Identification of homozygosity-rich regions in the Holstein genome.

In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1-2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.

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.

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.

[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.

[Genomic selection of milk cattle. The practical application over five years].

Genomic selection is a method based on the use of single nucleotide polymorphisms (SNPs) as markers for detecting animal or plant genotype values. The review describes the genomic selection of milk cattle 5 years after the design of dense SNP chips. References to the application of genomic selection to other animal and plant species are given. The main principles of constructing linear and nonlinear mathematical models that allow one to determine genomic estimates in animals are briefly described. Particular attention is focused on the accuracy and the phenomenon of the additivity ofgenomic estimates, as well as to the prospective use of various genomic selection schemes that consider it over dozens of generations. Information including international organizations that provide the consolidation of genomic information from different countries aimed at designing global reference populations of milk cattle is reported. The results of the practical application of genomic selection to detecting of the breeding value of milk cattle over 5 years are demonstrated in the table, which makes it possible to visually assess the achievements of this highly technological field of cattle breeding.

[Association of a single nucleotide substitution in intergenic region of chromosome 4 with traits of egg quality in domestic chickens].

The association of SNP2-1 with egg quality traits in domestic chickens was analyzed. SNP2-1 alleles were significantly associated with the thickness of eggshells in chickens of the UK-72 line. The substitution of the SNP2-1 allele Tfor the C allele had an effect of 35 +/- 15 microm, which corresponds to one standard deviation. For this trait, the effect of the Tallele was dominant. SNP2-1 was also associated with other traits, including shell weight, egg-laying capacity in 60-week-old chickens (line UK-72), and egg weight in 60-week-old chickens (line cross CD). Thus, the QTL marked with SNP2-1 has a pleiotropic effect that depends on the chicken strain. Candidate genes located on chromosome 4 in close vicinity of SNP2-1 are discussed.

[Study of the association between alleles of the growth hormone receptor and prolactin receptor genes of bulls and the milk productivity of their daughters].

A substitution of thyrosine for phenylalanine (F297Y) in the transmembrane domain of the growth hormone receptor (GHR) was tested for significance for breeding evaluation of bulls of the holstenized Black-and-White breed. The breeding value was estimated by the method of daughter yield deviation to contemporaries with modification. The frequency of genotype FF in the bulls examined was 0.37, lower than in Holstein bulls (0.67). The F297Y substitution exerted the greatest effect on the milk fat content (1.5 sigma) and milk yield (0.8 sigma) and a lower effect on the milk fat yield (0.6 sigma), milk protein yield (0.5 sigma), and milk protein content (0.6 sigma). The GHR4.2 single nucleotide substitution (SNP) in the promoter of the GHR gene did not affect the milk production traits. A substitution of asparagine for serine (S18N) in the transmembrane domain of the prolactin receptor (PRLR) was also examined, but it did not significantly affect the milk production parameters. The results are discussed in the context of the hypothesis that multiplicity of causal mutations of a particular gene is common and should be taken into account in the genetics of quantitative traits.

[Association of the DGAT1 gene polymorphism in stud bulls with milk productivity in cows].

The substitution of lysine for alanine (K232A) in the acyl-CoA-diacylglycerol acyltransferase, which is encoded by the DGAT1 gene, was tested for the significance for breeding evaluation of stud bulls of the holsteinized Black-and-White breed. The breeding value (deviation of milk productivity in daughters compared with cows of the same age) was estimated by the DYDC (daughter yield deviation to contemporary) method with modification. The frequency of allele 232K in the bulls examined was 0.28, lower than in Holstein bulls (0.4-0.6). The greatest effect of the A232K substitution was observed for the percent fat content in milk (1.4 sigma) and milk yield (0.76 sigma), and a lower effect was established for the milk protein yield (0.47 sigma) and percent protein content in milk (0.44 sigma). In the case of milk fat yield, the effect was nonsignificant. A method was proposed for converting the data on fat yield in order to obtain significant results in this case as well. The effect of the A232K substitution was estimated at 154 kg for milk yield, 2.8 kg for protein yield, 0.079% for percent fat content, and 0.015% for percent protein content. The results are discussed in the context of multiple pleiotropic effects of the K232A substitution in the DGAT1 gene. It is proposed that the K232A substitution of the DGAT1 gene be used as a golden standard in comparisons of the effect on milk productivity for the total gene set. This approach will allow a meta-analysis of the gene effects in spite of the differences in dairy cattle breeds and methods used to analyze their breeding value. In view of more than 30-year experience of using sperm of Holstein stud bulls, including those bred in North America, it was noted that the effect of the A232K substitution on milk productivity traits agreed well with the data reported for the North American commercial population of Holstein cattle.

