Vol 55, No 1 (2019)

This review presents characteristics of the HD-Zip family of homeobox-containing genes unique to plants, and their involvement in molecular mechanisms of resistance to certain adverse environmental factors (such as drought, deficiency of light, and pathogens) is considered. The importance of the HD-Zip genes in modulating and combining the signals from different hormone-dependent genetic cascades controlling the adaptation of plants to various external factors is demonstrated.

Over the past decade, there has been an active study of the interactions between the population of transposable elements (TEs) and the rest of the genome. Many regulatory sequences of TEs have been used for different genes regulation and genome organization. These regulatory sequences can be transcription factor binding sites, enhancers, and insulators. TEs may contain promoters that can be domesticated during substitution of original gene promoters or during de novo formation of long noncoding RNAs. In addition, there are many examples of domestication of TE-encoded proteins, for example, transposases, proteases, and Gag proteins. This review highlights the role of TEs in the evolution of gene regulatory networks and the principles determining it.

Genetic typing of the anthrax causative agent is used in epidemiological investigations of infection outbreaks and serves as a tool for studying the evolution of this pathogenic species. Analytical, technical, and economic possibilities of the most common modern methods of genetic typing of B. anthracis have been studied on the basis of our own and published data. It was established that canSNP genotyping distinguishes 10 genotypes among 23 strains of B. anthracis with a diversity index DI of 0.8261. DI for MLST is no more than 0.5495–0.5790, depending on the sample of strains. DI for MLVA15, 25, and 31 is the same and equal to 0.9881. SNP analysis of the core region of genomes of 181 strains provides the highest discrimination (DI = 1). MVLST with a DI of 0.9960, like SNR analysis, reveals differences between genotypes of isolates from the same outbreak. CanSNP13 genotyping is quite sufficient as a preliminary stage of genotyping for the separation of strains into the main genetic lines. MLST of B. anthracis is impractical owing to low resolution and laboriousness, and MVLST, despite its high resolution, is impractical owing to the length and laboriousness of the study. The identity of isolates from the same anthrax outbreak can be confirmed using MLVA15–31; the subtle differences between them are the methods of SNR and SNP analysis of the core region of the genome.

In cultivated tomato hybrids (Marglobe × Mo938), the anthocyanin-free gene shows linked inheritance with the d (dwarf) gene on chromosome 2, but with a recombination frequency approximately three times higher than that according to the genetic map and in other hybrids with the Marglobe line. Cytological analysis of the mother pollen cells of the hybrids (Marglobe × Mo938) revealed no abnormalities of meiotic division and segregation of chromosomes, as well as no decrease in fertility. By means of the functional allelism test, it was established that, unlike Mo500, Mo504, and Mo755 marker tomato lines, in Mo938 the anthocyanin-free trait is not determined by the aw (anthocyanin without) or aa (anthocyanin absent) genes of chromosome 2. Using the F₂ progeny of interspecies hybrids (Mo938 × Solanum pimpinellifolium), independent inheritance of the anthocyanin-free gene relative to the wv (white virescent) and d marker genes, as well as to six SSR anchor markers distributed at different sites of chromosome 2, was established. Thus, the Mo938 tomato line carries the d and wv markers on chromosome 2, as well as the anthocyanin-free gene not belonging to chromosome 2.

Pinus nigra Arn. ssp. pallasiana (Lamb.) Holmboe (Anatolian black pine) is the second most widespread coniferous pine species in Turkey after the red pine. Mobile genetic elements are capable of jumping from their positions to others within the genome and constitute 15–90% of plant genomes. In this study, barley-specific BAGY2, Nikita and Sukkula retrotransposon movements were examined in the stems and needles of Anatolian endemic Pinus nigra ssp. pallasiana var. pyramidata and var. Seneriana. Moreover, multiple alignment analyses were also performed to observe the relationships among sequences found in angiosperms and gymnosperms. Polymorphisms were calculated as 0–11% for BAGY2, 0–56% for Nikita and 0–76% for Sukkula between stems and needles in var. pyramidata. There was no polymorphism in var. Seneriana. Homomorphic band profiles were observed among all needle samples in BAGY2, Nikita and Sukkula analyses both in var. pyramidata and var. Seneriana. Furthermore, we detected few similar sequences among retrotransposons identified in different plants. There is almost no research related to retrotransposons in Anatolian black pine’s endemic varieties. This is the first study to investigate the movements of barley-specific retrotransposons in Pinus nigra. Our results are expected to contribute knowledge about these endemic plants, and even the evolutionary relationships between angiosperms and gymnosperms.

