Use Of Molecular Genetic Markers Research Articles

Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals.

Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in environmental pollution such as water pollution and soil degradation as well as alterations in the composition and concentration of environmental gases. These changes are affecting not only biodiversity loss but also affecting the physio-biochemical processes of crop plants, resulting in a stress-induced decline in crop yield. To overcome such problems and ensure the supply of food material, consistent efforts are being made to develop strategies and techniques to increase crop yield and to enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication and initially remained dependent on phenotype-based selection for crop improvement. But it has grown through cytological and biochemical methods, and the newer contemporary methods are based on DNA-marker-based strategies that help in the selection of agronomically useful traits. These are now supported by high-end molecular biology tools like PCR, high-throughput genotyping and phenotyping, data from crop morpho-physiology, statistical tools, bioinformatics, and machine learning. After establishing its worth in animal breeding, genomic selection (GS), an improved variant of marker-assisted selection (MAS), has made its way into crop-breeding programs as a powerful selection tool. To develop novel breeding programs as well as innovative marker-based models for genetic evaluation, GS makes use of molecular genetic markers. GS can amend complex traits like yield as well as shorten the breeding period, making it advantageous over pedigree breeding and marker-assisted selection (MAS). It reduces the time and resources that are required for plant breeding while allowing for an increased genetic gain of complex attributes. It has been taken to new heights by integrating innovative and advanced technologies such as speed breeding, machine learning, and environmental/weather data to further harness the GS potential, an approach known as integrated genomic selection (IGS). This review highlights the IGS strategies, procedures, integrated approaches, and associated emerging issues, with a special emphasis on cereal crops. In this domain, efforts have been taken to highlight the potential of this cutting-edge innovation to develop climate-smart crops that can endure abiotic stresses with the motive of keeping production and quality at par with the global food demand.

Роль полиморфизмов генов-регуляторов артериального давления в патогенезе преэклампсии

Aim: To analyze the information presented in scientific publications on the role of polymorphic variants of genes responsible for the regulation of blood pressure (BP) in the pathogenesis of preeclampsia (PE). Key points. Genome-wide association studies conducted for PE confirms the multifactorial nature of its pathogenesis and demonstrates a number of BP regulator genes, polymorphic variants of which are associated with its development. A review of the literature showed that PE and diseases of the cardiovascular system have similar mechanisms of inheritance. Conclusion. The use of molecular genetic markers of PE opens up new opportunities for personalized prediction of this gestational complication and increase the effectiveness of preventive measures. Keywords: preeclampsia, blood pressure regulation genes, genetic polymorphisms, prognosis.

Characteristics of the nucleotide composition and de novo structure of 28S rRNA gene of intestinal flukes (Echinostomatidae) and genetic distance among species (suborder Echinostomata)

The family Echinostomatidae includes four genera, Echinostoma, Hypoderaeum, Echinoparyphium, and Artyfechinostomum, which are of public epidemiological and pathogenic importance. The morphological similarity of species requires differentiating methods, and the use of molecular genetic markers is mainly encountered. The 28S rRNA gene sequence in the family Echinostomatidae is an important marker for the analysis of the interspecies and phylogenetic relationships. However, information about the structure and composition of the complete 28S rRNA gene in Echinostomatidae is limited. In this study, the complete 28S rRNA sequences (3,881–3,883 bp) of four species, including Echinostoma revolutum (designated Erev-MSD15-TH), E. malayanum (Emal-EMI3-TH), E. miyagawai (Emiy-RED11-TH), and Hypoderaeum conoideum (Hcon-RED42-TH) were obtained and analyzed for their genetic characteristics. All had complex secondary structures, containing numerous branches, “hairpins”, and “loops” that provide stability of the rRNA gene. The de novo structural pattern and the "skew" value in the nucleotide use of E. revolutum, E. malayanum, E. miyagawai, and H. conoideum were analyzed. The nucleotide usage of A, T, G, C and A+T and G+C of 28S rRNA in all species of the family Echinostomatidae was similar, in which A and T usage were almost equal, and G and C were slightly different in the range of 7–8%, so the skewness for AT was very low negative value (–0.029 to –0.045), and for GC was not very high (0.163 to 0.172). The genetic distance estimated among strains within a species (intra-specific level) was very low in both the Echinostomatidae (0.05%) and the Fasciolidae families (0–0.03%), and that among different species (inter-specific level) was higher. However, among species in different families (inter-familial level) the genetic distance was highest, at 3.80–4.86%, as seen between Echinostoma and Fasciola species. The 28S rRNA gene dataset obtained from four species of the intestinal flukes (family Echinostomatidae) in this study contribute to the understandings of genetic markers in the suborder Echinostomata for use in diagnostic, phylogenetic, taxonomic, epidemiological, and population genetics studies.