[SNP assisted total genomic selection as a possible accelerator of traditional selection].

Selection using single nucleotide polymorphism (SNP) markers scattered throughout the genome or genomic selection (GS) is considered. This approach permits simultaneous selection of most quantitative trait loci (QTLs) determining the selected trait. According to expert assessment, GS makes it possible to save 92% of the funds spent on traditional selection and is twice as efficient as the latter.

[Analysis of chromosomal localization of loci controlling milk production traits in cattle].

Analysis of the pattern of the chromosomal localization of quantitative trait loci (QTLs) is necessary for comprehensively understanding their functions. The chromosomal localization of QTLs controlling milk production traits has been studied in cattle chromosomes. The distribution of QTLs between chromosomes has proved to be binomial. Their distribution along each chromosome was, in general, uniform, except for the QTLs controlling the somatic cell score (SCS), which tended towards telomeric location. However, there are chromosomes either enriched with or particularly poor in QTLs. The QTL distribution patters are the most similar for the milk yield (M) and milk protein yield (P) and for milk fat yield (F) and milk fat content (%F). The pattern of the SCS QTLs stands out among those of other QTLs. The distance between the QTLs of contrasting traits is the shortest for M and P QTLs, longer for M and milk protein content (%P) QTLs, and still longer for M and %F QTLs, which may be explained by QTL pleiotropy, a common phenomenon in cattle.

[Genetic mapping of loci responsible for milk quality parameters in dairy cattle].

The review presents a definition of loci controlling quantitative traits (quantitative trait loci, QTLs) and localization of all currently known QTLs responsible for milk production traits in dairy cattle. The QTL number and chromosome localization are verified, with special reference to chromosomes 1, 3, 6, 14, 20, and 23. In a number of cases, close location of QTLs for mastitis and for milk production traits was found. Some aspects of QTL pleiotropy and epistasis are discussed and mapping methods of major QTLs are listed.

[The detection of the location in cattle chromosomes of a gene presumably determining testis development]. / Vyiavlenie lokalizatsii v khromosomakh krupnogo rogatogo skota gena, predpolozhitel'no opredeliaiushchego razvitie testisov.

The localization of the putative testis determining gene (TDF) was established with isotopic and nonisotopic methods of in situ hybridization in prometaphasic chromosomes of cattle. The results of both the methods were seen to coincide. The sites of hybridization have been revealed in X-chromosome (R-bands, q2.1 and q2.3.1). TDF was also localized in the proximal part of the long Y-chromosome arm.

[The heterochromatin regions of the mitotic chromosomes in cattle]. / Geterokhromatinovye uchastki mitoticheskikh khromosom krupnogo rogatogo skota.

Cytochemical and molecular peculiarities of heterochromatic regions of bovine chromosomes have been studied, using specific fluorochrome staining induced decondensation, in situ hybridization, pretreatment of restriction enzymes. The heterochromatin of autosomes demonstrated a strong homogeneity. In chromosome Y two small specific heterochromatic regions were found lacking a long repeated tandem block of nucleotides enriched in GC base pairs and having no tandem block of Bkm repeats (10(4) b.p.). This class repeats are probably interspersed in the bovine genome. A rather seldom character of mammalian karyotypes is the absence of cytochemical heterochromatin in the X chromosome.

[Aggregation of heterochromatin regions of chromosomes in Drosophila melanogaster neuroblasts]. / Agregatsiia geterokhromatinovykh raionov khromosom v neiroblastakh Drosophila melanogaster.

Interaction of heterochromatic regions was studied during interphase and mitosis. The interphasic heterochromatin unites, producing 1-8 H-chromocentres. A lack of synapsis between heterochromatic regions in prophase is shown to be a result of hypotonic treatment. It is mentioned that adhesion of sister chromatids was used for heterochromatin localization. The results are discussed in connection with the supposed interaction between heterochromatin and membrane.

[Staining of interphase and metaphase chromosomes with Procion Yellow 4RS]. / Okrashivanie interfaznykh i metafaznykh khromosom s pomoshch'iu protsionovogo zheltogo 4RS.

A method for staining proteins by procion yellow 4RS on preparates of metaphase and interphase chromosomes is suggested. It is shown that the dye is not bound to either native or denatured DNA in solution.

[Preparation of polytene chromosomes from isolated cell nuclei of the salivary glands of Drosophila]. / Prrparaty politennykh khromosom iz izolirovannykh iader kletok sliunnykh zhelez Drosofili.

A method is proposed for preparation of polytene chromosomes free of cytoplasmic substance. The nuclei are isolated using triton X-100 and squashed in 60% propionic acid solution.