A. M. Kudryavtsev

Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats

Molecular markers based on retrotransposon insertions are widely used for various applications including phylogenetic analysis. Multiple cases were described where retrotransposon-based markers, namely sequence-specific amplification polymorphism (SSAP), were superior to other marker types in resolving the phylogenetic relationships due to their higher variability and informativeness. However, the patterns of evolutionary relationships revealed by SSAP may be dependent on the underlying retrotransposon activity in different periods of time. Hence, the proper choice of retrotransposon family is essential for obtaining significant results. We compared the phylogenetic trees for a diverse set of diploid A-genome wheat species (Triticum boeoticum, T. urartu and T. monococcum) based on two unrelated retrotransposon families, BARE-1 and Jeli. BARE-1 belongs to Copia class and has a uniform distribution between common wheat (T. aestivum) genomes of different origin (A, B and D), indicating similar activity in the respective diploid genome donors. Gypsy-class family Jeli was found by us to be an A-genome retrotransposon with >70% copies residing in A genome of hexaploid common wheat, suggesting a burst of transposition in the history of A-genome progenitors. The results indicate that a higher Jeli transpositional activity was associated with T. urartu versus T. boeoticum speciation, while BARE-1 produced more polymorphic insertions during subsequent intraspecific diversification; as an outcome, each retrotransposon provides more informative markers at the corresponding level of phylogenetic relationships. We conclude that multiple retroelement families should be analyzed for an image of evolutionary relationships to be solid and comprehensive.

Modern HPC cluster virtualization using KVM and palacios

In this paper we explore the potential of virtualization being applied to High Performance Computing (HPC). We demonstrate the importance of proper NUMA architecture emulation when running HPC task inside virtual machines on multiple NUMA hosts. We assess KVM/QEMU and Palacios hypervisors and, with proper tuning of hypervisor (including NUMA emulation), we reduce the performance degradation from 10–60% to 1–5% on many tests from HPC Challenge and NAS Parallel Benchmark suites. All tests are performed on modern HPC cluster with high-speed Infiniband interconnect. The cluster nodes are 2-socket 12-core systems, up to 8 nodes were used for computation. Comparing KVM/QEMU and Palacios hypervisors, we conclude that in general the results with NUMA emulation enabled are similar, with KVM providing more stable and predictable results while Palacios being much better on fine-grained tests at a large scale, but showing abnormal performance degradation on a few tests. We believe that the main advantage of Palacios with respect to performance is the reduced amount of noise generated by the virtualization system. This advantage is getting more important when the scale of the system grows.

Virtualizing HPC applications using modern hypervisors

In this paper we explore the prospects of virtualization technologies being applied to high performance computing tasks. We use an extensive set of HPC benchmarks to evaluate virtualization overhead, including HPC Challenge, NAS Parallel Benchmarks and SPEC MPI2007. We assess KVM and Palacios hypervisors and, with proper tuning of hypervisor, we reduce the performance degradation from 10-60% to 1-5% in many cases with processor cores count up to 240. At the same time, a few tests provide overhead ranging from 20% to 45% even with our enhancements. We describe the techniques necessary to achieve sufficient performance. These include host OS tuning to decrease noise level, using nested paging with large pages for efficient guest memory allocation, and proper NUMA architecture emulation when running virtual machines on NUMA hosts. Comparing KVM/QEMU and Palacios hypervisors, we conclude that in general the results with proper tuning are similar, with KVM providing more stable and predictable results while Palacios being much better on fine-grained tests at a large scale, but showing abnormal performance degradation on a few tests.

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 accessions 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 accessions from the Middle East, Trans-Caucasia, the Pyrenean Peninsula, and the Balkans. Two genetically isolated ancient branches of durum wheat were isolated. A “southern” branch included mostly accessions from the Mediterranean region, the Middle East, and Trans-Caucasia. A “northern” branch included Russian and Ukrainian durum wheat accessions and varieties obtained on their basis. An additional group included durum wheat accessions 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.

Genetic diversity of common wheat varieties at the gliadin-coding loci

One hundred and fifty Russian and foreign winter common wheat varieties were examined by the PAGE method. A total of 70 alleles were identified at six gliadin-coding loci. It was demonstrated that 42% of varieties were heterogeneous, i.e., were represented by a number of genotypes, while 52% of varieties were homogeneous. A unique combination of gliadin alleles was typical of 91.3% of examined varieties, while 8.7% of varieties had identical alleles of all gliadin-coding loci and were indistinguishable. Frequent and rare alleles were identified, with the former accounting for 18.6% of all alleles. It was demonstrated that allelic diversity at the Gli-2 loci (47 alleles) was almost twice that at the Gli-1 loci (23 loci) and was determined by the number of rare alleles. New alleles for the winter common wheat, including three alleles of the GliA2 locus and two alleles of the Gli-B2 locus, were determined. A tendency toward a reduction of the genetic diversity level in modern varieties, which was due to the use of identical parental varieties in breeding programs, was identified.