Gene polymorphisms role of blood coagulation in myocardial infarction development in patients with malignant tumors of thoracoabdominal localization

Aim. To evaluate the role of polymorphic variants of blood coagulation genes (F2, F5, F7, F13, FGB, ITGA2, ITGB3, PAI-1) in the development of myocardial infarction in patients with malignant tumors of thoracoabdominal localization.
 Materials and methods. The study included 143 patients with thoracoabdominal tumors operated in the oncological Department of surgical methods of treatment No.11 (thoracic Oncology) of the thoracoabdominal Department of the Blokhin National Medical Research Center of Oncology in 20182019. The study group (n=62) consisted of patients with a history of myocardial infarction or in the perioperative period. The control group (n=81) included patients who did not have severe concomitant cardiovascular diseases, including a family history. Molecular genetic study to determine the gene polymorphisms of blood coagulation were performed in the laboratory of clinical oncogenetic of the Blokhin National Medical Research Center of Oncology with use of reagents Cardiogenetic Thrombophilia (LLC DNA-Technology, Russia, RU No. FSR 2010/08414 from 22.11.2016).
 Results. In the study group, 90.3% (n=56) of cases showed polymorphism -675 5G4G of the PAI-1 gene (SERPINE1, a plasminogen activator inhibitor) associated with a decrease in the activity of the fibrinolytic system and an increased risk of thrombosis. In the control group, this mutation was observed significantly less frequently in 67.9% (n=55) of cases (p0.001). In the group of patients with myocardial infarction, polymorphism 807 CT of the ITGA2 (integrin a2) gene responsible for platelet aggregation was detected in 66.1% (n=41) compared to 19.8% (n=16) in the control group (p0.0001). Polymorphism 1565 TC of the ITGB3 gene (platelet-derived fibrinogen receptor) responsible for fibrinogen-induced platelet aggregation was observed in 25.8% (n=16) of cases in the group of patients with myocardial infarction and in 12.4% (n=10) of cases in the group of patients without concomitant severe cardiovascular pathology (p0.05). In 48.4% (n=30) of patients of the study group, genetic disorders of the FGB gene (fibrinogen, missense mutation -455GA) were also registered, which resulted in the development of dysfibrinogenemia, leading to increased blood thrombogenicity; in the control group, this mutation was 2 times less common 25.9% (n=21) of cases (p0.01). Polymorphism 1691 GA of the F5 gene (coagulation factor V, Leiden factor), which is considered one of the most significant genetic risk factors for thrombosis in Caucasians, was detected in 4.8% (n=3) of cases in the study group, while this mutation was not found in the control group. Polymorphism 20210 GA of the F2 gene (coagulation factor II prothrombin), which is a key protein of the coagulation cascade associated with increased blood levels of prothrombin, was observed in 3.2% (n=2) of patients after myocardial infarction; in the control group, the carrier of this polymorphism was not found in any case. Disorders in the genes that promote hypocoagulation were also noted. Among patients who had a myocardial infarction, polymorphism 10976 GA of the F7 gene (coagulation factor VII) was detected in 17.7% (n=11) of cases, polymorphism 103 GT of the F13 gene (coagulation factor XIII) in 41.9% (n=26) of cases. In patients of the control group, these genetic aberrations were found: in 18.5% (n=15) of cases a mutation in the F7 gene (p0.05) and in 45.7% (n=37) in the F13 gene (p0.05), respectively.
 Conclusion. Based on the results of a molecular genetic study of factors associated with thrombogenic risk, a statistically significant difference in the frequency of occurrence of polymorphisms of genes involved in the process of thrombosis (polymorphisms: -455 GA of the FGB gene, 807 CT of the ITGA2 gene, 1565 TC of the ITGB3 gene, -675 5G4G of the PAI-1 gene) in patients who had a myocardial infarction, compared with patients without severe concomitant cardiovascular diseases. The frequency of 1691 GA polymorphism of the F5 gene, one of the most significant genetic risk factors for thrombosis, reached 4.8%. The obtained data on the use of molecular genetic markers of thrombophilia in patients with malignant tumors of thoracoabdominal localization allow us to identify a group of patients with a high risk of developing perioperative myocardial infarction and take additional measures for the prevention and treatment of thrombotic complications.

