Assessment of the level of allelic polymorphism of SSR markers and genetic distances of some grape varieties of the South of Russia of different ecological-geographical groups

Представлены результаты оценки генетического разнообразия 24 местных сортов юга России, поддерживаемых на ампелографической коллекции ФГБУН «ВННИИВиВ «Магарач». ДНК-типирование сортов и оценка аллельного разнообразия выполнено с использованием 9 ядерных (nSSR) и 3 хлоропластных (cpSSR) микросателлитных локусов. Уровень полиморфизма nSSR локусов составил 100 %. Всего было идентифицировано 73 аллеля, в среднем 9.1 аллеля /локус. Минимальное количество аллелей идентифицировано в локусах ssrVrZAG64 и ssrZag83. Наибольшее количество аллелей выявлено в локусе ssrVvUCH29 (13 аллелей), диапазон размера которых составил 203 п.н. - 309 п.н. В результате анализа полиморфизма сpSSR-локусов идентифицировано 4 хлоротипа: А, В, С, D. Наиболее распростанен в группе изученных сортов хлоротип D (58 %). В статье обсуждается происхождение сортов на основе анализа их гаплотипов. По результатами анализа аллельного полиморфизма nSSR-локусов рассчитана матрица генетических дистанций, значения которой находились в диапазоне 0,33-0,94, построена дендрограмма, отражающая взаимоотношения между образцами. По степени генетического сходства выделились 3 основных кластера, в которых наблюдалась дифференциация или тенденция к дифференциации по эколого-географическим группам. The assessment results of genetic diversity of 24 local varieties of the South of Russia, maintained in the ampelographic collection of the FSBSI Institute Magarach are presented. DNA typing of cultivars and assessment of allelic diversity was performed using 9 nuclear (nSSR) and 3 chloroplast (cpSSR) microsatellite loci. The level of polymorphism of nSSR loci was 100%. A total of 73 alleles were identified with an average of 9.1 alleles per locus. The minimal number of alleles was observed in the ssrVrZAG64 and ssrZag83 loci. The biggest number of alleles was found in the ssrVvUCH29 locus (13 alleles), the size range of which was 203 bp-309 bp. As a result of polymorphism analysis of cpSSR loci, 4 chlorotypes were identified: A, B, C, D. Chlorotype D is the most widespread in the group of the studied cultivars (58%). The article discusses the origin of varieties based on the analysis of their haplotypes. Based on the results of the analysis of allelic polymorphism of nSSR loci, a matrix of genetic distances was calculated, the values of which were in the range of 0.33-0.94, and a dendrogram, reflecting the relationship between the samples, was constructed. According to the degree of genetic similarity, 3 main clusters were distinguished, in which differentiation or a tendency towards differentiation by ecological-geographical groups was observed.

STUDY OF GENETIC DIVERSITY AND ANALYSIS OF THE DEGREE OF SIMILARITY IN SOME APPLE AND PLUM VARIETIES USING RAPD MARKERS

Molecular evaluation of germplasm is an important step in breeding programs, and the application of molecular biological techniques has led to important results in terms of both within- and between-species variability of traits. The RAPD technique has been successfully used to reveal allelic polymorphism as well as to measure genetic similarity. In this study, the genetic diversity of 25 genotypes and cultivars for apple species and 26 genotypes and cultivars for plum species was assessed with six RAPD markers. All these cultivars belong to the ex situ collection of apple and the ex situ collection of plum at the Research Institute for Fruit Growing Pitesti. The average number of amplified bands was 19.2 for apple and 17.66 for plum. Statistical analysis of intraspecific allelic polymorphism was expressed using the PIC (Polymorphic Information Content) index, which takes into account the allelic frequency. Two statistical indices were used to quantify genetic diversity: the Shannon index and the Simpson index. The degree of similarity between varieties was analyzed using the NTSYSpc version 2.1. Following RAPD analyses, the allele sizes of the analyzed varieties were within the range quoted in the literature, the genetic profiles of the studied varieties suggesting a medium to high genetic diversity, except for markers OPBC-04 and OPBB-05 for plum species, which expressed a high genetic diversity. Genetic distances calculated based on polymorphism of migrated bands in agarose gel confirmed the known genealogies of the apple and plum varieties studied. Thus, the smallest genetic distance for apple species was found between 'Jonagold' and 'Golden Delicious', 'Pionier' and 'Rustic', 'Jonathan' and 'Idared', 'Wagener Premiat' and 'Granny Smith', 'Remar' and 'Aura', 'Romus 3' and 'Rome Beauty', and the largest between Malus floribunda and the other genotypes studied. In plum, the smallest genetic distance was found between 'Dani' and 'Tita', 'Roman' and 'Tuleu gras', 'Dara' and 'Haganta', 'Romanța' and 'Stanley', 'Anna Spath' and 'Renclod Violet', and the largest between 'Lama', 'Black Diamond' and the other genotypes studied.