The genetic diversity of ten microsatellite loci is examined in samples of Arctic rainbow smelt. The expected heterozygosity estimates vary in the range of 12.6–83.9% (mean 55.3%). The degree of genetic differentiation is statistically significant: θ = 2.8%, 95% CI (1.4–4.9%). The greatest differences are found between datasets of smelt in Eastern and Western Kamchatka. The samples from Lake Nerpich’e demonstrate the maximum estimates of divergence from the other datasets from both the western and eastern coasts.

Chronic obstructive pulmonary disease (COPD) is a multifactorial chronic inflammatory disease of the respiratory system. A key phenomenon of COPD pathogenesis is inflammation. The goal of the present study was to investigate the association of COPD with alleles and genotypes of the genes that encode chemokines and chemokine receptors (CCL11, CX3CR1, CCR5, CCL5, CXCL12, CCL2, and CCL17), adhesion molecules (PECAM1 and ICAM1), and serum amyloid A1 (SAA1). It was found that COPD was associated with the C allele and the TC genotype of SAA1 (rs1136743C>T) (P = 0.0001, OR = 1.58 and P = 0.00001, OR = 2.15, respectively); this association was confirmed in the subgroups differentiated by smoking status. Markers of COPD risk were also the CG genotype of PECAM1 (rs281865545G>C) (P = 0.028, OR = 1.36) and the GG genotype of ICAM1 (rs5498A>G), which were significantly associated with the disease in smokers (P = 0.005, OR = 1.66). The AA genotype of CCL2 (rs1024611A>G) was associated with the disease in nonsmokers (P = 0.037, OR = 1.82). The GG genotype of PECAM1 (rs281865545G>C) and the AA genotype of CX3CR1 (rs3732378A>G) were associated with higher vital capacity (P = 0.014 and P = 0.04, respectively). Subjects with the GG genotype of ICAM1 (rs5498A>G) exhibited lower forced expiration volume in 1 s and lower forced vital capacity (P = 0.025 and P = 0.029, respectively).

The Human Leukocyte Antigen (HLA) system represents a distinctive marker in identifying population groups since they exhibit a very high level of polymorphism that reveals remarkable frequency variation in human populations. In this study the gene frequencies of HLA class II DRB1, DQB1 and DQA1 alleles were studied in 100 randomly chosen individuals from region of Vojvodina, Serbia, with an aim to establish the genetic relationship between Vojvodina population and selected populations of European and non-European descent. DNA low resolution typing for DRB1, DQA1 and DQB1 was done using a standardized PCR-SSOP. Genetic distances between Vojvodina and 28 populations were computed based on frequency of DRB1 alleles. Phylogenetic trees were constructed using the neighbour-joining algorithm. The distribution of the observed genotypes is in Hardy–Weinberg equilibrium for all studied systems. The most frequent alleles were HLA-DQA1*01 (0.475), HLA-DQB1*05 (0.3), HLA-DRB1*11 (0.14). Two locus haplotype analysis identified HLA-DQB1*05-DQA1*01 (0.22), HLA-DQB1*03-DQA1*05 (0.135) and HLA-DQB1*06-DQA1*01 (0.1075) as the common haplotypes in Vojvodina population. Compared to other populations, Vojvodina appear to be genetically related to Balkan population, in particular Croatia, Slovenia and Bosnia and Herzegovinia. In conclusion, genetic distance matrix estimated using alleles at HLA-DRB1 locus, indicates that Vojvodina population is related to present-day nearby populations, Polish, Russians, Germans and French but not to Albanians from Kosovo and Bulgarians.