Biomarkers of myocardial fibrosis and their genetic regulation in patients with heart failure

Currently, the development of chronic heart failure (CHF) is considered from the perspective of pathological structural remodeling of myocardium and fibrosis. Despite the widespread use of molecular genetic markers in clinical practice, only a small number of them are used to evaluate remodeling processes, as well as to predict potential complications associated with heart failure (HF). In addition, the relationship between many biomarkers with instrumental and histological confirmation of myocardial fibrosis has not yet been determined. Myocardial fibrosis remains quite debatable and controversial subject, which actualizes the further study of this direction. The discovery of pathogenetic and diagnostic markers of myocardial fibrosis could contribute to the development of targeted therapy. Of particular interest is the search for possible pathogenetic markers, since this is relevant for clinical practice.

Development of blast-resistant rice varieties based on application of DNA technologies

Diseases of crops are the main reason for the decrease in yield and product quality. Blast is the most dangerous disease in all areas of world rice cultivation. The most effective, economically viable, and environmentally friendly strategy to combat it is the development of resistant varieties. The use of molecular genetic markers (DNA markers) linked to the loci of blast resistance is relevant in this direction. The objective of the study was to introgress and pyramid genes effective in the south of Russia for race-specific resistance to blast Pi ta, Pi-b, Pi-1, Pi-2, Pi-33, Pi-40 into the genotypes of highly productive rice varieties of domestic breeding to obtain new forms resistant to P. oryzae. To achieve this, varieties Flagman and Boyarin were hybridized with the donors of resistance to blast IR-36, Bl-1, C101-Lac, C101Lac-A-51, IR 83260-2-10-5-2-1-B, which have the genes Pi-ta, Ρi-b, Pi-1 + Pi-33, Pi-2, Pi-40, respectively, with a growing season of more than 150 days. Three backcrosses were carried out and the breeding material was obtained. Several samples with high rates of milled rice quality and blast resistance, productivity, and other economically valuable traits were identified. The program for combining the genes of resistance to blast was performed. The hybridization of the obtained genotypes with the integrated Pi genes between themselves in their various combinations was carried out. The result was a breeding variety with three resistance genes (Pi-1; Pi-2; Pi-33). The cultivation of such varieties in production will reduce the use of chemical protective equipment and avoid pollution of grain ecosystems.