Population-specific diversity of the immunoglobulin constant heavy G chain (IGHG) genes

Human immunoglobulin G (IgG) molecules, IgG1, IgG2 and IgG3, exhibit substantial inter-individual variation in their constant heavy chain regions, as discovered by serological methods. This polymorphism is encoded by the IGHG1, IGHG2, and IGHG3 genes and may influence antibody function. We sequenced the coding fragments of these genes in 95 European Americans, 94 African Americans, and 94 Black South Africans. Striking differences were observed between the population groups, including extremely low amino acid sequence variation in IGHG1 among South Africans, and higher IGHG2 and IGHG3 diversity in individuals of African descent compared to individuals of European descent. Molecular definition of the loci illustrates a greater level of allelic polymorphism than previously described, including the presence of common IGHG2 and IGHG3 variants that were indistinguishable serologically. Comparison of our data with the 1000 Genome Project sequences indicates overall agreement between the datasets, although some inaccuracies in the 1000 Genomes Project are likely. These data represent the most comprehensive analysis of IGHG polymorphisms across major populations, which can now be applied to deciphering their functional impact.

Influencing factors on the severity of clinical and laboratory manifestations of carbohydrate malabsorption syndrome in early-aged children with rotavirus infection

Purpose — to determine the role of the lactase gene MCM6 allelic polymorphism 13910 C/T and the concomitant food allergy (FA) and atopic dermatitis (AD) on the formation of carbohydrate malabsorption syndrome manifestations in early-aged children with rotavirus infection (RVI). Materials and methods. 60 children aged 1–24 months with RVI were examined. The determination of single nucleotide polymorphism 13910 C/T of the MCM6 gene was performed by real-time polymerase chain reaction and the content of total Ig E in serum was determined by enzyme immunoassay for all children on the day of hospitalization. Total amount of carbohydrates in feces (Benedict's test) and the level of lactose in feces (Malfatti's test) were also determined in the dynamics of the disease (on the 3rd, 5th, 7th, 10th day). The analysis of the carbohydrate malabsorption syndrome clinical and laboratory signs was carried out in subgroups depending on the genotype 13910 C/T of the MCM6 gene and concomitant allergic pathology. Results. No significant differences were found in the maximum daily frequency of diarrhea, its duration and the frequency of intestinal colic and flatulence registration in children with genotypes C/C, C/T and T/T -13910 of the MCM6 gene (p>0.05). There was no statistically significant difference in the total level of carbohydrates and lactose in feces at all stages of the disease (p>0.05 on the 3rd, 5th, 7th, 10th). Children with concomitant FA and AD had 1.3 and 2 times higher daily frequency of liquid bowel movements during the height of the disease (p<0.05 on the 5th and 7th days, respectively), 1.3 times longer diarrhea (p<0.05), 1.6 and 1.8 times higher incidence of flatulence and intestinal colic (p<0.05). These children had 3 and 3.3 times higher Benedict's test values (p<0.01), as well as 3 and 2.5 times higher Malfatti's test values (p<0.01; p<0.05, respectively) on the 3rd and 5th days of RVI, respectively, than in patients without allergies, with a gradual decrease in this difference during the period of convalescence (p>0.05 on the 10th day). Conclusions. The allelic polymorphism 13910 C/T of the MCM6 gene does not affect the degree of oligosaccharide metabolism disorders in the intestines in early-aged children with RVI. Against the background of concomitant food allergy and atopic dermatitis in children with RVI, there are more pronounced laboratory signs of carbohydrate malabsorption, and, as a consequence, diarrhea more pronounced during the height of the disease with a higher incidence of flatulence and intestinal colic. The research was carried out in accordance with the principles of the Helsinki declaration. The study protocol was approved by the Local Ethics Committee of the participating institution. The informed consent of the patient was obtained for conducting the studies. No conflict of interest was declared by the author. Key words: rotavirus infection, early-aged children, carbohydrate malabsorption syndrome, lactase gene polymorphism, food allergy, atopic dermatitis.

