Russian version of Russian Journal of Genetics (1022-7954).
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Publications in this journal
Article: The 5q31 region in two African populations as a facet of natural selection by infectious diseases.[show abstract] [hide abstract]
ABSTRACT: Cases of extreme natural selection could lead either to rapid fixation or extinction of alleles depending on the population structure and size. It may also manifest in excess of heterozygosity and the locus concerned will be displaying such drastic features of allele change. We suspect the 5q31 in chromosome 5 to mirror situation of such extreme natural selection particularly that the region encompasses genes of type 2 cytokine known to associate with a number of infectious and non-infectious diseases. We typed two sets of single nucleotide polymorphisms (SNPS) in two populations: an initial limited set of only 4 SNP within the genes of IL-4, IL-13, IL-5 and IL-9 in 108 unrelated individuals and a replicating set of 14 SN P in 924 individuals from the same populations with disregard to relatedness. The results suggest the 5q31 area to be under intense selective pressure as indicated by marked heterozygosity independent of Linkage Disequilibrium (LD); difference in heterozygosity, allele, and haplotype frequencies between generations and departure from Hardy-Weinberg expectations (DHWE). The study area is endemic for several infectious diseases including malaria and visceral leishmaniasis (VL). Malaria caused by Plasmodiumfalciparum, however, occurs mostly with mild clinical symptoms in all ages, which makes it unlikely to account for these indices. The strong selection signals seems to emanate from recent outbreaks of VL which affected both populations to varying extent.Genetika 02/2013; 49(2):279-88.
Article: R-ISSR - for fingerprinting, mapping and identification of new genomic loci in rye (secale cereale l.).[show abstract] [hide abstract]
ABSTRACT: The results of the research confirming the possibility of applying various combinations of RAPD and ISSR primers in one multiplex PCR and the generation of a new type of R-ISSR products for the rye genome were presented in this work. The following was applied in the research: five rye genotypes including two inbred lines (153/79-1 and Otl-3), hybrid F1 and two bulks (tolerant and susceptible) formed from recombinant inbred lines - RILs (F9) varying in the response to abiotic stress caused by nutrient deficiencies at the seedling stage. While evaluating the possibility of applying R-ISSR to the assessment of the rye variability, five of its genotypes were amplified separately with the RAPD and ISSR primers in each PCR reaction. These primers were combined in R-ISSR amplifications. The products of RAPD, ISSR and R-ISSR amplification were separated in 1.5% agarose gel. 32 R-ISSR combinations were examined, combining 20 and 8 selected RAPD and ISSR primers, respectively. 658 loci were amplified, including 230 RAPD, 180 ISSR and 271 R-ISSR, including 157 new loci. Over 91 loci were found, with an identical electrophoretic mobility for three methods. It was shown that R-ISSR products with electrophoretic mobility on agarose gels, identical to the co-migrating RAPD or ISSR, are not products of RAPD or ISSR, but they possess sequences of heteroamplicons - R-ISSR. The occurrence of sequences of primers used to R-ISSR was demonstrated while sequencing seven selected products of the above type. The ISSR primers with a low Tm were proven to generate repeatable fingerprints in the thermal profile of the reaction specific for RAPD and combined with the RAPD primer - repeatable R-ISSR profiles. A similar range of variability as described in RAPD or ISSR was observed in the R-ISSR profiles. The correlation coefficient between genetic similarity matrices for five rye genotypes, calculated with the Mantel test, amounted to rABC = 0.870.Genetika 02/2013; 49(2):214-23.