Biochemical and histological indicators of blood and m. longissimus dorsi of young bulls of Kazakh white-headed breed of different genotypes by the CAPN1 and GH genes

The use of molecular genetic markers for productivity is one of the modern approaches in breeding beef cattle. The article presents the results of the studies on the influence of genotypes by the calpain (CAPN1) and growth hormone (GH) genes on live weight, fatty acid composition of blood plasma, quantitative and qualitative indicators of meat of young cattle of Kazakh white-headed breed. It was established that animals of the homozygous geno-types СС–CAPN1 and VV-GH had a larger live weight and its average daily gain on the 240th and 365th days. Their superiority over the GG and LL genotypes was 13.8% (P<0.05) and 6.9%; 14.6% (P<0.05) and 6.9%, respectively. The carriers of the desirable alleles in the homozygous state had the sum of unsaturated fatty acids higher by 6.3% and 7.1%, respectively, than the young bulls, in which genotypes they were absent. The predominance of unsaturated fatty acids over saturated fatty acids also determined lower values of lipid me-tabolism direction index (0.92 and 1.00) in the animals with the desirable genotype. Muscle tissue of animals of the СС and VV genotypes was characterized by a higher level of protein, fat by 0.28–2.13 abs. per cent, energy value, and the quantity of muscle fibers with a smaller diameter per unit area compared to the GG and LL genotypes by on average 8.7% and 25.5% (P<0.01). Due to the greater number of interfiber fat inclusions, muscle tissue of the desirable genotypes received higher marbling scores. The obtained data testify to the prospects of replication of animals, which genotype has the desirable alleles for further improvement of traits of meat productivity of Kazakh white-headed breed.

The International Society of Urological Pathology Consultation on Molecular Pathology of Urogenital Cancer.

The 2019 Consultation Conference on the molecular pathology of urogenital cancers was organized by the International Society of Urological Pathology (ISUP) to have an understanding of the current use of molecular-genetic markers and to make recommendations on their application in prostate, bladder, renal, testicular, and penile cancer. This brief introductory article describes the organization of this conference and provides its rationale and main findings.

Efficiency of using SNP markers in the MSTN gene in the selection of the Pushkin breed chickens

In the poultry industry, indicators reflecting the growth rate of young stock and the exterior characteristics of chickens are important benchmarks for breeding. Traditional selection based on phenotypic evaluation is characterized by low efficiency with a low character inheritance ratio and is difficult to apply in small groups of animals and birds bred in bioresource collections. The use of molecular genetic markers associated with economically important traits makes it possible to carry out early selection of birds. This entails an increase in the profitability of the poultry industry. Recently, single nucleotide polymorphisms (SNPs) have served as convenient markers for selection purposes. For five generations (P1–P5), an experimental selection of hens of the Pushkin breed was carried out for live weight. It was based on selection for single nucleotide polymorphism rs313744840 in the MSTN gene. As a result, a significant increase in the frequency of allele A in this gene, from 0.11 to 0.50, took place. The association of SNP markers with meat qualities in the experimental group led to changes in the exterior profile of an adult bird at 330 days of age. The individuals with the AA and AG genotypes had the greatest live weight and longest body. As a result of selection, the bird on average became larger due to an increase in the number of heterozygous individuals with long bodies and large chest girths. The depth of the chest and the width of the pelvis increased due to an increase in the frequency of allele A in the experimental population. A tendency towards an increase in these indicators with the substitution of G with A in the genotype was found. Saturation of the population with desirable alleles led to an increase in the average live weight of the chickens. Analysis of the exterior parameters of adult birds showed that this growth is achieved by increasing the depth and volume of the bird body, and not by increasing the length of the limbs. Thus, marker selection carried out for five generations in the experimental population of Pushkin breed chickens to increase body weight has reliably (p < 0.001) changed the exterior profile of adult birds.

Actuality of molecular genetic studies in aquaculture

In the present article, it was considered the state and prospects of modern molecular genetic research in aquaculture, an overview of the methods of studying the genetic structure by using different types of markers. As a result of the use of molecular genetic markers, it is possible to evaluate intraspecific genetic polymorphism, to carry out the certification of repair broodstocks and further formation of parent pairs of producers by alternative genotypes in order to improve the quality of the genetic material of fish tribal resources in order to control the reproduction efficiency in the conditions of domestic fish farms.

