis of genetic differences between populations and breeds has become possible at a previously unattainable level. The Wright's fixation index (Fst) and the principal component analysis (PCA) are widely used methods in animal genetics studies. In paper we compared the power of these methods, their complementing each other and which of them is the most powerful. RESULTS: Comparative analysis of the power Principal Components Analysis (PCA) and Fst were carried out to reveal genetic differences between herds of Holsteinized cows. Totally, 803 BovineSNP50 genotypes of cows from 13 herds were used in current study. Obtained Fst values were in the range of 0.002-0.012 (mean 0.0049) while for rare SNPs with MAF 0.0001-0.005 they were even smaller in the range of 0.001-0.01 (mean 0.0027). Genetic relatedness of the cows in the herds was the cause of such small Fst values. The contribution of rare alleles with MAF 0.0001-0.01 to the Fst values was much less than common alleles and this effect depends on linkage disequilibrium (LD). Despite of substantial change in the MAF spectrum and the number of SNPs we observed small effect size of LD - based pruning on Fst data. PCA analysis confirmed the mutual admixture and small genetic difference between herds. Moreover, PCA analysis of the herds based on the visualization the results of a single eigenvector cannot be used to significantly differentiate herds. Only summed eigenvectors should be used to realize full power of PCA to differentiate small between herds genetic difference. Finally, we presented evidences that the significance of Fst data far exceeds the significance of PCA data when these methods are used to reveal genetic differences between herds. CONCLUSIONS: LD - based pruning had a small effect on findings of Fst and PCA analyzes. Therefore, for weakly structured populations the LD - based pruning is not effective. In addition, our results show that the significance of genetic differences between herds obtained by Fst analysis exceeds the values of PCA. Proposed, to differentiate herds or low structured populations we recommend primarily using the Fst approach and only then PCA.

[The use of cytoflavin in the acute period of hemorrhagic stroke]. / Ispol'zovanie tsitoflavina v ostrom periode gemorragicheskogo insul'ta.

AIM: To evaluate the efficacy of cytoflavin in the dose of 10 ml/day in the complex therapy in acute period of hemorrhagic stroke. MATERIAL AND METHODS: Sixty patients were examined in the acute period of hemorrhagic stroke (HS). The NIHSS, the Rivermead Mobility Index, the Rankin scale and the Barthel Index of Activities of Daily Living were used. Patients were divided into 2 groups: the main group included 30 patients who received cytoflavin in addition to basic therapy. The control group included 30 patients who received basic therapy. RESULTS AND CONCLUSION: In the main group, there were a significant decrease in the severity of neurological symptoms assessed with the NIHSS in the 10th day of treatment and a more pronounced improvement in the indicators of functional activity on the Rankin scale and daily life on the Barthel index to the level of 'moderate dependence', while the level of 'pronounced dependence' remained in the control group. Thus, the probability of favorable outcome was higher in the main group. Inclusion of cytoflavin in the therapy scheme of patients in the acute period of HS increased the efficacy of treatment.

[Study cytoflavin dose-dependent effect in the treatment of acute ischemic stroke]. / Izuchenie dozozavisimogo effekta tsitoflavina v terapii ostrogo perioda ishemicheskogo insul'ta.

AIM: To compare the efficacy of cytoflavin in doses of 10 and 20 ml/day in the complex pharmacological therapy of patients with acute ischemic stroke. MATERIAL AND METHODS: Eighty-six patients, aged from 43 to 85 years, were examined. Patient's status was assessed using the NIHSS, the Rankin scale, the Barthel index and the Rivermead mobility index. Patients were stratified into 3 groups: patients of group 1 received standard treatment, patients of group 2 received cytoflavin in dose of 10 ml/day in addition to standard treatment and patients of group 3 were treated with cytoflavin in dose of 20 ml/day in addition to standard treatment. RESULTS AND CONCLUSION: Cytoflavin in doses of 10 and 20 ml/day significantly promotes the regression of neurological deficit, improves day-to-day activity, and therefore, improves functional independence in daily life. The dose-dependent effect of the drug was shown. The use of cytoflavin in dose of 20 ml/day resulted in the more rapid regress of neurological symptoms during inpatient treatment and higher indices of daily activities and functional independence of patients that was important for the further rehabilitation.

[Genome-Wide Analysis of Across Herd F(st) Heterogeneity in Holsteinized Livestock].

To form a reference population necessary for genomic selection of dairy cattle, it is important to acquire information on the genetic diversity of the original population. Our report is the first among the studies on breeding of farm animals to implement Wright's F-statistics for this purpose. Genotyping of animals was performed using BovineSNP50 chip. In total, we genotyped 499 heifers from 13 breeding farms in the Leningrad oblast. We calculated Weir and Cockerham's F(st) estimate for all pairwise combinations of herds of breeding farms and the values obtained were in the range of 0.016-0.115 with the mean of 0.076 ± 0.002. Theoretical F(st) values for the same pairwise combinations of herds were calculated using the ADMIXTURE program. These values were significantly (p < 0.05) higher than Weir and Cockerham's F(st) estimates and fell in the range of 0.063-0.136 with the mean of 0.100 ± 0.001. We discuss the reasons for this discrepancy between the two sets of F(st) data. The obtained F(st) values were used to identify reliable molecular and genetic differences between the herds. The ADMIXTURE program breaks the pool of 476 heifers into 16 subpopulations, the number of which is close to the number of herds used in the experiment. Results of the comparison between F(st) values obtained using SNP markers with published data obtained on microsatellites are in support of the common opinion that microsatellite analysis results in underestimation of F(st) values. On the whole, the obtained across-herd F(st) values are in the range F(st) data reported for cattle breeds. Results of comparison of F(st) values with the data on the origin of bulls imported from different countries lead to the conclusion on the expediency of the use of F(st) indicators to assess heterogeneity of the herds. Thus, we have demonstrated that use of F(st) data provides the means to assess genetic diversity of cattle herds and is a necessary step in the formation of a reference population for dairy cattle.

[Experience with using selective angiography of the mesenteric arteries in patients with cicatricial esophageal stenosis]. / Opyt primeneniia selektivnoi angiografii bryzheechnykh srterii u bol'nykh s rubtsovym suzheniem pishchevoda.

The authors have used selective angiography of the upper and lower mesenterial arteries in patients with scary constriction of the esophagus in order to obtain data of blood supply of the colon before operation of esophagus plasty and to give preliminary grounds for surgical tactics. The method was used in 37 patients operated upon. In ten of them angiography of the upper mesenterial arteries has shown contrasted veins. Coincidence of the pathway of arteries and veins was noted in 1 patient. Angiography of the lower mesenterial artery has shown coincidence of the pathway of arteries and veins in 16 cases, i.e. in all the cases where the venous phase was fulfilled.