Article: Genotype x environment interaction patterns for grain yield of spring barley in different regions of Kazakhstan.[show abstract] [hide abstract]
ABSTRACT: Barley plays an important role in agricultural sector of Kazakhstan and it is grown in many different climate zones over 1.5 min hectares annually. Therefore development of optimal cultivars for specific environments is a major challenge for barley breeding community in Kazakhstan. One of the approaches to address this question is to test large collection of commercial cultivars and advanced lines over a number of environmental sites that reflect major spatial and temporal climate variations in the country. In this work 103 cultivars and advanced lines of spring barley bred in six different breeding stations of Kazakhstan were grown in different testing sites in seven regions over 2009-2011 years. The major tasks of this research were to evaluate genotype x x environment interactions and assess grain yield in associations with developmental stages of barley, such as heading date and seed maturation date. The results suggest that (i) heading and seed maturation dates are significantly correlated with grain yield in specific regions and may have opposite correlation indexes in response to environmental conditions; (ii) accessions of different bred origin vary in their ability to exhibit environmentally-dependent plastic responses; (iii) spatial variation was more important than temporal variation in GxE interactions; (iv) biplot analysis is effective approach in identification of best suitable and stable accessions for both broad and narrow environments. The obtained results are further contribution to understanding of complex mechanisms of genotype x environment interactions.Genetika 02/2013; 49(2):224-34.
Article: Aeluropus littoralis NaCl-induced vacuolar H(+)-ATPase subunit c: molecular cloning and expression analysis.[show abstract] [hide abstract]
ABSTRACT: The vacuolar H(+)-ATPase (VHA) is a universal component of eukaryotic organisms that is responsible for establishing and maintaining intracellular pH gradients across specialized organellar membranes, and influences the transport of cations into the vacuoles of plant cells. A cDNA clone (AlVHA-c) encoding the c subunit of V-ATPase was isolated from the monocot halophyte Aeluropus littoralis. The DNA sequence of AlVHA-c showed significant homology with V-ATPase subunit c of millet, rice and Zea mays. The deduced amino acid sequence of AlVHA-c and other reported c subunits were compared, and sequence relationships have been drawn to know their genetic relatedness. Semi-quantitative RT-PCR analysis of salt-treated A. littoralis plants revealed that subunit c of V-ATPase is regulated by NaCl treatment at transcriptional level in a tissue-specific manner. The increased V-ATPase subunits amounts of A. littoralis provide the energy for the compartmentalization of sodium in response to salinity.Genetika 12/2012; 48(12):1380-8.
Article: Population genetic structure and historical demography of Oratosquilla oratoria revealed by mitochondrial DNA sequences.[show abstract] [hide abstract]
ABSTRACT: Genetic diversity, population genetic structure and molecular phylogeographic pattern of mantis shrimp Oratosquilla oratoria in Bohai Sea and South China Sea were analyzed by mitochondrial DNA sequences. Nucleotide and haplotype diversities were 0.00409-0.00669 and 0.894-0.953 respectively. Neighbor-Joining phylogenetic tree clustered two distinct lineages. Both phylogenetic tree and median-joining network showed the consistent genetic structure corresponding to geographical distribution. Mismatch distributions, negative neutral test and "star-like" network supported a sudden population expansion event. And the time was estimated about 44000 and 50000 years ago.Genetika 12/2012; 48(12):1410-7.
Article: Isolation and characterization of microsatellite markers in Chinese herb of Dendrobium loddigesii.[show abstract] [hide abstract]
ABSTRACT: As an invaluable herb, Dendrobium loddigesii is widely used in Chinese medicinal field. In order to develop a convenient and efficient identification method and investigate the genetic diversity and structure of this species, twelve microsatellite loci were isolated from two microsatellite-enriched libraries. Twenty-six individuals from Baise population were analysed. The observed and expected heterozygosities ranged from 0.174 to 0.617 and from 0.182 to 0.608, respectively. These microsatellite loci characterized from D. loddigesii will contribute to research on the individual authentication, population structure, genetic diversity and conservation of this species and its similar species.Genetika 10/2012; 48(10):1237-40.