GENETIC STRUCTURE OF UKRAINIAN MOUNTAIN CARPATHIAN SHEEP BY USE OFMICROSATELLITE LOCI

Significant reduction of sheep population and the lack of clear selection-breeding work in Ukraine, have led to partial and in some cases complete loss of specific gene pools of local breeds. Intensification of the selection process accelerates absorption of uncompetitive breeding material, which primarily is mostly local (native) breeds, reducing their number, in consequence of which is rapidly decreasing natural diversity of animals. Using crossed with imported breeds doesn't solve the general problem of reconstruction and development of the sheep industry, while resulting in the loss of local breeds features, increasing the number of diseases, including genetically caused ones. The natural basis of Carpathian Mountain sheep is native (local) thick-fiber wool sheep, a typical representative of such sheep breed is Tsakel. Since the middle of last century, by a long reproductive crossbreeding of local thick-fiber wool ewes of Carpathian Mountain sheep with the rams of Tsigay breed, a Ukrainian Carpathian Mountain sheep breed combined with wool-milk-meat-sheep skin direction of productivity was created, and, in 1993, was approved. To study the polymorphism of microsatellite loci and molecular genetic estimation of Ukrainian Mountain Carpathian sheep we investigated the use of molecular genetic markers – microsatellite DNA sequences recommended by FAO for assessing biodiversity sheep. Material was taken from both sexes sheep of different age groups in "Bansko" farm, Rakhiv district – mountainous area and "Saldobosh" farm, Khust district, Transcarpathian region – low-lying area in the amount of 49 head. Genetic analysis of groups of sheep by the use of DNA markers was conducted based on the recommended list of the International Society for Animal Genetics (ISAG), for assessing sheep biodiversity by using different fluorescent coloring for labelling fragments. Given the criteria and recommendations of ISAG, we selected 11 microsatellite loci: Oar304, HSC, Oar129, MAF214, Oar11, INRA063, CSRD247, SPS113, D5S2, MAF65, McM527. The analysis revealed significant genetic differences in the use of microsatellite markers in sheep of this breed. We found a total of 106 alleles, which number ranges from 6 (D5S2 locus) to 13 (INRA63 locus). The identified alleles were used to determine polymorphism of markers. Based on the calculation of allele frequencies heterozygosity values (H), polymorphic information content (PIC) and inbreeding coefficient (FIS) were determined. The results showed that the markers had a high degree of polymorphism. The polymorphic information content (PIC) averaged 0,740 and ranged from 0,53 (Oar304 locus) to 0,84 (HSC locus). In our studies, the highest polymorphism was typical for INRA 063 locus, which consisted of 13 alleles with polymorphic information content (PIC) – 0,838 and observed heterozygosity (HO) – 0,857. High variability was also detected for loci HSC, Oar11 and SPS113, where it was identified more than 9 alleles, and the value of PIC and HO varied from 0,74 and 0,84 (SPS113) to 0,89 and 0,81 (Oar11). The lowest polymorphism was noted for Oar304 locus where it was found 9 allelic variants, but two of them (164 and170 bp) had much higher frequency of 0,28 and 0,57. PIC and HO values for this locus were 0,53 and 0,47, respectively. The other markers exhibited a similar polymorphism, with the number of alleles in the range of 8-11 and PIC and HO values ranging from 0,65 and 0,61 (Oar129) to 0,72 and 0,70 (MAF65). Thus, information on the genetic structure of Ukrainian Mountain Carpathian sheep breed and its diversity at the genomic level was obtained by use of 11 microsatellite loci. The specific features of the structure of the gene pool were revealed. The analysis showed a significant genetic variability of the studied microsatellite loci. Totally 106 alleles were identified that were used to determine the discussed polymorphism markers. The highest polymorphism was characterized for Oar 11, INRA063 and SPS113 loci which had more than 9 alleles, whereas the index of polymorphism (PIC) and actual heterozygosity (HO) exceeded 0,80. The lowest polymorphism was revealed for Oar304 locus and at the presence of 9 alleles, PIC and HO values were 0,53 and 0,47 respectively. Average inbreeding coefficient had low negative value (0,070), indicating almost absent inbreeding within the studied breed. The obtained information at the appropriate assessment using classical methods of selection and breeding makes it possible to control the genetic structure directly with DNA markers, and the creation of targeted groups of animals through genetic selection based on appropriate economic characteristics.