D1S111 and 33.4 Polymorphism as a Tool of Genetic Identity among Egyptians

Background The variable number tandem repeats (VNTR) are highly polymorphic markers. Due to their high polymorphic content, VNTR constitute useful tools in population genetic studies in understanding population and ethnic migrations throughout history. They also constitute preferred systems for DNA “fingerprinting”, criminal and forensic examinations and paternity testing, evaluating hematopoietic chimerism and in determining the origin of leukemic cells in patients with recurrent disease after BMT. Aim of the Work To standardize PCR protocols of 2 VNTR loci (D1S111/33.6 and 33.4) in order to detect allelic polymorphism among Egyptians as a tool in following up the chimeric status after allogenic stem cell transplantation. Patients and Methods The current study was conducted at Clinical Pathology Department of Ain Shams University Hospital between January 2018 and December 2019, a total of 130 subjects [65 pairs (allogenic stem cell transplantation donors and their recipients)] were included. D1S111/33.6 and 33.4 VNTR loci were evaluated in every subject by PCR technique to study their relative distribution and number of informative alleles detected in order to be used in chimerism follow up and population studies. Results Five alleles were found at D1S111/33.6 in 130 subjects with molecular weight ranging from 364 to 993 bp, frequency of homozygous alleles were 30.8% and it was 69.2% for heterozygous, 90 out of the total 130 subjects were heterozygous for 33.6, that means that the heterozygosity index for D1S111/33.6 is 69.2%, from the 65 pairs tested 31 pair were informative or discriminative with discriminative power 47.69%. For 33.4 we tried many PCR programs but no bands were detected at all. Conclusion D1S111/33.6 VNTR polymorphism is a dependable cost effective method in following up of allogenic stem cell transplantation recipients.

Assessment of Microsatellite Markers (SSRs) For Genetic Diversity in Asparagus Officinalis L. And Allied Species

The present study was hypothesized to evaluate a set of SSRs for the assessment of genetic variations in Asparagus officinalis L. and their allied species. Nine genic SSR markers were especially developed for Asparagus genome and employed for DNA profiling studies of Asparagus species. These SSRs markers have revealed the allelic polymorphism ranging from 1.0 to 2.0. Allele frequency was found highest for psbD-trnL (1.0), petB (1.0) and AG7 (1.0), while it was lowest for ZHD1 (0.1). Polymorphism Information content (PIC) was highest for TC7 (0.9) while it was lowest (0.0) for psbD-trnL, petB and AG7 respectively. The genetic similarity coefficients were found to range from 0.42 to 1.0. The UPGMA clustering algorithm based on SSRs data have clustered Asparagus species into 4 groups (I, II, III & IV) indicating Asparagus officinalis (L.) cultivars and allied species in the first clade, while Asparagus officinalis (L.) ‘Gersengum’, Asparagus densiflorus (Kunth) Jessop, and Asparagus racemosus willd. were clustered in separate clades respectively. The present study has endorsed the origin status of Asparagus officinalis and their allied species. A. officinalis cultivars and other allied Asparagus species are clustered in separate clades, and it was revealed that they have monophyletic origin. It was established that SSRs markers could be informative markers for the differentiation of Asparagus officinalis cultivars, and their allied Asparagus species. Bangladesh J. Bot. 50(3): 595-602, 2021 (September)

