Comparative peculiarities of genomic diversity in Gallus gallus domesticus chickens with decorative plumage: the muffs and beard phenotype.

Throughout history, humans have been attempting to develop the ornamental features of domestic animals in addition to their productive qualities. Many chicken breeds have developed tufts of elongated feathers that jut out from the sides and bottom of the beak, leading to the phenotype known as muffs and beard. It is an incomplete autosomal dominant phenotype determined by the Mb locus localised on chromosome GGA27. This project aimed to analyse the genetic diversity of chicken breeds using full genomic genotyping with the Chicken 60K BeadChip. A total of 53,313 Single Nucleotide Polymorphisms were analysed. DNA was obtained from breeds with the muffs and beard as a marker phenotype: Faverolles (n = 20), Ukrainian Muffed (n = 18), Orloff (n = 20), Novopavlov White (n = 20), and Novopavlov Coloured (n = 15). The Russian White (n = 20) was selected as an alternative breed without the muffs and beard phenotype. The chickens are owned by the Centre of Collective Use "Genetic Collection of Rare and Endangered Breeds of Chickens" (St. Petersburg region, Pushkin), and are also included in the Core Shared Research Facility (CSRF) and/or Large-Scale Research Facility (LSRF). Multidimensional scaling revealed that the Novopavlov White and the Novopavlov Coloured populations formed a separate group. The Ukrainian Muffed and the Orloff have also been combined into a separate group. Based on cluster analysis, with the cross-validation error and the most probable number of clusters K = 4 taken into account, the Orloff was singled out as a separate group. The Ukrainian Muffed exhibited a notable similarity with the Orloff under the same conditions. At K = 5, the populations of the Novopavlov White and the Novopavlov Coloured diverged. Only at K = 6, a distinct and separate cluster was formed by the Ukrainian Muffed. The Russian White had the greatest number of short (1-2 Mb) homozygous regions. If the HOXB8 gene is located between 3.402 and 3.404 Mb on chromosome GGA27, homozygous regions are rarely found in the chickens with the muffs and beard phenotype. Scanning the chicken genome with the Chicken 60K BeadChip provided enough information about the genetic diversity of the chicken breeds for the peculiarities of the development of the ornamental muffs and beard phenotypes in them to be understood. For example, Phoenix bantams, whose tail feathers grow throughout their lives, require greater consideration of husbandry conditions.

16A system of molecular markers to identify alleles of the Rht-B1 and Rht-D1 genes controlling reduced height in bread wheat.

Mutant alleles of the Rht-B1 and Rht-D1 (Reduced height) genes are widely used in bread wheat breeding for the development of intensive-type cultivars. These genes and their f lanking regions have been sequenced and the point mutations leading to the nonsense codons (Rht-B1b, Rht-B1e, Rht-B1p and Rht-D1b alleles) and various insertions (Rht-B1c, Rht-B1h and Rht-B1i-1) associated with a change in plant height have been described. DNA-markers based on the allele-specif ic PCR have been developed to identify single-nucleotide changes. However, the use of such technique imposes stringent PCR conditions, and the resulting data are not always unambiguous. An alternative can be found in the CAPS technology: it detects differences in sequences by digesting PCR products. In the absence of restrictases capable of digesting DNA at the point mutation site, restriction sites can be introduced into the primer sequence (derived CAPS). The aim of this study was to propose a system of CAPS-, dCAPS- and STS-markers for identifying alleles of the reduced height genes frequently used in breeding programs. Three CAPS have been developed to identify the Rht-B1b, Rht-D1b, Rht-B1p alleles, as well as two dCAPS for Rht-B1b, Rht-B1e. STS-markers for the insertion-containing alleles Rht-B1c, Rht-B1h and Rht-B1i-1 have been selected from publications. The proposed markers were tested during the genotyping of 11 bread wheat accessions from the VIR collection with the abovementioned mutant alleles and the wild-type Rht-B1a and Rht-D1a. The presence of nonsense mutations was also conf irmed by the results of allele-specif ic PCR. This marker system, along with the existing ones, can be used to identify dwarf ing alleles of the Rht-B1 and Rht-D1 genes in bread wheat for genetic screening of accessions from ex situ collections and/or for marker-assisted selection.