Article: The point mutation induced by the low-energy N+ ion implantation in impatiens balsamine genome.[show abstract] [hide abstract]
ABSTRACT: To investigate the effect of genome mutations induced by low energy ions implantation in higher plants, genome mutation of Impatiens balsamine mutant induced by low energy N+ ion implantation were analyzed by the RAPD, ISSR and genome sequence. Six out of the 121 ISSR primers and 6 out of the 135 RAPD primers showed that polymorphism ratios between mutants and wild type were 4.96% and 2.89%, respectively. Sequence analysis revealed that base deletions, insertions, and substitutions were observed in the mutant genome comparable to wild type. N+ induced point mutations were mostly base substitution (77.4%), no duplication, long fragments insertions and deletions was found. In all point mutation, adenine (A) was most sensitive to the N+ ion implantation in impatiens. The transition was mainly A --> guanine (G) (15.90%) and thymine (T) --> cytosine (C) (12.55%). Transversion happened in A <--> T (16.74%), which much higher than C <--> G(5.02%), G <--> T(6.69%), A <--> C (7.11%) bases. These findings indicate that low energy ions being a useful mutagen were mostly cause the point mutation in impatiens.Genetika 10/2012; 48(10):1179-84.
Article: QTL and epistatic analyses of heterosis for seed yield and three yield component traits using molecular markers in rapeseed (Brassica napus L.).[show abstract] [hide abstract]
ABSTRACT: Aiming to explore the basis of heterosis in rapeseed, QTLs for yield and three yield component traits were mapped and the digenic interactions were detected in an F2 population derived from a cross between two elite rapeseed lines, SI-1300 and Eagle, in this study. Twenty-eight QTLs were detected for the four yield traits, with only two of them detected simultaneously in the Wuhan and Jingmen environments. Additive, partial dominance, dominance, and overdominance effects were all identified for the investigated traits. Dominance (including partial dominance) was shown by 55% of the QTLs, which suggests that dominance is a major genetic basis ofheterosis in rapeseed. At the P < or = 0.01 level with 1000 random permutations, 108 and 104 significant digenic interactions were detected in Wuhan and Jingmen, respectively, for the four yield-related traits using all possible locus pairs of molecular markers. Digenic interactions, including additive by additive, additive by dominance, and dominance by dominance, were frequent and widespread in this population. In most cases (78.3%), the interactions occurred among marker loci for which significant effects were not detected by single-locus analysis. Some QTLs (57.1%) detected by single-locus analysis were involved in epistatic interactions. It was concluded that epistasis, along with dominance (including partial dominance), is responsible for the expression of heterosis in rapeseed.Genetika 10/2012; 48(10):1171-8.
Article: Haplotype variation of estrogen receptor-alpha (ER-alpha) gene exon 4 in Turkish sheep breeds.[show abstract] [hide abstract]
ABSTRACT: Estrogen receptor a (ERalpha) gene has previously been found to related with sexual development and reproduction. In this study, on the basis of the sequences of human, cattle and caprine estrogen receptor a (ERalpha) genes, available in the GenBank database, sets of PCR primers were designed and used to amplify the ovine ERalpha gene exon 4 region. We identified six single nucleotide polymorphisms (SNP) in the ERalpha exon 4. Some variations determined for exon 4 g.43A > G, p.T43A; g.49C > T, p.L49F; g.178A > T, p.T178S led to changes in the amino acids, but no amino acid changes were determined in g. 18G > C, g.27C > T, g.96G > A. These fragments were deposited in the GenBank database under accession number: JF262030-JF262035. It was noted in particular that White Karaman and Awassi breeds were similar to each other, whereas the Chios breed had a different variation.Genetika 10/2012; 48(10):1185-9.
Article: Genetic and morphological variation of three freshwater lake populations of Coilia ectenes (Engraulidae).[show abstract] [hide abstract]
ABSTRACT: Population structure of the important commercial fish, Coilia ectenes, was investigated in samples from three freshwater lakes in the Eastern China using a multivariate approach of morphometrics and mitochondrial DNA control region sequencing. A total of eighteen morphological distances of truss method and eight morphometric variables were taken from each fish. Multivariate analyses of the morphometric data revealed significant morphological differences among the three lake populations, especially for those samples from Taihu Lake. Discriminant functions were used to compare sites, and these permitted an 83% success rate in distinguishing fish from the three sites. However, no obviously geographical differentiation was found among those populations of C. ectenes based on the genetic data. In the AMOVA analysis, only 2.2% genetic variability came from different populations, and most of them were present within the sub-populations. Experience a recent population expansion and some movement of fish among those areas, quite possibly enough to bring about relative genetic homogeneity, but there is insufficient to prevent the three populations from differing phenotypically. The diversified environmental factors may be playing an important role in shaping morphological variations among those populations.Genetika 10/2012; 48(10):1200-6.
