In recent years, the number of genome-wide association studies (GWAS) carried out for various economically important animal traits has been increasing. GWAS discoveries provide summary statistics ...that can be used both for targeted marker-oriented selection and for studying the genetic control of economically important traits of farm animals. In contrast to research in human genetics, GWAS on farm animals often does not meet generally accepted standards (availability of information about effect and reference alleles, the size and direction of the effect, etc.). This greatly complicates the use of GWAS results for breeding needs. Within the framework of human genetics, there are several technological solutions for researching the harmonized results of GWAS, including one of the largest, the GWAS-MAP platform. For other types of living organisms, including economically important agricultural animals, there are no similar solutions. To our knowledge, no similar solution has been proposed to date for any of the species of economically important animals. As part of this work, we focused on creating a platform similar to GWAS-MAP for working with the results of GWAS of sheep, since sheep breeding is one of the most important branches of agriculture. By analogy with the GWAS-MAP platform for storing, unifying and analyzing human GWAS, we have created the GWAS-MAP|ovis platform. The platform currently contains information on more than 34 million associations between genomic sequence variants and traits of meat production in sheep. The platform can also be used to conduct colocalization analysis, a method that allows one to determine whether the association of a particular locus with two different traits is the result of pleiotropy or whether these traits are associated with different variants that are in linkage disequilibrium. This platform will be useful for breeders to select promising markers for breeding, as well as to obtain information for the introduction of genomic breeding and for scientists to replicate the results obtained.
Inversion heterozygotes are expected to suffer from reduced fertility and a high incidence of chromosomally unbalanced gametes due to recombination within the inverted region. Non-homologous synapsis ...of the inverted regions can prevent recombination there and diminish the deleterious effects of inversion heterozygosity. The choice between non-homologous and homologous synapsis depends on the size of inversion, its genetic content, its location in relation to the centromere and telomere, and genetic background. In addition, there is a class of inversions in which homologous synapsis is gradually replaced by non-homologous synapsis during meiotic progression. This process is called synaptic adjustment. The degree of synaptic adjustment depends critically on the presence and location of the COs (crossovers) within the inversion loop. Only bivalents without COs within the loop and those with COs in the middle of the inversion can be completely adjusted and became linear.
Results of theoretical analysis of dielectric permittivity perturbations in lithium niobate crystal with periodically poled domain structure are presented. The deviation of periodical domain ...structure duty cycle from 0.5 and the electric bias field created by point defects are taken into consideration. The isotropic diffraction with many maxima is considered as a boundary problem for symmetric propagation of probing beam. The agreement between numerical analysis and experimental study of the isotropic diffraction patterns performed for laser beam polarized along domain walls and propagating along polar axis through the periodically poled domain structure confirmed the proposed theoretical model.
Having information such as an estimation of the processing time or possibility of system outage (abnormal behaviour) helps to assist to monitor system performance and to predict its next state. The ...current cyber-infrastructure of the ATLAS Production System presents computing conditions in which contention for resources among high-priority data analyses happens routinely, that might lead to significant workload and data handling interruptions. The lack of the possibility to monitor and to predict the behaviour of the analysis process (its duration) and system's state itself provides motivation for a focus on design of the built-in situational awareness analytic tools.
Most true lizards (Lacertidae) share a conservative karyotype, consisting of 18 pairs of macrochromosomes and one microchromosome pair. Homeologues of the microchromosome are present in other ...squamates and even in chickens. No structural autosomal microchromosome polymorphisms have been described previously in lizards. We found homozygous and heterozygous carriers of a microchromosome variant in a Siberian population of the sand lizard,
Linnaeus, 1758. The variant microchromosome was almost twice as long as the standard one. In heterozygotes at pachytene, the microchromosomes firstly pair in proximal regions and the central part of the longer axial element undergoes foldback synapsis, then its distal region pairs with the distal region of the standard partner. At metaphase-I, the heteromorphic microchromosome bivalents have a proximal chiasma. The content of the additional segment was Ag-NOR, C-like DAPI, CMA3 negative. FISH with telomere PNA probe did not detect interstitial (TTAGGG)
sequences in the heteromorphic and any other bivalents. Both homo- and heterozygous carriers were phenotypically normal. The presence of homozygotes shows that heterozygotes are fertile. Reduction in the number of microchromosomes is a clear trend in squamate evolution, as a result of microchromosomes fusing together or with macrochromosomes. Our findings indicate that gaining additional DNA may lead to a transformation of microchromosomes into small macrochromosomes without fusion.