Tissue geometry drives deterministic organoid patterning.

Epithelial organoids are stem cell­derived tissues that approximate aspects of real organs, and thus they have potential as powerful tools in basic and translational research. By definition, they self-organize, but the structures formed are often heterogeneous and irreproducible, which limits their use in the lab and clinic. We describe methodologies for spatially and temporally controlling organoid formation, thereby rendering a stochastic process more deterministic. Bioengineered stem cell microenvironments are used to specify the initial geometry of intestinal organoids, which in turn controls their patterning and crypt formation. We leveraged the reproducibility and predictability of the culture to identify the underlying mechanisms of epithelial patterning, which may contribute to reinforcing intestinal regionalization in vivo. By controlling organoid culture, we demonstrate how these structures can be used to answer questions not readily addressable with the standard, more variable, organoid models.

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.

[Molecular markers in the genetic analysis of crossability of bread wheat with rye]. / Молекулярные маркеры в генетическом анализе скрещиваемости мягкой пшеницы с рожью.

Bread wheat (Triticum aestivum L.), the varieties of which are widely used for the grain production, is difficultly crossable with related species of Triticeae Dum. This factor limits the chance of introduction of alien genetic material into the wheat gene pool and the possibility of new varieties breeding with good adaptation to adverse environmental factors. The crossability between wheat and related species is controlled by Kr1-Kr4 genes (Crossability with Rye, Hordeum and Aegilops spp.) and the SKr gene (Suppressor of crossability). SKr and Kr1 have the largest influence on the trait. In the case of the recessive alleles, these genes do not function and the quantity of hybrid seeds after pollination with alien species can achieve more than 50 %. SKr is located on 5BS between the GBR0233 and Xgwm234 markers, closely linked with the markers Xcfb341, TGlc2 and gene12. Kr1 was mapped on 5BL, proximally to the Ph1 gene, between the EST-SSR markers Xw5145 and Xw9340. The markers of SKr were used to control the transfer of its recessive allele into other wheat genotypes, which made it possible to obtain highly crossable forms. However, the advantages of using the SKr and Kr1 markers in marker-assisted selection and in the screening of ex situ collections are not sufficiently studied. The published Kr1 sequence for varieties with different crossability offers great prospects, because it will be possible to create allele-specific markers. In this review, the following issues are considered: genetic resources created by wheat and rye hybridization, the geographical distribution of easy-to-cross forms of wheat, genetic control of the wheat and rye compatibility, advances of the use of molecular markers in the mapping of Kr-genes and their transmission control.

Haplotype structure and copy number polymorphism of the beta-defensin 7 genes in diverse chicken breeds.

Beta-defensins is a family of avian peptides related to the innate immune system. Copy number variation was recently reported for the avian beta-defensin 7 gene (AvBD7) between the highly inbred Leghorn and Fayoumi lines. Here, we examined copy number variants in 35 different chicken breeds and found that 31 of them have at least the same representation of the duplicated AvBD7 allele. We also found haplotypes upstream of the AvBD6 regions that are strongly linked to the AvBD7 duplication. We observed a strong linkage disequilibrium spanning of the upstream region of the AvBD6 gene, with two SNPs being flanking markers to detect duplication of the AvBD7.

[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.

[Genealogical Analysis of the Use of Aegilops (Aegilops L.) Genetic Material in Wheat (Triticum Aestivum L.)].

A genealogical analysis of accessions in the global gene pool of the wheat database GRIS4.0 showed that the use of the genetic material of Aegilops in wheat breeding began about half a century ago. During this time, more than 1350 varieties and 9000 lines, the pedigree of which contains Aegilops species, were created in different regions of the world. The spatial and temporal dynamics of the distribution of wheat varieties containing the genetic material of Aegilops was investigated. Analysis of the data showed that most commercial varieties with a pedigree including Ae. tauschii and/or Ae. umbellulata were created and grown in North America. More than 70% of the varieties were produced with Ae. ventricosa, which is common in western and central Europe. A gradual increase in the proportion of varieties with Aegilops genetic material was recorded from 1962 to 2011. The percentage of varieties created with the involvement of Ae. umbellulata increased from 1-5% in the 1960s to 25-29% in the 2000s. Those created with Ae. tauschii increased from 0% to 14-18%, and those created with Ae. ventricosa increased from 1% to 34-37%. The increases in the number of these varieties indicates that the resistance genes from Aegilops species retain their effectiveness. Genealogical analysis of the varieties in which resistance genes from Aegilops were postulated revealed that varieties or lines that were sources of identified genes were often absent in the pedigree. This may be due to an incorrect pedigree record or errors in the identification of resistance genes by phytopathological testing and/or the use of molecular markers, or confusion in nurseries. Preliminary analysis of pedigrees provides an opportunity to reveal discrepancies between the pedigree and postulated genes.