Article: Morphological characteristics and chromosome behaviour in F1, F2 and BC1 progenies between Chrysanthemum x morifolium and Ajania pacifica.[show abstract] [hide abstract]
ABSTRACT: The garden chrysanthemum (Chrysanthemum x morifolium) variety 'Aoyunhuoju' (2n = 6x = 54) was crossed as female with Ajania pacifica (2n = 10x = 90) to produce an intergeneric F1 hybrid, which was used both as a source ofF2 progeny and as a parent for a first back-cross with 'Aoyunhuoju'. The morphology of all of the F1 hybrids and hybrid derivatives was intermediate with respect to the two parents, although the BC1 progenies resembled 'Aoyunhuoju' more closely than any of the F1 and F2 progenies did. In the F1 hybrid, the density of silvery hairs on the lower leaf surface and along the margin of the leaf was lower than in A. pacifica, while that in the BC1 generation, this trait was less prominent than in the F1. The somatic chromosome number of the F1, F2 (with an exception of F2-6 of a mainly 63) and BC1 generations was 2n = 8x = 72, 2n = 8x = 72 and 2n = 7x = 63 respectively, as expected. The hybrids and their derivatives retained a variable degree of fertility. There was a low frequency of meiotic chromosome pairing failure in all three hybrid generations, with most of the chromosomes involved as bivalents. Some BC1 individuals show potential for commercialization thanks both to their flower shape and the inheritance of the silvery leaf trait from A. pacifica.Genetika 08/2012; 48(8):951-61.
Article: Comparative analysis of the role of JNK signaling pathway in regulating cell proliferation and apoptosis of rat liver regeneration and rat acute hepatic failure.[show abstract] [hide abstract]
ABSTRACT: To compare the role of JNK signaling pathway in rat liver regeneration (LR) and in rat acute hepatic failure (AHF) occurrence at the gene transcription level, Rat Genome 230 2.0 array was used to detect the gene expression profiles of the two processes, and bioinformatics and systems biology methods were applied to analyze the physiological activities uncovered by their gene expression profiles in this study. The results showed that 240 genes were included in the array above, though there were 302 genes related to forty two paths of JNK signaling pathway. Array detection results demonstrated that 52 genes were significantly expressed during LR, 20 genes in AHF occurrence, and 15 genes in both of above two processes. Synergy values of these genes were calculated using a mathematical model established by our lab, which revealed the following. The cell proliferation-promoting effects of paths 1, 16 and paths 1-17 of JNK signaling pathway were stronger than the control at 6-12 h and 72 h of LR, respectively, while the cell proliferation-promoting effects of paths 1-17 and the cell proliferation-inhibiting effects of path 34-35 were weaker at 6h of AHF occurrence. The cell apoptosis-promoting effects of paths 22-23 were much stronger at 6, 12 and 72 h of LR and at 12, 24 h of AHF occurrence. In conclusion, thirty eight paths of JNK signaling pathway regulate cell proliferation and apoptosis in both LR and AHF occurrence.Genetika 08/2012; 48(8):909-17.
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ABSTRACT: We investigated the population genetic structure of wild boars from Vojvodina (Serbia), Slavonija (Croatia) and Bosnia using four microsatellite markers. All loci presented a high degree of polymorphism and a total of 76 alleles (mean 19 alleles per locus) were detected. Average observed heterozygosity (Ho) value was 0.60. Deviation from Hardy-Weinberg equilibrium was found due to significant heterozygote deficiency detected for three of the four analyzed loci and for all populations. F(IS) value over all loci and all populations was 0.29, and the effective number of migrants based on private alleles was 1.64. Sufficient levels of gene flow were found between all populations and the spatial structure showed slightly closer nuclear gene pool affinity of Vojvodina and Slavonija populations in relation of Bosnia population.Genetika 08/2012; 48(8):1007-11.