The Big Data processing needs of the ATLAS experiment grow continuously, as more data and more use cases emerge. For Big Data processing the ATLAS experiment adopted the data transformation approach, ...where software applications transform the input data into outputs. In the ATLAS production system, each data transformation is represented by a task, a collection of many jobs, submitted by the ATLAS workload management system (PanDA) and executed on the Grid. Our experience shows that the rate of task submission grows exponentially over the years. To scale up the ATLAS production system for new challenges, we started the ProdSys2 project. PanDA has been upgraded with the Job Execution and Definition Interface (JEDI). Patterns in ATLAS data transformation workflows composed of many tasks provided a scalable production system framework for template definitions of the many-tasks workflows. These workflows are being implemented in the Database Engine for Tasks (DEfT) that generates individual tasks for processing by JEDI. We report on the ATLAS experience with many-task workflow patterns in preparation for the LHC Run 2.
An unusual supernumerary chromosome has been reported for two related avian species, the zebra and Bengalese finches. This large, germline-restricted chromosome (GRC) is eliminated from somatic cells ...and spermatids and transmitted via oocytes only. Its origin, distribution among avian lineages, and function were mostly unknown so far. Using immunolocalization of key meiotic proteins, we found that GRCs of varying size and genetic content are present in all 16 songbird species investigated and absent from germline genomes of all eight examined bird species from other avian orders. Results of fluorescent in situ hybridization of microdissected GRC probes and their sequencing indicate that GRCs show little homology between songbird species and contain a variety of repetitive elements and unique sequences with paralogs in the somatic genome. Our data suggest that the GRC evolved in the common ancestor of all songbirds and underwent significant changes in the extant descendant lineages.
To make insight into the cytological basis of reproductive isolation, we examined chromosome synapsis and recombination in sterile male and female hybrids between Microtus arvalis and M. levis. These ...sibling species differ by a series of chromosomal rearrangements (fusions, inversions, centromere shifts and heterochromatin insertions). We found that meiosis in male hybrids was arrested at leptotene with complete failure of chromosome pairing and DNA double-strand breaks repair. In the female hybrids meiosis proceeded to pachytene; however, the oocytes varied in the degree of pairing errors. Some of them demonstrated almost correct chromosome pairing, while most of them contained a varying number of univalents and multivalents with extensive regions of asynapsis and non-homologous synapsis. Variation between oocytes was probably caused by stochasticity in the ratio of homologous to non-homologous pairing initiations. We suggest that substantial chromosomal and genetic divergence between the parental species affects preliminary alignment of homologues, homology search and elimination of ectopic interhomologue interactions that are required for correct homologous pairing. Apparently, pairing failure in male and aberrant synapsis in female vole hybrids followed by meiotic silencing of unsynapsed chromatin cause apoptosis of gametocytes and sterility.
Hybrid zones between chromosome races of the common shrew (
) provide exceptional models to study the potential role of chromosome rearrangements in the initial steps of speciation. The Novosibirsk ...and Tomsk races differ by a series of Robertsonian fusions with monobrachial homology. They form a narrow hybrid zone and generate hybrids with both simple (chain of three chromosomes) and complex (chain of eight or nine) synaptic configurations. Using immunolocalisation of the meiotic proteins, we examined chromosome pairing and recombination in males from the hybrid zone. Homozygotes and simple heterozygotes for Robertsonian fusions showed a low frequency of synaptic aberrations (<10%). The carriers of complex synaptic configurations showed multiple pairing abnormalities, which might lead to reduced fertility. The recombination frequency in the proximal regions of most chromosomes of all karyotypes was much lower than in the other regions. The strong suppression of recombination in the pericentromeric regions and co-segregation of race specific chromosomes involved in the long chains would be expected to lead to linkage disequilibrium between genes located there. Genic differentiation, together with the high frequency of pairing aberrations in male carriers of the long chains, might contribute to maintenance of the narrow hybrid zone.
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