The transitivity of the Hardy-Weinberg law

The reduction of multi-allelic polymorphisms to variants with fewer alleles, two in the limit, is addressed. The Hardy-Weinberg law is shown to be transitive in the sense that a multi-allelic polymorphism that is in equilibrium will retain its equilibrium status if any allele together with its corresponding genotypes is deleted from the population. Similarly, the transitivity principle also applies if alleles are joined, which leads to the summation of allele frequencies and their corresponding genotype frequencies. These basic polymorphism properties are intuitive, but they have apparently not been formalized or investigated. This article provides a straightforward proof of the transitivity principle, and its usefulness in practical genetic data analysis with multi-allelic markers is explored. In general, results of statistical tests for Hardy-Weinberg equilibrium obtained with polymorphisms that are reduced by deletion or joining of alleles are seen to be consistent with the formulated transitivity principle. We also show how the transitivity principle allows one to identify equilibrium-offending alleles, and how it can provide clues to genotyping problems and evolutionary changes. For microsatellites, which are widely used in forensics, the transitivity principle implies one expects similar results for statistical tests that use length-based and sequence-based alleles. High-quality autosomal microsatellite databases of the US National Institute of Standards and Technology are used to illustrate the use of the transitivity principle in testing both length-based and sequence-based microsatellites for Hardy-Weinberg proportions. Test results for Hardy-Weinberg proportions for the two types of microsatellites are seen to be largely consistent and can detect allele imbalance.

Comprehensive analysis of the 5-HTTLPR allelic polymorphism effect on behavioral and neurophysiological indicators of executive control in people from different ethnic groups in Siberia

The allelic polymorphism of the serotonin transporter’s gene 5-HTTLPR is considered as one of the factors determining an individual genetic predisposition to the development of a wide range of affective disorders, including depression. Many studies have shown that the climatic and social conditions of people’s life can have a significant impact on the connections of 5-HTTLPR with the risk of depression. The stop-signal paradigm (SSP) is an experimental method allowing evaluating an individual ability to the self-control of behavior in a changing environment. In the SSP experiment, a subject should either press one of several buttons quickly after the appearance of the target stimuli or suppress the already started movement if an inhibitory signal follows the target stimulus. The aim of this study is a research of associations between the allelic the 5-HTTLPR polymorphism and the individual scores of the personal anxiety level, as well as the behavioral and neurophysiological indicators of the ability to self-control over motor reactions in the SSP. The study was conducted among people from three ethno-regional groups: healthy Caucasoids from Novosibirsk, the Mongoloid groups of the indigenous population of the Tuva Republic and Sakha Republic (Yakutia). Genetic, ethnographic, and psychological influences on an individual’s ability to control motor responses were compared. The amplitude of the premotor peak of the evoked brain potential was used as a neurophysiological marker of the person’s readiness to the execution of target-directed activity. It was revealed that the frequency of the S-allele polymorphism 5-HTTLPR was significantly higher for both mongoloid groups compared to the Caucasoids. The S/S genotype was associated with an increased level of personal anxiety and at the same time with a better ability to the self-control of behavior in the SSP experiment. Anxiety level, participants’ sex, ethnicity, and allelic polymorphism 5-HTTLPR had a statistically significant effect on the amplitude of the premotor readiness potential recorded under the SSP conditions in the frontal and parietal-occipital cortical regions. Our data support the hypothesis that the S/S genotype of the 5-HTTLPR polymorphism may be associated with more success in adapting to the climatic conditions connected with high life risk in comparison to L/L and L/S genotypes.

Exploiting the allelic polymorphism at microsatellite loci to underpin the genetic status of Cirrhinus mrigala in wild populations

An adequate knowledge regarding the genetic issues of natural populations is imperative for developing conservation and stock improvement plans. The present research work was aimed to assess the genetic variability and structuring patterns in six natural populations of Cirrhinus mrigala from Punjab province, Pakistan. The PCR based amplification of targeted loci was carried out by employing a total of 12 microsatellite markers. Based on the study inferences, moderate level of genetic diversity was observed in all the populations. The average number of alleles (Na) varied from 3.750 to 4.416 and those of effective number of alleles ranged between 3.112 to 3.856 in all the examined populations. The mean values of observed and expected heterozygosity were measured as 0.563 to 0.685 and 0.669 to 0.739, respectively. The average values of inbreeding coefficient (FIS) ranged from 0.019 to 0.184. Significant deviation from HWE was detected in 9 out of 72 tests. Among all the population pairs, low to moderate level of genetic differentiation was found. After applying AMOVA, it was revealed that most of the variations (81.15%) lied within individuals. The UPGMA dendrogram resulted in two distinct clusters. The present study inferences would be helpful for setting up effective strategies to avoid the loss of genetic variability in C. mrigala populations.