Polymorphisms in the GHRL gene and their associations with traits of economic interest in beef cattle.

The hormone ghrelin is produced in the stomach wall, has an orexigenic function, stimulates growth hormone secretion, and affects the energy balance of the animal. Therefore, the ghrelin gene (GHRL) is considered to be a good candidate marker for the identification of traits of great economic importance in cattle, such as those associated with feed intake, growth, and carcass quality. The use of molecular genetic markers associated with such traits permits the earlier and more accurate identification of superior animals, thus reducing the interval between generations, and increasing the genetic gain. Six SNPs were found in the GHRL gene, located in intron 3, intron 4, and exon 5. The positions of the SNPs on the gene and the substitutions were: g.2184A>G, g.2347T>C, g.4469T>C, g.4548A>G, g.4663T>C, and g.4729T>C (GenBank accession No. JX565585). After analysis of linkage disequilibrium, association tests were performed between four SNPs with the traits year weight for males, yearling weight for females, dry matter intake, loin eye area, and rump fat thickness (P ≤ 0.05). Therefore, GHRL is an important candidate gene that may be used to identify genetic variations that influence traits of economic importance in beef cattle.

The use of Molecular Genetic Markers and PCR for DNA Diagnostics in Raw Materials Derived From Fruit and Berries

A general description of molecular genetic markers is provided in the present article. The classification of DNA markers used for identification of raw materials of plant origin is presented. The most appropriate method for identifying raw materials derived from fruit and berries is chosen using study reports. The use of PCR for determining the quantitative and qualitative composition of the raw materials is considered. DNA regions used for PCR diagnostics of raw material derived from fruit and berries are characterized. The significance of amplification for a PCR test is outlined. The optimal PCR conditions have been selected and the advantages of this method have been revealed in the present study. Amplification profiles of DNA from the samples have been analyzed using different primers. Experiments with different primers allowing for identification of the raw material were carried out. The possibility of using a complex including a common gene and a variable gene for the identification of raw materials derived from fruit and berries has been considered. The sequence of DNA regions has been analyzed. The possibility of using a ribosomal RNA gene for generic and interspecific differentiation of DNA samples has been demonstrated. The significance of oligonucleotide primers and PCR product length for the reliability of the whole genotyping system has been elucidated. A scheme of PCR-based DNA profiling has been developed. Two types of the procedure were compared and the most appropriate type was chosen according to cost efficiency.

THE Analysis of CEBPA, NPM1, FLT3 and P53 gene mutations in groups of patients with myelodysplastic syndrome and acute nonlymphocytic leukaemia

The article presents the molecular genetic analysis of the prevalence of somatic mutations in FLT3, NPM1, CEBPA, and p53 genes in a group consisting of 23 patients with myelodysplastic syndrome MDS (option - refractory anemia with excess blasts, RAEB) and 97 patients with acute nonlymphoblastic leukemia (ANLL). It was ascertained that FLT3-ITD mutations in the group of patients with MDS RAEB occur with the prevalence of 8,7 ± 5,9 %, while in the group with ANLL they are observed in 22,7 ± 4,3 % cases. FLT3 D835 mutations were detected only in the ANLL group with the prevalence of 7.2±2.6 %. NPM1 gene mutations were detected in 8,7 ± 5,9 % of MDS RAEB cases and in 21,6 ± 4,2 % of ANLL cases. CEBPA somatic mutations were found in 11,3 ± 3,2 % of ANLL cases, while the group of MDS RAEB was free of them. Mutations in the p53 gene were detected in 17,4 ± 7,9 % of MDS RAEB cases and in 10,3 ± 0,3 % of ANLL cases. All the detected CEBPA and p53 gene mutations were described by means of direct sequencing. The analysis results show that the use of molecular genetic markers in combination with cytogenetic ones makes it possible to expand the group with prognostic markers by 41,3 % in comparison with the use of only cytogenetic data.