[The effectiveness of molecular markers for the identification of Lr28, Lr35, and Lr47 genes in common wheat].

The effectiveness of molecular markers for the identification of leaf rust resistance genes Lr28, Lr35, Lr47 transferred to common wheat was assessed the using samplesof Triticum spp. and Aegilops spp. from Ae. speltoides. Markers Sr39F2/R3, BCD260F1/35R2 of gene Lr35 and PS10 of Lr47 gene were characterized by high efficiency and were revealed in a line of common wheat containing these genes, and samples of Ae. speltoides (their donor). Marker SCS421 of Lr28gene and markers Sr39#22r, Sr39#50s, BE500705 of Lr35/Sr39 genes turned out to be less specific. Marker SCS421 was amplified in the samples of the T. timopheevii species, and markers Sr39#22r, Sr39#50s--in the Ae. speltoides, Ae. tauschii, T. timopheevii, line KS90WRC010 (Lr41), the sort of common wheat In Memory of Maistrenko, obtained using synthetic hexaploid T. timopheevii x Ae. tauschii and introgressive lines obtained using Ae. speltoides. Marker BE500705, which indicates the absence of Lr35/Sr39 genes, was not revealed in lines TcLr35 and MqSr39, in Ae. speltoides, Ae. tauschii and T. boeoticum (kk-61034, 61038). Analysis of the nucleotide sequences of amplification products obtained with the markers SCS421 and Sr39#22r indicated their low homology with TcLr28 and TcLr35. Using molecular markers, we showed a different distribution of Lr28 (77%), Lr35 (100%) and Lr47 (15%) genes in 13 studied samples ofAe. speltoides. In introgressive lines derived from Ae. speltoides, contemporary Russian sorts of common wheat and triticale variants Lr28, Lr35, Lr47 genes were not revealed.

Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example.

Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.

[Global diversity of durum wheat Triticum durum desf. for alleles of gliadin-coding loci].

Genetic diversity for the alleles of gliadin-coding loci was studied with 465 durum wheat cultivars from 42 countries. A total of 108 alleles were identified for four loci; 60 alleles were described for the first time. Broad diversity of rare gliadin-coding alleles was observed. The highest genetic diversity was characteristic of durum wheat cultivars from the Middle East, Trans-Caucasia, the Pyrenean Peninsula, and the Balkans. Two genetically isolated ancient branches were isolated. A southern branch included mostly cultivars from the Mediterranean region, the Middle East, and Trans-Caucasia. A northern branch included Russian and Ukrainian durum wheat cultivars and varieties obtained on their basis. An additional group included durum wheat cultivars that had been obtained in several past decades on the basis of the material of international breeding centers (CIMMYT and ICARDA) and had low genetic diversity.

[Diversity and the origin of the European population of Triticum dicoccum (Schrank) Schuebl. as revealed by chromosome analysis].

Cluster analysis of the Triticum dicoccum chromosome passports by artificial neural networks and UPGMA divided the European T. dicoccum population into two groups, West European and Volga-Balkan. The West European T. dicoccum accessions displayed a predominance of the marker translocation T7A:5B (67% of the accessions), which was also found in a few accessions from other countries (Turkey, Iran, and northern Africa), and were similar in chromosome C-banding patterns. The Volga-Balkan T. dicoccum accessions differed in the C-banding patterns of some chromosomes from the West European accessions, thus probably originating from another founder population. It was assumed that the T. dicoccum accessions carrying the T7A:5B translocation had a common origin and that the wild T. dicoccum population of the Middle East (Syria and Lebanon) contributed to the origin of West European T. dicoccum.