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ABSTRACT: Sickle cell disease (SCD) is an inherited autosomal recessive disorder. We aimed to describe the spectrum of haplotyes of BS-gene and to investigate a relationship with disease phenotype in patients with SCD in Southern Iran. We didn't find any significant association between BS-globin gene haplotypes and clinical severity of the disease in an Iranian population. The exact mechanism by which the BS-globin gene polymorphism affects clinical presentation is not obvious; however, further detailed studies at the molecular level, with a larger sample size are required to show the mechanisms that influence the clinical presentation of SCD in Iranian population.Genetika 07/2012; 48(7):890-3.
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ABSTRACT: We designed in vitro study to determine possible genotoxic effects oftacrolimus (FK-506), which is used as a potent immunosuppressive drug, by using sister chromatid exchange (SCEs), chromosome aberration (CAs), micronuclei tests (MN) and cell growth kinetics such as mitotic index (MI) and replication index (RI) in human lymphocytes. The cells were treated with 5, 25, 50, and 100 ng/mL concentrations of tacrolimus, for 24 h and 48 h treatment periods. Tacrolimus induced CA and MN frequency at all concentrations for 24 and 48 h In additon, it induced the SCE at the highest concantration for 24 h and at 25 and 100 ng/mL for 48 h. Tacrolimus decreased MI at all concentrations (except 5 ng/mL) for all treatment periods. It also inhibited the RI at 50 and 100 ng/mL concentrations for 24 h and at all concentrations for 48 h. Treatments given with tacrolimus result in the enhance of the different endpoints ofgenotoxicity, suggesting its mutagenic action on lymphocytes in vitro.Genetika 06/2012; 48(6):762-7.
Article: [Gene pool of ethnic groups of the caucasus: results of integrated study of the Y chromosome and mitochondrial DNA and genome-wide data].[show abstract] [hide abstract]
ABSTRACT: Genetic diversity has been analyzed in 22 ethnic groups of the Caucasus on the basis of data on Y-chromosome and mitochondrial DNA (mtDNA) markers, as well as genome-wide data on autosomal single-nucleotide polymorphisms (SNPs). It has been found that the West Asian component is prevailing in all ethnic groups studied except for Nogays. This Near Eastern ancestral component has proved to be characteristic of Caucasian populations and almost entirely absent in their northern neighbors inhabiting the Eastern European Plain. Turkic-speaking populations, except Nogays, did not exhibit an increased proportion of Eastern Eurasian mtDNA or Y-chromosome haplogroups compared to some Abkhaz-Adyghe populations (Adygs and Kabardians). Genome-wide SNP analysis has also shown substantial differences of Nogays from all other Caucasian populations studied. However, the characteristic difference of Nogays from other populations of the Caucasus seems somewhat ambiguous in terms of the R1a1a-M17(M198) and R1b1b1-M73 haplogroups of the Y chromosome. The state of these haplogroups in Turkic-speaking populations of the Caucasus requires further study.Genetika 06/2012; 48(6):750-61.