Genetic divergence and taxonomic status of chars of the genus Salvelinus

The chars of the genus Salvelinus (Salmonidae) are characterized by high phenotypic diversity within lake or river basins, which creates some difficulties for determining the taxonomic (species) status of their forms and populations. The lack of the commonly accepted species concept complicates the situation. Based on the dominant biological species concept the reveal of the reproduction isolation of such forms or populations under conditions of sympatry can be the foundation for establishing the species status. The use of molecular genetic markers is a key approach to determining the degree of reproductive isolation and genetic divergence of populations. The paper compares and summarizes our and literary data on genetic studies of several species of the chars in the Russian Far East and northeast with regard to controversial issues of their species status. Using various molecular genetic markers, the validity of the species status of white char (S. albus) compared to the sympatric northern Dolly Varden (S. malma malma) was analyzed. The absence of the complete reproductive isolation between these chars makes it possible to consider S. albus as an ecotype or a form of S. m. malma, but not as a separate species. In pairs of sympatric S. m. malma-S. taranetzi and S. m. malma-S. levanidovi, the genetically well-expressed reproductive isolation was determined, which confirms their supposed status as separate species. The character of genetic differences for allozyme markers in the Asian allopatric population of S. m. malma and S. alpinus and the evidence of the reproductive isolation by microsatellite loci in sympatric Alaskan populations of these chars correspond to their status of separate species. The results of an analysis of mitochondrial genomes are evidence of their relatively recent divergence and possible hybridization between these species during their evolution. Significant genetic differences, including karyological differences between allopatric forms of northern and southern forms of Dolly Varden (S. m. malma-S. m. krascheninnikivi) correspond to the level of the species differentiation. However, the degree of their reproductive isolation in sympatry remains unknown. The data on mtDNA make it possible to suggest hybridization between these forms of Dolly Varden in their evolutionary past. The possibilities of using different molecular markers to identify the contemporary and historical isolation, and the evolution of contemporary char species and forms, which complicate the determination of their taxonomic status, are discussed.

Research gap analysis for application of biotechnology to sustaining US forests

Research gap analysis for application of biotechnology to sustaining US forests

From population genetics to population genomics of forest trees: Integrated population genomics approach

Early works by Altukhov and his associates on pine and spruce laid the foundation for Russian population genetic studies on tree species with the use of molecular genetic markers. In recent years, these species have become especially popular as nontraditional eukaryotic models for population and evolutionary genome-wide research. Tree species with large, cross-pollinating native populations, high genetic and phenotypic variation, growing in diverse environments and affected by environmental changes during hundreds of years of their individual development, are an ideal model for studying the molecular genetic basis of adaptation. The great advance in this field is due to the rapid development of population genomics in the last few years. In the broad sense, population genomics is a novel, fast-developing discipline, combining traditional population genetic approaches with the genome-wide level of analysis. Thousands of genes with known function and sometimes known genome-wide localization can be simultaneously studied in many individuals. This opens new prospects for obtaining statistical estimates for a great number of genes and segregating elements. Mating system, gene exchange, reproductive population size, population disequilibrium, interaction among populations, and many other traditional problems of population genetics can be now studied using data on variation in many genes. Moreover, population genome-wide analysis allows one to distinguish factors that affect individual genes, allelles, or nucleotides (such as, for example, natural selection) from factors affecting the entire genome (e.g., demography). This paper presents a brief review of traditional methods of studying genetic variation in forest tree species and introduces a new, integrated population genomics approach. The main stages of the latter are: (1) selection of genes, which are tentatively involved in variation of adaptive traits, by means of a detailed examination of the regulation and the expression of individual genes and genotypes, with subsequent determination of their complete allelic composition by direct nucleotide sequencing; (2) examination of the phenotypic effects of individual alleles by, e.g., association mapping; and (3) determining the frequencies of the selected alleles in natural population for identification of the adaptive variation pattern in the heterogeneous environment. Through decoding the phenotypic effects of individual alleles and identification of adaptive variation patterns at the population level, population genomics in the future will serve as a very helpful, efficient, and economical tool, essential for developing a correct strategy for conserving and increasing forests and other commercially valuable plant and animal species.