[Genetic differentiation of hexaploid wheat inferred from analysis of microsatellite loci].

Landraces of wheat can serve as important potential sources for extending the genetic basis of selection cultivars. Analysis of microsatellites and typing of polymorphism in a representative sample of 347 genotypes, including landraces and selection cultivars, was performed using a set of 38 selected oligonucleotide primer pairs. Classification of genotypes with respect to the level of their similarity was performed using cluster analysis. The data obtained pointed to genetic differentiation of hexaploid wheat. The groups of cultivars, the formation of which was thought to be associated with the main old areas of wheat cultivation in Europe and Asia, were identified. The basis of each of the groups was formed by landraces of common wheat. The differences between the groups identified were associated with multiple changes in the wheat genome and were expressed as quantitative differences in the allele frequencies of microsatellite loci. The results of the study are of interest in terms of understanding the structure of wheat genetic diversity and revealing the pathways of evolution of this culture.

[Analysis of intraspecific divergence of hexaploid wheat Triticum spelta L. by chromosome C-banding]. / Analiz vnutrividovoi divergentsii geksaploidnoi pshenitsy Triticum spelta L. s pomoshch'iu metoda differentsial'nogo okrashivaniia khromosom.

Intraspecific divergence of hexaploid wheat Triticum spelta was studied by chromosome C-banding in 41 accessions of different geographic origins. The spelt accessions did not differ in karyotype structure or heterochromatin distribution from common wheat, but showed greater intraspecific polymorphism for chromosome rearrangements (translocations, inversions) and banding patterns. On evidence of C-banding patterns, spelt was assumed to occupy an intermediate position between tetraploid and hexaploid wheat species. Accessions of the Asian spelt subspecies had more diverse banding patterns than European accessions. A relatively high frequency of chromosome rearrangements was observed in Iranian accessions. Visual analysis revealed high uniformity of chromosome banding patterns in T. spelta populations of Afghanistan, Spain, and Germany (Bavarian group), suggesting a significant role of the founder effect in their evolution.

[Levels of lipid peroxidation products and activity of antiradical defense enzymes in blood of patients with Bechterew disease]. / Soderzhanie produktov perekisnogo okisleniia lipidov i aktivnost' fermentov antiradikal'noi zashchity v krovi bol'nykh bolezn'iu Bekhtereva.

AIM: To study lipid peroxidation (LPO) in Bechterev's disease (BD) treated with antiinflammatory and antioxidant drugs. MATERIAL AND METHODS: LPO was estimated in 75 BD patients before medication and during this treatment. 30 healthy volunteers served control. RESULTS: Levels of LPO products was high but activity of antioxidant defense enzymes low in BD patients. CONCLUSION: Antiinflammatory drugs meloxicam, indometacin and an antioxidant drug triovit depressed LPO activity, improve the patients' condition and results of functional tests.

[Study of a collection of Triticum spelta L. wheat species using gliadin polymorphism]. / Issledovanie kollektsii vida pshenitsy Triticum spelta L. po polimorfizmu gliadinov.

Using gliadins, endosperm storage proteins of kernels, as markers, the genetic diversity of 170 samples from the Triticum spelta L. collection of the Vavilov Institute of Plant Industry was studied. High intraspecific polymorphism of the gliadin electrophoretic patterns was revealed. On the basis of similarity of the gliadin electrophoretic patterns, groups of samples were isolated, and the genetic structurization of the collection was performed.

[Changes in rheological properties of blood in patients with chronic glomerulonephritis]. / Izmenenie reologicheskikh svoistv krovi u bol'nykh khronicheskim glomerulonefritom.

The study of rheological blood properties in patients with chronic glomerulonephritis (CGN) demonstrates an increase in red blood cells aggregation and blood viscosity 3-4-fold while red blood cells deformability is two times less compared to healthy subjects. These findings well correlated with plasma fibrinogen and protein/lipid ratio of plasma and red blood cells. The highest informative value is associated with middle-sized and maximum-sized red blood cells aggregates which are significally related with a clinical form of the disease and its activity. The evidence obtained in the study is indicative of profound microcirculatory abnormalities in CGN patients necessitating administration of active antiaggregate therapy.