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ABSTRACT: Cattle are the most important livestock in India and play a pivotal role in agrarian economy. There are 34 recognized breeds of cattle and number of unexplored lesser known populations. The present study is a contribution towards determining genetic variation and understanding the relationship among four lesser known populations. A total of 194 unrelated DNA samples from three cattle populations of Orissa (Binjharpuri, Ghumsuri, Motu) and Hill cattle of Kumaun (Kumauni) were collected from respective breeding tracts. Genotyping was done with 23 bovine microsatellite markers as suggested by International Society for Animal Genetics (ISAG) and FAO (DAD-IS) on automated sequencer. The average observed heterozygosity in the four populations lie within the narrow range of 0.623 +/- 0.04 in Binjharpuri to 0.664 +/- 0.03 in Kumauni. Mean estimates of observed and expected heterozygosity over all loci and breeds were 0.651 +/- 0.02 and 0.720 +/- 0.01, respectively. In the overall population, the homozygote excess (F(IT)) of 0.132 +/- 0.03, was partly due to the genetic differentiation among breeds (F(ST) = 0.044 +/- 0.01) and, to a larger extent, to a significant homozygote excess within breeds (F(IS) = 0.094 +/- 0.03). The phylogenetic reconstruction from a UPGMA clustering based on Nei's Standard genetic distance yielded a tree with Binjharpuri and Ghumsuri on a single node and Motu and Kumauni on separate nodes. The most probable clustering detected by STRUCTURE in population was three. Binjharpuri and Ghumsuri animals were assigned to one cluster with high proportion of membership.Genetika 06/2012; 48(6):719-25.
Article: [Characterization of the Bellevalia sarmatica (Georgi) woronow populations from Volgograd oblast using molecular genetic identification].[show abstract] [hide abstract]
ABSTRACT: DNA samples obtained from the populations of the Red Data Book species Bellevalia sarmatica (Georgi) Worovow from Volgograd oblast were examined using RAPD and AFLP analyses. DNA marking revealed considerable differences in the levels of interpopulation and intraspecific polymorphism of the Bellevalia. Furthermore, RAPD analysis, despite of lower levels of interpopulation polymorphism identified, made it possible to obtain clearer data on population subdivision upon statistical treatment of the results. The results of this study can be used in developing conservation strategies for maintenance of the species abundance and genetic diversity, as well as in elaborating the criteria for construction genetic collections.Genetika 06/2012; 48(6):706-12.
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ABSTRACT: The character of chromosome pairing in meiocytes was studied in F1 wheat-rye Triticum aestivum L. x Secale cereale L. (ABDR, 4x = 28) hybrids with three types of chromosome behavior: reductional, equational, and equational + reductional. A high variation of the frequencies of bivalents and ring univalents was observed in meiocytes with the reductional or equational + reductional type of chromosome behavior. The type of chromosome division was found to affect the bivalent and ring univalent frequencies. Chromosome pairing occurred in 10.28% of meiocytes with the reductional chromosome behavior, 0.93% of meiocytes with the equational chromosome behavior, and 10.81% of meiocytes with the equational + reductional chromosome behavior. On average, 0.13 bivalents per cell formed in meiocytes of the hybrid population. C-banding and genomic in situ hybridization (GISH) showed that both rye and wheat chromosomes produced ring univalents. The role of the Ph genes in regulating the bivalent formation in meiocytes with different types of chromosome behavior is discussed.Genetika 06/2012; 48(6):698-705.
Article: Identification of a specific scar marker for detection of Tilletia foetida (Wall) Liro pathogen of wheat.[show abstract] [hide abstract]
ABSTRACT: Common bunt is one of the most important destructive diseases of wheat worldwide and is a domestic quarantined disease in China. However, a rapid and efficient method to identify the corresponding pathogens is currently limited. The objective of the present study was to develop a diagnostic molecular marker specific towards Tilletia foetida (Wall) Liro, a causal agent of the bunt disease. One specific DNA fragment for T. foetida (286 bp in length) was amplified using an Amplified Fragment Length Polymorphism (AFLP) assay and, this fragment was cloned and sequenced. One pair of specific primers (SC(286-1)/SC(286-2)), which was designed according to the sequence, could specifically amplify the corresponding fragment in all of the T. foetida isolates employed from both the People's Republic of China and United States, whereas this fragment could not be amplified by the other fungal species tested. Therefore, a specific Sequence Characterized Amplified Region (SCAR) marker was developed. This SCAR marker could distinguish T. foetida from related pathogenic fungi efficiently and could be used for the early diagnosis of the common bunt of wheat in the field, and provide an efficient way for disease surveillance and disease forecasting in cereal crop.Genetika 06/2012; 48(6):776-80.
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