Choosing the right molecular genetic markers for studying biodiversity: from molecular evolution to practical aspects

The use of molecular genetic markers (MGMs) has become widespread among evolutionary biologists, and the methods of analysis of genetic data improve rapidly, yet an organized framework in which scientists can work is lacking. Elements of molecular evolution are summarized to explain the origin of variation at the DNA level, its measures, and the relationships linking genetic variability to the biological parameters of the studied organisms. MGM are defined by two components: the DNA region(s) screened, and the technique used to reveal its variation. Criteria of choice belong to three categories: (1) the level of variability, (2) the nature of the information (e.g. dominance vs. codominance, ploidy, ... ) which must be determined according to the biological question and (3) some practical criteria which mainly depend on the equipment of the laboratory and experience of the scientist. A three-step procedure is proposed for drawing up MGMs suitable to answer given biological questions, and compiled data are organized to guide the choice at each step: (1) choice, determined by the biological question, of the level of variability and of the criteria of the nature of information, (2) choice of the DNA region and (3) choice of the technique.

Identification and characterization of microsatellites for striped bass from repeat-enriched libraries

Striped bass (Morone saxatilis) is economically important in the US due to its value as an aquaculture species and in supporting commercial and recreational fisheries, especially those off the Atlantic coast and in the Gulf of Mexico. Modern strategies for managing fishery populations and aquaculture broodstocks employ the use of molecular genetic markers to identify individuals, assign parentage, and characterize population genetic structure and levels of inbreeding and migration. As part of a collaborative effort to utilize molecular genetic technologies in striped bass breeding programs we generated microsatellite markers for use in population genetic studies, broodstock selection and management strategies, and the construction of a genetic map. We developed 345 new microsatellite markers for striped bass, a subset (n=71) of which was characterized by genotyping samples from two striped bass broodstock populations to evaluate marker polymorphism, percent heterozygosity, Hardy–Weinberg equilibrium (HWE), linkage disequilibrium (LD) and utility for population genetic studies.

Single Marker and Haplotype Analysis of the Chicken Apolipoprotein B Gene T123G and D9500D9- Polymorphism Reveals Association with Body Growth and Obesity

Apolipoprotein B (apoB) is synthesized in the mammalian small intestine and liver, where it serves an essential role in the assembly and secretion of triglyceride-rich lipoproteins and is the constituent of very low density lipoprotein, intermediate density lipoprotein, and low density lipoprotein (LDL), and is the ligand for the LDL receptor. The present study was designed to investigate the effects of the apoB gene on chicken growth and deposition of adipose tissues. The Northeast Agricultural University broiler lines divergently selected for abdominal fat were used. Two novel polymorphisms, a synonymous mutation T→G at 123 of 26th exon, and a 9 bp deletion at 500 bp after the stop code TGA of the apoB gene were found, and then the association between these 2 polymorphisms and traits were detected using both single marker and haplotype analysis. Results showed that the haplotype of the 2 polymorphisms of apoB gene was linked with potential major loci or genes affecting the body growth and fatness traits. The results of the present study not only suggest a primary function of apoB gene in the chicken, but also suggest that the use of molecular genetic markers associated with the apoB gene can be used in a selection program for low abdominal fat.