Catalogue of alleles of gliadin-coding loci in durum wheat (Triticum durum Desf.).

Gliadins are seed storage proteins which are characterized by high intervarietal polymorphism and can be used as genetic markers. As a result of our work, a considerably extended catalogue of allelic variants of gliadin component blocks was compiled for durum wheat; 74 allelic variants for four gliadin-coding loci were identified for the first time. The extended catalogue includes a total of 131 allelic variants: 16 for locus Gli-A1(d), 19 for locus Gli-B1(d), 41 for locus Gli-A2(d), and 55 for locus Gli-B2(d). The electrophoretic pattern of the standard cultivar and a diagram are provided for every block identified. The number of alleles per family is quite small for loci Gli-A1(d) and Gli-B1(d) of durum wheat, as contrasted to loci Gli-A2(d) and Gli-B2(d) that are characterized by large families including many alleles. The presence of large block families determines a higher diversity of durum wheat for loci Gli-A2(d) and Gli-B2(d) as compared to Gli-A1(d) and Gli-B1(d). The catalogue of allelic variants of gliadin component blocks can be used by seed farmers to identify durum wheat cultivars and evaluate their purity; by breeders, to obtain homogenous cultivars and control the initial stages of selection; by gene bank experts, to preserve native varieties and the original biotypic composition of cultivars.

Analysis of sequences of ITS1 internal transcribed spacer and 5.8S ribosome gene of Malus species

The nucleotide sequence of the ITS1-5.8S ribosomal DNA spacer fragment was determined for 41 samples of the Malus species. The total length of compared sequences ranged from 389 to 392 bp. The nucleotide sequence of the 5.8S gene within the genus was highly conserved. The level of polymorphism of ITS1 region comprised 14%. Both species- and group-specific substitutions were identified. The analysis of M. orientalis and M. turkmenorum sequences revealed their full identity, which indicates the need to perform more research with a larger number of samples of both species from other collections to clarify the taxonomic status of the M. turkmenorum species. The previous findings on the synonymy of species M. baccata, M. mandshurica, M. pallasiana, and M. sachalinensis were also confirmed.

Analysis of the ITS1/ITS2 nuclear spacers and the secondary structure of 5.8S rRNA gene in endemic species Bellevalia sarmatica (Pall. ex Georgi) Woronow and related species of the subfamily scilloideae

Sequence variability of the ITS spacers and 5.8S rRNA gene was examined in 11 accessions of the subfamily Scilloideae, including seven accessions of rare and endangered species Bellevalia sarmatica from Volgograd region. The intraspecific polymorphism level of the examined ITS1–5.8S–ITS2 sequence of B. sarmatica accessions constituted 1.3%. The phylogenetic position of B. sarmatica within the genus Bellevalia was determined. It was demonstrated that B. sarmatica belonged to the section Nutantes, and the most closely related species were B. webbiana and B. dubia. Nucleotide substitutions in the 5.8S rRNA gene sequence of the analyzed Scilloideae accessions were identified and studied. The predicted secondary structure of 5.8S rRNA gene was constructed. It was demonstrated that in the examined accessions, mutations in the 5.8S rRNA gene were mainly localized in the third hairpin region and had no effect on the secondary structure of the 5.8S rRNA molecule.

AFLP analysis of genetic diversity in the genus Mallus Mill. (Apple)

The first molecular genetic analysis of the apple species and varieties from Russian collections with the AFLP marker system was performed in order to study the genetic diversity of the genus Malus, as well as to clarify the phylogeny and solve some systematic issues of the genus. Nienty-one apple accessions, including species from five sections of the genus Malus and hybrid species, were examined. The level of polymorphism constituted 90.2%. It was demonstrated that the classical taxonomy of the genus Malus, which identifies five sections based on differences in their morphological characters, is valid and may be used to classify apple species. The species assignment of the Antonovka landraces was established. All of them belonged to the species M. domestica. It was demonstrated that the Yakutskaya apple variety is a domesticated species of the section Gymnomeles, presumably, M. baccata. AFLP analysis confirmed the hybrid nature of many species. The relationships between apple varieties of the Golden group with American wild species were demonstrated. The data suggest that the species M. sieversii was the ancestor of not only the domesticated apple but also of other species of the Section Malus.

Interspecific polymorphism of the glucosyltransferase domain of the sucrose synthase gene in Malus and related Rosaceae species

The sequences that encode the main functional glucosyltransferase domain of sucrose synthase genes have been identified for the first time in 14 Malus species and related Rosaceae species, and their polymorphism was investigated. Single nucleotide polymorphisms leading to amino acid substitutions in the protein sequence, including the conservative transmembrane motif sequence common to all sucrose synthase genes of higher plants, were detected in the studied sequences.